From f4b38f8132f5268f87bedc923cafaa83337d7348 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Fri, 30 Aug 2024 20:55:20 +0100 Subject: [PATCH 1/6] Update Turing to v0.34 --- Manifest.toml | 242 ++++++++++++++++++++++++-------------------------- Project.toml | 2 +- _quarto.yml | 2 +- 3 files changed, 120 insertions(+), 126 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 6f8f1feae..3b5e8c298 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "4dbb593d041b187abd261fc4e92a2df5baf55b80" +project_hash = "e0661388214f9e03749b3fccc86939dfd3853246" [[deps.ADTypes]] git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" @@ -182,9 +182,9 @@ version = "7.7.1" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "ce2ca959f932f5dad70697dd93133d1167cf1e4e" +git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.2" +version = "1.10.3" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -327,12 +327,6 @@ git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.18.0+2" -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" - [[deps.Cassette]] git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" uuid = "7057c7e9-c182-5462-911a-8362d720325c" @@ -373,14 +367,15 @@ weakdeps = ["SparseArrays"] ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.ChangesOfVariables]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "2fba81a302a7be671aefe194f0525ef231104e7f" +deps = ["LinearAlgebra"] +git-tree-sha1 = "799b25ca3a8a24936ae7b5c52ad194685fc3e6ef" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.8" -weakdeps = ["InverseFunctions"] +version = "0.1.9" +weakdeps = ["InverseFunctions", "Test"] [deps.ChangesOfVariables.extensions] ChangesOfVariablesInverseFunctionsExt = "InverseFunctions" + ChangesOfVariablesTestExt = "Test" [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] @@ -395,16 +390,16 @@ uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.15.7" [[deps.CodecBzip2]] -deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "f8889d1770addf59d0a015c49a473fa2bdb9f809" +deps = ["Bzip2_jll", "TranscodingStreams"] +git-tree-sha1 = "e7c529cc31bb85b97631b922fa2e6baf246f5905" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.3" +version = "0.8.4" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "b8fe8546d52ca154ac556809e10c75e6e7430ac8" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.5" +version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] @@ -445,10 +440,10 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" [[deps.Compat]] deps = ["TOML", "UUIDs"] @@ -512,9 +507,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "d8a9c0b6ac2d9081bf76324b39c78ca3ce4f0c98" +git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.6" +version = "1.5.7" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -640,10 +635,10 @@ version = "2.35.0" weakdeps = ["OrdinaryDiffEq", "Sundials"] [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "ed0158e758723b4d429afbbb5d98c5afd3458dc1" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.22.0" +version = "5.23.0" weakdeps = ["ReverseDiff"] [deps.DiffEqNoiseProcess.extensions] @@ -669,9 +664,9 @@ version = "7.10.0" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "114474c54e14f9ae53b8a5088507560278db15c3" +git-tree-sha1 = "c2acd1de2c4c357928f9fb6b60b402d914621378" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.13" +version = "0.4.14" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -695,9 +690,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac" +git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.110" +version = "0.25.111" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -734,12 +729,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.DynamicHMC]] deps = ["ArgCheck", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "ProgressMeter", "Random", "SimpleUnPack", "Statistics", "TensorCast"] git-tree-sha1 = "9285af003a31272b4105c8e80d90b99eaf4b8c05" @@ -748,9 +737,9 @@ version = "3.4.7" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "f017bc2020220697b795ff636dc595537b9d271f" +git-tree-sha1 = "79ff677df43bbad59ee704819ec6ede5a9c71b29" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.28.2" +version = "0.28.3" weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "ReverseDiff", "ZygoteRules"] [deps.DynamicPPL.extensions] @@ -897,19 +886,24 @@ uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" version = "1.16.3" [[deps.FilePathsBase]] -deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +deps = ["Compat", "Dates"] +git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.21" +version = "0.9.22" +weakdeps = ["Mmap", "Test"] + + [deps.FilePathsBase.extensions] + FilePathsBaseMmapExt = "Mmap" + FilePathsBaseTestExt = "Test" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.11.0" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -1131,10 +1125,10 @@ uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "1.10.8" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.3.1+0" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] @@ -1149,10 +1143,10 @@ uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" version = "2.11.1+0" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.24" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1195,10 +1189,10 @@ uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34" version = "0.3.0" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.2.0+0" +version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1226,14 +1220,14 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "18c59411ece4838b18cd7f537e56cf5e41ce5bfd" +git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.15" -weakdeps = ["Dates"] +version = "0.1.16" +weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] - DatesExt = "Dates" + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -1257,15 +1251,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1361,9 +1355,9 @@ version = "0.0.29+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "17.0.6+0" [[deps.LRUCache]] git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" @@ -1785,9 +1779,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "c0fe113e9c72aa0c9a185fd3c5ca1daa51de1486" +git-tree-sha1 = "5b246fca5420ae176d65ed43a2d0ee5897775216" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.31.1" +version = "1.31.2" [[deps.MathProgBase]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1846,9 +1840,9 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.Mocking]] deps = ["Compat", "ExprTools"] -git-tree-sha1 = "ead0dbb33b6808578c385ffaab20d9b57053661b" +git-tree-sha1 = "2c140d60d7cb82badf06d8783800d0bcd1a7daa2" uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.8.0" +version = "0.8.1" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" @@ -1884,10 +1878,10 @@ uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" version = "0.6.5" [[deps.NLopt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9b1f15a08f9d00cdb2761dcfa6f453f5d0d6f973" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "3d1eefa627faeabc59ab9edbf00d17f70123ad69" uuid = "079eb43e-fd8e-5478-9966-2cf3e3edb778" -version = "2.7.1+0" +version = "2.8.0+0" [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -1897,9 +1891,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "190dcada8cf9520198058c4544862b1f88c6c577" +git-tree-sha1 = "ae52c156a63bb647f80c26319b104e99e5977e51" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.21" +version = "0.9.22" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2076,10 +2070,10 @@ uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" version = "0.1.14" [[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.2+0" +version = "1.3.3+0" [[deps.OrderedCollections]] git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" @@ -2117,9 +2111,9 @@ weakdeps = ["Requires", "TOML"] [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cb5a2ab6763464ae0f19c86c56c63d4a2b0f5bda" +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.52.2+0" +version = "1.54.1+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2175,9 +2169,9 @@ version = "1.4.1" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "082f0c4b70c202c37784ce4bfbc33c9f437685bf" +git-tree-sha1 = "45470145863035bb124ca51b320ed35d071cc6c2" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.5" +version = "1.40.8" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2200,10 +2194,10 @@ uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.4" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "9ff799e8fb8ed6717710feee3be3bc20645daa97" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.15" +version = "0.7.16" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -2225,9 +2219,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "d7f3f63331c7c8c81245b4ee2815b7d496365833" +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.23" +version = "0.4.24" weakdeps = ["ReverseDiff"] [deps.PreallocationTools.extensions] @@ -2277,9 +2271,9 @@ uuid = "92933f4c-e287-5a05-a399-4b506db050ca" version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.0" +version = "1.2.1" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] @@ -2338,10 +2332,10 @@ uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -2443,15 +2437,15 @@ version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21" +git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.2+0" +version = "0.4.3+0" [[deps.Roots]] deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "3484138c9fa4296a0cf46a74ca3f97b59d12b1d0" +git-tree-sha1 = "12e0a0e549c8545db615a2ec48664d56e1aad44d" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.6" +version = "2.1.7" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -2509,10 +2503,15 @@ uuid = "e9a6253c-8580-4d32-9898-8661bb511710" version = "0.1.9" [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "10499f619ef6e890f3f4a38914481cc868689cd5" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "e39c5f217f9aca640c8e27ab21acf557a3967db5" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.8" +version = "0.3.10" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLSensitivity]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote"] @@ -2661,10 +2660,10 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.8.10" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "Static"] -git-tree-sha1 = "c3668ff1a3e4ddf374fc4f8c25539ce7194dcc39" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.6.0" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -2723,9 +2722,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "5cf6c4583533ee38639f73b880f35fc85f2941e0" +git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.7.3" +version = "0.7.4" [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -2789,10 +2788,9 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] StructArraysStaticArraysExt = "StaticArrays" [[deps.StructIO]] -deps = ["Test"] -git-tree-sha1 = "010dc73c7146869c042b49adcdb6bf528c12e859" +git-tree-sha1 = "c581be48ae1cbf83e899b14c07a807e1787512cc" uuid = "53d494c1-5632-5724-8f4c-31dff12d585f" -version = "0.3.0" +version = "0.3.1" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -2907,22 +2905,18 @@ version = "0.5.24" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "5158100ed55411867674576788e710a815a0af02" +git-tree-sha1 = "da45269e1da051c2a13624194fcdc74d6483fad5" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.34" +version = "0.2.35" weakdeps = ["PDMats"] [deps.Tracker.extensions] TrackerPDMatsExt = "PDMats" [[deps.TranscodingStreams]] -git-tree-sha1 = "96612ac5365777520c3c5396314c8cf7408f436a" +git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.1" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.2" [[deps.Transducers]] deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] @@ -2974,9 +2968,9 @@ version = "1.5.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "a11ea6fcba56924d2dd151b3ec5a6dd553a3b65c" +git-tree-sha1 = "e4ccbd30d20705f0a4e208dd414e0fb812ab8287" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.33.3" +version = "0.34.0" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3106,9 +3100,9 @@ version = "1.6.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d" +git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.1+0" +version = "2.13.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] @@ -3303,9 +3297,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.53.0+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3326,10 +3320,10 @@ uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] @@ -3349,10 +3343,10 @@ uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" version = "1.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libinput_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] diff --git a/Project.toml b/Project.toml index cdfa84dd5..422d12f8a 100644 --- a/Project.toml +++ b/Project.toml @@ -52,4 +52,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.33" +Turing = "0.34" diff --git a/_quarto.yml b/_quarto.yml index 856afea87..258aba908 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -32,7 +32,7 @@ website: text: Team right: # Current version - - text: "v0.33" + - text: "v0.34" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html From 5d2129cda2f9b2a8576ca2f92680902905b56e15 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Fri, 30 Aug 2024 22:59:11 +0100 Subject: [PATCH 2/6] Add more Quarto build artifacts to gitignore --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index efe4be87b..209e22c85 100644 --- a/.gitignore +++ b/.gitignore @@ -23,3 +23,6 @@ versions.qmd tmp.gif .venv venv + +404.html +site_libs From 0b3bb94a8641a8ad42322a41ac866c79e6f44911 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Fri, 30 Aug 2024 23:14:44 +0100 Subject: [PATCH 3/6] Separate developers>contributing into its own section --- _quarto.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/_quarto.yml b/_quarto.yml index 258aba908..bbc4c44f1 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -97,11 +97,15 @@ website: - text: "Gaussian Process Latent Variable Models" href: tutorials/12-gplvm/index.qmd - - section: "For Developers (PPL)" + - section: "Developers: Contributing" collapse-level: 1 contents: - text: "How to Contribute" href: tutorials/docs-01-contributing-guide/index.qmd + + - section: "Developers: PPL" + collapse-level: 1 + contents: - tutorials/docs-05-for-developers-compiler/index.qmd - text: "A Mini Turing Implementation I: Compiler" href: tutorials/14-minituring/index.qmd @@ -109,7 +113,7 @@ website: href: tutorials/16-contexts/index.qmd - tutorials/docs-06-for-developers-interface/index.qmd - - section: "For Developers (Inference)" + - section: "Developers: Inference" collapse-level: 1 contents: - tutorials/docs-04-for-developers-abstractmcmc-turing/index.qmd From 345edd3c607c2d6e88701f8da81f5dc678dd7df7 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Fri, 30 Aug 2024 23:42:54 +0100 Subject: [PATCH 4/6] Update contributing guide --- .../docs-01-contributing-guide/index.qmd | 29 ++++++++++++++----- 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/tutorials/docs-01-contributing-guide/index.qmd b/tutorials/docs-01-contributing-guide/index.qmd index 2726c1d9b..f5d973e19 100755 --- a/tutorials/docs-01-contributing-guide/index.qmd +++ b/tutorials/docs-01-contributing-guide/index.qmd @@ -2,17 +2,28 @@ title: Contributing --- -Turing is an open-source project. If you feel that you have relevant skills and are interested in contributing, please get in touch. You can contribute by opening issues on GitHub, implementing things yourself, and making a pull request. We would also appreciate example models written using Turing. +Turing is an open-source project and is [hosted on GitHub](https://github.com/TuringLang). +We welcome contributions from the community in all forms large or small: bug reports, feature implementations, code contributions, or improvements to documentation or infrastructure are all extremely valuable. +We would also very much appreciate examples of models written using Turing. -Turing has a [style guide](#style-guide). Reviewing it before making a pull request is not strictly necessary, but you may be asked to change portions of your code to conform with the style guide before it is merged. +### How to get involved -### What Can I Do? +Our outstanding issues are tabulated on our [issue tracker](https://github.com/TuringLang/Turing.jl/issues). +Closing one of these may involve implementing new features, fixing bugs, or writing example models. -Look at the [issues](https://github.com/TuringLang/Turing.jl/issues) page for an outstanding issue. For instance, you could implement new features, fix bugs or write example models. +You can also join the `#turing` channel on the [Julia Slack](https://julialang.org/slack/) and say hello! -### Git Workflow +If you are new to open-source software, please see [GitHub's introduction](https://guides.github.com/introduction/flow/) or [Julia's contribution guide](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md) on using version control for collaboration. -For more information on how the Git workflow typically functions, please see the [GitHub's introduction](https://guides.github.com/introduction/flow/) or [Julia's contribution guide](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md). +### Documentation + +Each of the packages in the Turing ecosystem (see [Libraries](/library)) has its own documentation, which is typically found in the `docs` folder of the corresponding package. +For example, the source code for DynamicPPL's documentation can be found in [its repository](https://github.com/TuringLang/DynamicPPL.jl). + +The documentation for Turing.jl itself consists of the tutorials that you see on this website, and is built from the separate [`docs` repository](https://github.com/TuringLang/docs). +None of the documentation is generated from the Turing.jl repository; in particular, the API that Turing exports does not currently form part of the documentation. + +Other sections of the website (anything that isn't a package, or a tutorial)—for example, the list of libraries—is built from the [`turinglang.github.io` repository](https://github.com/TuringLang/turinglang.github.io). ### Tests @@ -38,7 +49,11 @@ Or otherwise, set the global `ARGS` variable, and call `include("test/runtests.j ### Style Guide -Most Turing code follows the [Blue: a Style Guide for Julia](https://github.com/JuliaDiff/BlueStyle). These conventions were created from a variety of sources including Python's [PEP8](http://legacy.python.org/dev/peps/pep-0008/), Julia's [Notes for Contributors](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md), and Julia's [Style Guide](https://docs.julialang.org/en/v1/manual/style-guide/). +Turing has a [style guide](#style-guide). +Reviewing it before making a pull request is not strictly necessary, but you may be asked to change portions of your code to conform with the style guide before it is merged. + +Most Turing code follows [Blue: a Style Guide for Julia](https://github.com/JuliaDiff/BlueStyle). +These conventions were created from a variety of sources including Python's [PEP8](http://legacy.python.org/dev/peps/pep-0008/), Julia's [Notes for Contributors](https://github.com/JuliaLang/julia/blob/master/CONTRIBUTING.md), and Julia's [Style Guide](https://docs.julialang.org/en/v1/manual/style-guide/). #### Synopsis From 2688c37ef03aea20464a49515a56a8c548703d75 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 2 Sep 2024 15:02:08 +0100 Subject: [PATCH 5/6] Apply suggestions from code review Co-authored-by: Markus Hauru --- tutorials/docs-01-contributing-guide/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tutorials/docs-01-contributing-guide/index.qmd b/tutorials/docs-01-contributing-guide/index.qmd index f5d973e19..02a3f94a7 100755 --- a/tutorials/docs-01-contributing-guide/index.qmd +++ b/tutorials/docs-01-contributing-guide/index.qmd @@ -21,9 +21,9 @@ Each of the packages in the Turing ecosystem (see [Libraries](/library)) has its For example, the source code for DynamicPPL's documentation can be found in [its repository](https://github.com/TuringLang/DynamicPPL.jl). The documentation for Turing.jl itself consists of the tutorials that you see on this website, and is built from the separate [`docs` repository](https://github.com/TuringLang/docs). -None of the documentation is generated from the Turing.jl repository; in particular, the API that Turing exports does not currently form part of the documentation. +None of the documentation is generated from the [main Turing.jl repository](https://github.com/TuringLang/Turing.jl); in particular, the API that Turing exports does not currently form part of the documentation. -Other sections of the website (anything that isn't a package, or a tutorial)—for example, the list of libraries—is built from the [`turinglang.github.io` repository](https://github.com/TuringLang/turinglang.github.io). +Other sections of the website (anything that isn't a package, or a tutorial) — for example, the list of libraries — is built from the [`turinglang.github.io` repository](https://github.com/TuringLang/turinglang.github.io). ### Tests @@ -49,7 +49,7 @@ Or otherwise, set the global `ARGS` variable, and call `include("test/runtests.j ### Style Guide -Turing has a [style guide](#style-guide). +Turing has a style guide, described below. Reviewing it before making a pull request is not strictly necessary, but you may be asked to change portions of your code to conform with the style guide before it is merged. Most Turing code follows [Blue: a Style Guide for Julia](https://github.com/JuliaDiff/BlueStyle). From e839f3f9d9fd037dc054cd49a03f72021a64eb47 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 2 Sep 2024 15:05:05 +0100 Subject: [PATCH 6/6] en dash --- tutorials/docs-01-contributing-guide/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/docs-01-contributing-guide/index.qmd b/tutorials/docs-01-contributing-guide/index.qmd index 02a3f94a7..3ee296ef8 100755 --- a/tutorials/docs-01-contributing-guide/index.qmd +++ b/tutorials/docs-01-contributing-guide/index.qmd @@ -23,7 +23,7 @@ For example, the source code for DynamicPPL's documentation can be found in [its The documentation for Turing.jl itself consists of the tutorials that you see on this website, and is built from the separate [`docs` repository](https://github.com/TuringLang/docs). None of the documentation is generated from the [main Turing.jl repository](https://github.com/TuringLang/Turing.jl); in particular, the API that Turing exports does not currently form part of the documentation. -Other sections of the website (anything that isn't a package, or a tutorial) — for example, the list of libraries — is built from the [`turinglang.github.io` repository](https://github.com/TuringLang/turinglang.github.io). +Other sections of the website (anything that isn't a package, or a tutorial) – for example, the list of libraries – is built from the [`turinglang.github.io` repository](https://github.com/TuringLang/turinglang.github.io). ### Tests