From 9ac86d1089deaf2fd1d2692affaf8ee85d0fe4b1 Mon Sep 17 00:00:00 2001 From: yebai Date: Sat, 19 Aug 2023 01:28:51 +0000 Subject: [PATCH] Update manifest files --- tutorials/00-introduction/Manifest.toml | 56 +++++----- .../01-gaussian-mixture-model/Manifest.toml | 56 +++++----- .../02-logistic-regression/Manifest.toml | 56 +++++----- .../03-bayesian-neural-network/Manifest.toml | 60 ++++++----- .../04-hidden-markov-model/Manifest.toml | 56 +++++----- tutorials/05-linear-regression/Manifest.toml | 56 +++++----- .../06-infinite-mixture-model/Manifest.toml | 56 +++++----- tutorials/07-poisson-regression/Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../09-variational-inference/Manifest.toml | 56 +++++----- .../Manifest.toml | 100 +++++++++--------- tutorials/11-probabilistic-pca/Manifest.toml | 60 ++++++----- tutorials/12-gaussian-process/Manifest.toml | 60 ++++++----- .../13-seasonal-time-series/Manifest.toml | 56 +++++----- tutorials/14-minituring/Manifest.toml | 52 ++++----- .../docs-00-getting-started/Manifest.toml | 56 +++++----- .../docs-01-contributing-guide/Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- tutorials/docs-08-using-turing/Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- .../docs-12-using-turing-guide/Manifest.toml | 60 ++++++----- .../Manifest.toml | 52 ++++----- .../Manifest.toml | 56 +++++----- .../Manifest.toml | 56 +++++----- 31 files changed, 956 insertions(+), 832 deletions(-) diff --git a/tutorials/00-introduction/Manifest.toml b/tutorials/00-introduction/Manifest.toml index 97f7916bc..38d766132 100644 --- a/tutorials/00-introduction/Manifest.toml +++ b/tutorials/00-introduction/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/01-gaussian-mixture-model/Manifest.toml b/tutorials/01-gaussian-mixture-model/Manifest.toml index acfe5b335..7b17c7ca7 100644 --- a/tutorials/01-gaussian-mixture-model/Manifest.toml +++ b/tutorials/01-gaussian-mixture-model/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/02-logistic-regression/Manifest.toml b/tutorials/02-logistic-regression/Manifest.toml index 7740030b9..9dcbe4078 100644 --- a/tutorials/02-logistic-regression/Manifest.toml +++ b/tutorials/02-logistic-regression/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -790,10 +794,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1021,9 +1025,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1072,9 +1076,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1168,9 +1172,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1478,9 +1482,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1580,9 +1584,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1780,9 +1784,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1816,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/03-bayesian-neural-network/Manifest.toml b/tutorials/03-bayesian-neural-network/Manifest.toml index b0316c702..d5663a31d 100644 --- a/tutorials/03-bayesian-neural-network/Manifest.toml +++ b/tutorials/03-bayesian-neural-network/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -453,9 +453,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -756,10 +760,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -987,9 +991,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1026,9 +1030,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1121,9 +1125,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1401,9 +1405,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1419,9 +1423,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1521,9 +1525,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1697,9 +1701,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1729,9 +1733,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/04-hidden-markov-model/Manifest.toml b/tutorials/04-hidden-markov-model/Manifest.toml index db6541d8b..0ec471a90 100644 --- a/tutorials/04-hidden-markov-model/Manifest.toml +++ b/tutorials/04-hidden-markov-model/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/05-linear-regression/Manifest.toml b/tutorials/05-linear-regression/Manifest.toml index 154c6c14a..9d6dfb73f 100644 --- a/tutorials/05-linear-regression/Manifest.toml +++ b/tutorials/05-linear-regression/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -511,9 +511,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -808,10 +812,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1039,9 +1043,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1078,9 +1082,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1185,9 +1189,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1500,9 +1504,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1613,9 +1617,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1813,9 +1817,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1845,9 +1849,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/06-infinite-mixture-model/Manifest.toml b/tutorials/06-infinite-mixture-model/Manifest.toml index cc9e97304..8435d2c27 100644 --- a/tutorials/06-infinite-mixture-model/Manifest.toml +++ b/tutorials/06-infinite-mixture-model/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -447,9 +447,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -708,10 +712,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -933,9 +937,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -972,9 +976,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1050,9 +1054,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1331,9 +1335,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1422,9 +1426,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1598,9 +1602,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1630,9 +1634,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/07-poisson-regression/Manifest.toml b/tutorials/07-poisson-regression/Manifest.toml index e97d16ded..0cef91119 100644 --- a/tutorials/07-poisson-regression/Manifest.toml +++ b/tutorials/07-poisson-regression/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -790,10 +794,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1021,9 +1025,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1072,9 +1076,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1168,9 +1172,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1478,9 +1482,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1580,9 +1584,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1780,9 +1784,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1816,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/08-multinomial-logistic-regression/Manifest.toml b/tutorials/08-multinomial-logistic-regression/Manifest.toml index c5d58dda8..660e3133f 100644 --- a/tutorials/08-multinomial-logistic-regression/Manifest.toml +++ b/tutorials/08-multinomial-logistic-regression/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -784,10 +788,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1015,9 +1019,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1066,9 +1070,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1162,9 +1166,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1472,9 +1476,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1569,9 +1573,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1763,9 +1767,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1795,9 +1799,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/09-variational-inference/Manifest.toml b/tutorials/09-variational-inference/Manifest.toml index 3f682995f..3a6f076ed 100644 --- a/tutorials/09-variational-inference/Manifest.toml +++ b/tutorials/09-variational-inference/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -533,9 +533,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -865,10 +869,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1096,9 +1100,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1135,9 +1139,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1242,9 +1246,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1563,9 +1567,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1682,9 +1686,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1899,9 +1903,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1936,9 +1940,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/10-bayesian-differential-equations/Manifest.toml b/tutorials/10-bayesian-differential-equations/Manifest.toml index 6f8b936f7..d61af3191 100644 --- a/tutorials/10-bayesian-differential-equations/Manifest.toml +++ b/tutorials/10-bayesian-differential-equations/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -171,9 +171,9 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "6e9b384d5e21452bc81cae3552c74f430e320985" +git-tree-sha1 = "106122bad983acd8e21aef3f7a7f91a3ac739077" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.35" +version = "0.17.36" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -208,10 +208,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -241,10 +241,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.5" [[deps.BoundaryValueDiffEq]] -deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "ed8e837bfb3d1e3157022c9636ec1c722b637318" +deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces"] +git-tree-sha1 = "039775034259dfc1f106b195f69af7741f90ef10" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "2.11.0" +version = "3.0.0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -472,9 +472,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "ed586656058844e48660c6d6fdb384e83afc50db" +git-tree-sha1 = "5f9126d4fb0a114ef122610a902f23736e90e93c" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.128.0" +version = "6.128.1" [deps.DiffEqBase.extensions] DiffEqBaseDistributionsExt = "Distributions" @@ -529,9 +529,9 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "1cfe0178410e1bb4b14058c537d0f347eb9d95dc" +git-tree-sha1 = "9b2fef0d520066196dbd6761bbc15da5e6282d9e" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.8.0" +version = "7.9.0" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] @@ -595,9 +595,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipsisNotation]] deps = ["StaticArrayInterface"] @@ -617,10 +621,10 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Printf", "Random"] -git-tree-sha1 = "5eb8de9b18c31683be5c7b5a5034aaf5e24dd068" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] +git-tree-sha1 = "1f85bc8a9da6118abb95d134efc68cf4a6957341" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.6" +version = "0.11.7" [[deps.EnzymeCore]] deps = ["Adapt"] @@ -630,9 +634,9 @@ version = "0.5.2" [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "dca536dc737737d14228b485bb46abeeecfa9695" +git-tree-sha1 = "ffa4926cc857bcc5c256825bd7273a6ac989eb34" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.78+0" +version = "0.0.80+0" [[deps.ExceptionUnwrapping]] deps = ["Test"] @@ -965,10 +969,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1246,9 +1250,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1296,9 +1300,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1402,9 +1406,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1480,9 +1484,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.6" +version = "1.7.7" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] @@ -1503,9 +1507,9 @@ version = "1.6.2" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4" +git-tree-sha1 = "2758190d4b01182e2278b772339daa83e209d45a" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.53.4" +version = "6.54.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1764,9 +1768,9 @@ version = "1.1.1" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1782,9 +1786,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1837,9 +1841,9 @@ version = "0.3.6" [[deps.SciMLSensitivity]] deps = ["Adapt", "ArrayInterface", "Cassette", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseDiffTools", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote", "ZygoteRules"] -git-tree-sha1 = "8f90cc3583e4f6e341f558a0c7c4b1b3d581cbb3" +git-tree-sha1 = "917ff87007015687aeca53cfd1cfff07cc6ec580" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.36.0" +version = "7.37.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1940,9 +1944,9 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2205,9 +2209,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -2242,9 +2246,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/11-probabilistic-pca/Manifest.toml b/tutorials/11-probabilistic-pca/Manifest.toml index d4a718fdc..55620e7cf 100644 --- a/tutorials/11-probabilistic-pca/Manifest.toml +++ b/tutorials/11-probabilistic-pca/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -481,9 +481,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -748,10 +752,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -973,9 +977,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1012,9 +1016,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1096,9 +1100,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1382,9 +1386,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1400,9 +1404,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1497,9 +1501,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1685,9 +1689,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1717,9 +1721,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/12-gaussian-process/Manifest.toml b/tutorials/12-gaussian-process/Manifest.toml index 3f154c4c1..a0d4a578e 100644 --- a/tutorials/12-gaussian-process/Manifest.toml +++ b/tutorials/12-gaussian-process/Manifest.toml @@ -34,9 +34,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -55,9 +55,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -174,10 +174,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -493,9 +493,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -772,10 +776,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1003,9 +1007,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1042,9 +1046,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1126,9 +1130,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1413,9 +1417,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1431,9 +1435,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1528,9 +1532,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1710,9 +1714,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1742,9 +1746,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/13-seasonal-time-series/Manifest.toml b/tutorials/13-seasonal-time-series/Manifest.toml index 6d5f5263e..84f0fadc9 100644 --- a/tutorials/13-seasonal-time-series/Manifest.toml +++ b/tutorials/13-seasonal-time-series/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/14-minituring/Manifest.toml b/tutorials/14-minituring/Manifest.toml index eaa6adf5c..030bcc1a3 100644 --- a/tutorials/14-minituring/Manifest.toml +++ b/tutorials/14-minituring/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -385,9 +385,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -539,10 +543,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] @@ -666,9 +670,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -705,9 +709,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -772,9 +776,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -959,9 +963,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1033,9 +1037,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1197,9 +1201,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" diff --git a/tutorials/docs-00-getting-started/Manifest.toml b/tutorials/docs-00-getting-started/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-00-getting-started/Manifest.toml +++ b/tutorials/docs-00-getting-started/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-01-contributing-guide/Manifest.toml b/tutorials/docs-01-contributing-guide/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-01-contributing-guide/Manifest.toml +++ b/tutorials/docs-01-contributing-guide/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-02-contributing-style-guide/Manifest.toml b/tutorials/docs-02-contributing-style-guide/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-02-contributing-style-guide/Manifest.toml +++ b/tutorials/docs-02-contributing-style-guide/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml index 800beb573..b03f7e47f 100644 --- a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml +++ b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-05-for-developers-compiler/Manifest.toml b/tutorials/docs-05-for-developers-compiler/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-05-for-developers-compiler/Manifest.toml +++ b/tutorials/docs-05-for-developers-compiler/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-06-for-developers-interface/Manifest.toml b/tutorials/docs-06-for-developers-interface/Manifest.toml index 7e0175174..fe5bc3ef8 100644 --- a/tutorials/docs-06-for-developers-interface/Manifest.toml +++ b/tutorials/docs-06-for-developers-interface/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml +++ b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-08-using-turing/Manifest.toml b/tutorials/docs-08-using-turing/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-08-using-turing/Manifest.toml +++ b/tutorials/docs-08-using-turing/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-09-using-turing-advanced/Manifest.toml b/tutorials/docs-09-using-turing-advanced/Manifest.toml index 065784c4b..5dbf6cc29 100644 --- a/tutorials/docs-09-using-turing-advanced/Manifest.toml +++ b/tutorials/docs-09-using-turing-advanced/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-10-using-turing-autodiff/Manifest.toml b/tutorials/docs-10-using-turing-autodiff/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-10-using-turing-autodiff/Manifest.toml +++ b/tutorials/docs-10-using-turing-autodiff/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml index b092f03b8..7315b3749 100644 --- a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml +++ b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -481,9 +481,13 @@ version = "3.4.6" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -742,10 +746,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -973,9 +977,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1012,9 +1016,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1096,9 +1100,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1388,9 +1392,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1485,9 +1489,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1696,9 +1700,9 @@ version = "1.3.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1728,9 +1732,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-12-using-turing-guide/Manifest.toml b/tutorials/docs-12-using-turing-guide/Manifest.toml index 4f426900d..a40c5eaa6 100644 --- a/tutorials/docs-12-using-turing-guide/Manifest.toml +++ b/tutorials/docs-12-using-turing-guide/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -752,10 +756,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -983,9 +987,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1022,9 +1026,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1112,9 +1116,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1178,9 +1182,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.6" +version = "1.7.7" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] @@ -1422,9 +1426,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1519,9 +1523,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1707,9 +1711,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1744,9 +1748,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml index 7d7d28135..7d45c2bb5 100644 --- a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml +++ b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -385,9 +385,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -539,10 +543,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] @@ -666,9 +670,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -705,9 +709,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -778,9 +782,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -965,9 +969,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1039,9 +1043,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1203,9 +1207,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" diff --git a/tutorials/docs-14-using-turing-quick-start/Manifest.toml b/tutorials/docs-14-using-turing-quick-start/Manifest.toml index 9f4ff6272..aaeebc883 100644 --- a/tutorials/docs-14-using-turing-quick-start/Manifest.toml +++ b/tutorials/docs-14-using-turing-quick-start/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml index e2883d662..92d961214 100644 --- a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -736,10 +740,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -961,9 +965,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "5ab83e1679320064c29e8973034357655743d22d" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.25" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1000,9 +1004,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "e89d1ea12c5a50057bfb0c124d905669e5ed4ec9" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.1" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1084,9 +1088,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1376,9 +1380,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1473,9 +1477,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1661,9 +1665,9 @@ version = "1.4.0" [[deps.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1697,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "607c142139151faa591b5e80d8055a15e487095b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.16.3" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions]