From 7ccaeb5fdd1c5eff8fb287b6479d09a960d6d545 Mon Sep 17 00:00:00 2001 From: pat-alt Date: Mon, 29 Apr 2024 13:42:09 +0200 Subject: [PATCH 1/3] updated --- README.md | 2 +- README.qmd | 2 +- .../figure-commonmark/cell-3-output-1.svg | 4054 ++++---- .../figure-commonmark/cell-8-output-1.svg | 9183 +++++++++-------- docs/Manifest.toml | 1918 ++-- docs/setup_docs.jl | 2 +- docs/src/_intro.qmd | 3 +- 7 files changed, 7878 insertions(+), 7286 deletions(-) diff --git a/README.md b/README.md index 8403196..5bf759b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ - # `JointEnergyModels.jl` + *Joint Energy Models in Julia.* [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliatrustworthyai.github.io/JointEnergyModels.jl/stable) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliatrustworthyai.github.io/JointEnergyModels.jl/dev) [![Build Status](https://github.com/juliatrustworthyai/JointEnergyModels.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/juliatrustworthyai/JointEnergyModels.jl/actions/workflows/CI.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/juliatrustworthyai/JointEnergyModels.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/juliatrustworthyai/JointEnergyModels.jl) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) [![License](https://img.shields.io/github/license/juliatrustworthyai/JointEnergyModels.jl)](LICENSE) [![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/JointEnergyModels/.png)](https://pkgs.genieframework.com?packages=JointEnergyModels) diff --git a/README.qmd b/README.qmd index a7dd409..f20046c 100644 --- a/README.qmd +++ b/README.qmd @@ -9,7 +9,7 @@ crossref: tbl-prefix: Table bibliography: bib.bib output: asis -jupyter: julia-1.8 +jupyter: julia-1.10 execute: freeze: auto eval: true diff --git a/README_files/figure-commonmark/cell-3-output-1.svg b/README_files/figure-commonmark/cell-3-output-1.svg index 80c8452..58006b3 100644 --- a/README_files/figure-commonmark/cell-3-output-1.svg +++ b/README_files/figure-commonmark/cell-3-output-1.svg @@ -1,2042 +1,2042 @@ - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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"a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -38,9 +52,9 @@ version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" +git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.1.0" +version = "0.4.0" [[deps.Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] @@ -55,10 +69,32 @@ uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" +deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "133a240faec6e074e07c31ee75619c90544179cf" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.3" +version = "7.10.0" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesExt = "ChainRules" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -69,34 +105,54 @@ git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" version = "0.1.0" +[[deps.AtomsBase]] +deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"] +git-tree-sha1 = "995c2b6b17840cd87b722ce9c6cdd72f47bab545" +uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a" +version = "0.3.5" + [[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] -git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" +git-tree-sha1 = "01b8ccb13d68535d73d2b0c23e39bd23155fb712" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" -version = "1.0.1" +version = "1.1.0" [[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" +git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.6" +version = "0.4.7" [[deps.BFloat16s]] deps = ["LinearAlgebra", "Printf", "Random", "Test"] -git-tree-sha1 = "dbf84058d0a8cbbadee18d25cf606934b22d7c66" +git-tree-sha1 = "2c7cc21e8678eff479978a0a2ef5ce2f51b63dff" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.4.2" +version = "0.5.0" [[deps.BSON]] -git-tree-sha1 = "2208958832d6e1b59e49f53697483a84ca8d664e" +git-tree-sha1 = "4c3e506685c527ac6a54ccc0c8c76fd6f91b42fb" uuid = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" -version = "0.3.7" +version = "0.3.9" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "7aa7ad1682f3d5754e3491bb59b8103cae28e3a3" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.3.40" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -107,67 +163,78 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.BitFlags]] -git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.7" +version = "0.1.8" + +[[deps.BitTwiddlingConvenienceFunctions]] +deps = ["Static"] +git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" +version = "0.1.5" [[deps.BufferedStreams]] -git-tree-sha1 = "bb065b14d7f941b8617bc323063dbe79f55d16ea" +git-tree-sha1 = "4ae47f9a4b1dc19897d3743ff13685925c5202ec" uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" -version = "1.1.0" +version = "1.2.1" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" +version = "1.0.8+1" [[deps.CEnum]] -git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" +git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.2" +version = "0.5.0" + +[[deps.CPUSummary]] +deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] +git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" +uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" +version = "0.2.4" [[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "SnoopPrecompile", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "c700cce799b51c9045473de751e9319bdd1c6e94" +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.9" +version = "0.10.14" [[deps.CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Preferences", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "8547829ee0da896ce48a24b8d2f4bf929cf3e45e" +deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics"] +git-tree-sha1 = "4e33522a036b39fc6f5cb7447ae3b28eb8fbe99b" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "4.1.4" +version = "5.3.3" +weakdeps = ["ChainRulesCore", "SpecialFunctions"] + + [deps.CUDA.extensions] + ChainRulesCoreExt = "ChainRulesCore" + SpecialFunctionsExt = "SpecialFunctions" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = 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"ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.24.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.11.5" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] @@ -259,11 +343,6 @@ git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.12.10" -[[deps.Combinatorics]] -git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" -uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" -version = "1.0.2" - [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" @@ -271,31 +350,52 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.6.1" +version = "4.14.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.1+0" +version = "1.1.0+0" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + + [deps.CompositionsBase.weakdeps] + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.ComputationalResources]] git-tree-sha1 = "52cb3ec90e8a8bea0e62e275ba577ad0f74821f7" uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3" version = "0.3.2" +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.4.1" + [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" +git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.1" +version = "1.5.5" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -304,21 +404,37 @@ uuid = "6add18c4-b38d-439d-96f6-d6bc489c04c5" version = "0.1.3" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" [[deps.CoordinateTransformations]] deps = ["LinearAlgebra", "StaticArrays"] -git-tree-sha1 = "681ea870b918e7cff7111da58791d7f718067a19" +git-tree-sha1 = "f9d7112bfff8a19a3a4ea4e03a8e6a91fe8456bf" uuid = "150eb455-5306-5404-9cee-2592286d6298" -version = "0.6.2" +version = "0.6.3" [[deps.CounterfactualExplanations]] -deps = ["CSV", "CUDA", "CategoricalArrays", "DataFrames", "Flux", "LaplaceRedux", "LazyArtifacts", "LinearAlgebra", "MLDatasets", "MLJBase", "MLJModels", "MLUtils", "MultivariateStats", "NearestNeighborModels", "Parameters", "Plots", "ProgressMeter", "Random", "Serialization", "SliceMap", "SnoopPrecompile", "Statistics", "StatsBase", "Tables", "UMAP"] -git-tree-sha1 = "fec2f4fff04fd9cb2a86e0957757bf9e42ad2f29" +deps = ["CategoricalArrays", "ChainRulesCore", "DataFrames", "DecisionTree", "Distributions", "Flux", "LazyArtifacts", "LinearAlgebra", "Logging", "MLJBase", "MLJDecisionTreeInterface", "MLUtils", "MultivariateStats", "PackageExtensionCompat", "ProgressMeter", "Random", "Serialization", "Statistics", "StatsBase", "Tables", "TaijaBase", "UUIDs"] +git-tree-sha1 = "be60a64de3a3b46940c402e6bd8a4d6a94208d9c" uuid = "2f13d31b-18db-44c1-bc43-ebaf2cff0be0" -version = "0.1.9" +version = "1.1.4" + + [deps.CounterfactualExplanations.extensions] + EvoTreesExt = "EvoTrees" + LaplaceReduxExt = "LaplaceRedux" + NeuroTreeExt = "NeuroTreeModels" + + [deps.CounterfactualExplanations.weakdeps] + EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" + LaplaceRedux = "c52c1a26-f7c5-402b-80be-ba1e638ad478" + NeuroTreeModels = "1db4e0a5-a364-4b0c-897c-2bd5a4a3a1f2" + +[[deps.CpuId]] +deps = ["Markdown"] +git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" +uuid = "adafc99b-e345-5852-983c-f28acb93d879" +version = "0.3.1" [[deps.Crayons]] git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" @@ -331,27 +447,27 @@ uuid = "dc8bdbbb-1ca9-579f-8c36-e416f6a65cce" version = "1.0.2" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.16.0" [[deps.DataDeps]] -deps = ["HTTP", "Libdl", "Reexport", "SHA", "p7zip_jll"] -git-tree-sha1 = "bc0a264d3e7b3eeb0b6fc9f6481f970697f29805" +deps = ["HTTP", "Libdl", "Reexport", "SHA", "Scratch", "p7zip_jll"] +git-tree-sha1 = "8ae085b71c462c2cb1cfedcb10c3c877ec6cf03f" uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" -version = "0.7.10" +version = "0.7.13" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.5.0" +version = "1.6.1" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -362,6 +478,12 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.DecisionTree]] +deps = ["AbstractTrees", "DelimitedFiles", "LinearAlgebra", "Random", "ScikitLearnBase", "Statistics"] +git-tree-sha1 = "526ca14aaaf2d5a0e242f3a8a7966eb9065d7d78" +uuid = "7806a523-6efd-50cb-b5f6-3fa6f1930dbb" +version = "0.12.4" + [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" @@ -369,13 +491,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.DensityInterface]] -deps = ["InverseFunctions", "Test"] -git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" -uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" -version = "0.4.0" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -385,25 +503,40 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.13.0" +version = "1.15.1" [[deps.Distances]] -deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.8" +version = "0.10.11" +weakdeps = ["ChainRulesCore", "SparseArrays"] + + [deps.Distances.extensions] + DistancesChainRulesCoreExt = "ChainRulesCore" + DistancesSparseArraysExt = "SparseArrays" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "13027f188d26206b9e7b863036f87d2f2e7d013a" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "22c595ca4146c07b16bcf9c8bea86f731f7109d2" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.87" +version = "0.25.108" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + DistributionsTestExt = "Test" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -412,10 +545,10 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.Documenter]] -deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "58fea7c536acd71f3eef6be3b21c0df5f3df88fd" +deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"] +git-tree-sha1 = "f15a91e6e3919055efa4f206f942a73fedf5dfe6" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.24" +version = "1.4.0" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -428,16 +561,28 @@ git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" +[[deps.EpollShim_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" +uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" +version = "0.0.20230411+0" + +[[deps.ExceptionUnwrapping]] +deps = ["Test"] +git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" +version = "0.1.10" + [[deps.Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.8+0" +version = "2.5.0+0" [[deps.ExprTools]] -git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" +git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.9" +version = "0.1.10" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -446,10 +591,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.2+2" +version = "4.4.4+1" [[deps.FFTViews]] deps = ["CustomUnitRanges", "FFTW"] @@ -459,9 +604,9 @@ version = "0.3.2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "f9818144ce7c8c41edf5c4c179c684d92aa4d9fe" +git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.6.0" +version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -483,30 +628,30 @@ version = "0.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.3" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12" +git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.20" +version = "0.9.21" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" +deps = ["LinearAlgebra"] +git-tree-sha1 = "57f08d5665e76397e96b168f9acc12ab17c84a68" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.11" +version = "1.10.2" +weakdeps = ["PDMats", "SparseArrays", "Statistics"] -[[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "03fcb1c42ec905d15b305359603888ec3e65f886" -uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.19.0" + [deps.FillArrays.extensions] + FillArraysPDMatsExt = "PDMats" + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -515,16 +660,22 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[deps.Flux]] -deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Zygote", "cuDNN"] -git-tree-sha1 = "3f6f32ec0bfd80be0cb65907cf74ec796a632012" +deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "a5475163b611812d073171583982c42ea48d22b0" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.13.15" +version = "0.14.15" -[[deps.FoldsThreads]] -deps = ["Accessors", "FunctionWrappers", "InitialValues", "SplittablesBase", "Transducers"] -git-tree-sha1 = "eb8e1989b9028f7e0985b4268dabe94682249025" -uuid = "9c68100b-dfe1-47cf-94c8-95104e173443" -version = "0.1.1" + [deps.Flux.extensions] + FluxAMDGPUExt = "AMDGPU" + FluxCUDAExt = "CUDA" + FluxCUDAcuDNNExt = ["CUDA", "cuDNN"] + FluxMetalExt = "Metal" + + [deps.Flux.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] @@ -532,23 +683,26 @@ git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" version = "2.13.93+0" -[[deps.Formatting]] -deps = ["Printf"] -git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" -uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" -version = "0.4.2" +[[deps.Format]] +git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" +uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8" +version = "1.3.7" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.35" +version = "0.10.36" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] -deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" +deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.4+0" +version = "2.13.1+0" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -556,62 +710,57 @@ git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" -[[deps.FunctionWrappers]] -git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" -uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" -version = "1.1.3" - [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "478f8c3145bb91d82c2cf20433e8c1b30df454cc" +git-tree-sha1 = "d3e63d9fa13f8eaa2f06f64949e2afc593ff52c2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.4" +version = "0.4.10" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] +git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.8+0" +version = "3.3.9+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "9ade6983c3dbbd492cf5729f865fe030d1541463" +git-tree-sha1 = "68e8ff56a4a355a85d2784b94614491f8c900cde" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.6.6" +version = "10.1.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" +git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.4" +version = "0.1.6" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "e9a9173cd77e16509cdf9c1663fda19b22a518b7" +git-tree-sha1 = "1600477fba37c9fc067b9be21f5e8101f24a8865" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.19.3" +version = "0.26.4" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "db730189e3d250d97515a91886de7e33aa8833e6" +git-tree-sha1 = "3437ade7073682993e092ca570ad68a2aba26983" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.2" +version = "0.73.3" [[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "47a2efe07729dd508a032e2f56c46c517481052a" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "a96d5c713e6aa28c242b0d25c1347e258d6541ab" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.2+0" +version = "0.73.3+0" [[deps.GZip]] -deps = ["Libdl"] -git-tree-sha1 = "039be665faf0b8ae36e089cd694233f5dee3f7d6" +deps = ["Libdl", "Zlib_jll"] +git-tree-sha1 = "0085ccd5ec327c077ec5b91a5f937b759810ba62" uuid = "92fee26a-97fe-5a0c-ad85-20a5f3185b63" -version = "0.5.1" +version = "0.6.2" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -625,11 +774,23 @@ git-tree-sha1 = "43ba3d3c82c18d88471cfd2924931658838c9d8f" uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b" version = "9.55.0+4" +[[deps.Git]] +deps = ["Git_jll"] +git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e" +uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" +version = "1.3.1" + +[[deps.Git_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "d18fb8a1f3609361ebda9bf029b60fd0f120c809" +uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" +version = "2.44.0+2" + [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.80.0+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -650,9 +811,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" +git-tree-sha1 = "3863330da5466410782f2bffc64f3d505a6a8334" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.8.0" +version = "1.10.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -660,22 +821,28 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HDF5]] -deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires", "UUIDs"] -git-tree-sha1 = "3dab31542b3da9f25a6a1d11159d4af8fdce7d67" +deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] +git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.16.14" +version = "0.17.2" + + [deps.HDF5.extensions] + MPIExt = "MPI" + + [deps.HDF5.weakdeps] + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" [[deps.HDF5_jll]] -deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.12.2+2" +version = "1.14.2+1" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "2c3ec1f90bb4a8f7beafb0cffea8a4c3f4e636ab" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.7.4" +version = "1.10.6" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -683,29 +850,52 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" +[[deps.HistogramThresholding]] +deps = ["ImageBase", "LinearAlgebra", "MappedArrays"] +git-tree-sha1 = "7194dfbb2f8d945abdaf68fa9480a965d6661e69" +uuid = "2c695a8d-9458-5d45-9878-1b8a99cf7853" +version = "0.3.1" + +[[deps.HostCPUFeatures]] +deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] +git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" +version = "0.1.16" + +[[deps.Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.10.0+0" + [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "432b5b03176f8182bd6841fbfc42c718506a2d5f" +git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.15" +version = "0.3.23" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.4" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "0ade27f0c49cebd8db2523c4eeccf779407cf12c" +git-tree-sha1 = "d05027a62b4c9a2223820a9fdeae1110ad3946a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.9" +version = "0.4.13" + +[[deps.IfElse]] +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" +uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" +version = "0.1.1" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] -git-tree-sha1 = "c54b581a83008dc7f292e205f4c409ab5caa0f04" +git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" -version = "0.6.10" +version = "0.6.11" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -713,11 +903,17 @@ git-tree-sha1 = "b51bb8cae22c66d0f6357e3bcb6363145ef20835" uuid = "c817782e-172a-44cc-b673-b171935fbb9e" version = "0.1.5" +[[deps.ImageBinarization]] +deps = ["HistogramThresholding", "ImageCore", "LinearAlgebra", "Polynomials", "Reexport", "Statistics"] +git-tree-sha1 = "f5356e7203c4a9954962e3757c08033f2efe578a" +uuid = "cbc4b850-ae4b-5111-9e64-df94c024a13d" +version = "0.3.0" + [[deps.ImageContrastAdjustment]] -deps = ["ImageCore", "ImageTransformations", "Parameters"] -git-tree-sha1 = "0d75cafa80cf22026cea21a8e6cf965295003edc" +deps = ["ImageBase", "ImageCore", "ImageTransformations", "Parameters"] +git-tree-sha1 = "eb3d4365a10e3f3ecb3b115e9d12db131d28a386" uuid = "f332f351-ec65-5f6a-b3d1-319c6670881a" -version = "0.3.10" +version = "0.3.12" [[deps.ImageCore]] deps = ["AbstractFFTs", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Graphics", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "Reexport"] @@ -725,23 +921,29 @@ git-tree-sha1 = "acf614720ef026d38400b3817614c45882d75500" uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" version = "0.9.4" +[[deps.ImageCorners]] +deps = ["ImageCore", "ImageFiltering", "PrecompileTools", "StaticArrays", "StatsBase"] +git-tree-sha1 = "24c52de051293745a9bad7d73497708954562b79" +uuid = "89d5987c-236e-4e32-acd0-25bd6bd87b70" +version = "0.1.3" + [[deps.ImageDistances]] deps = ["Distances", "ImageCore", "ImageMorphology", "LinearAlgebra", "Statistics"] -git-tree-sha1 = "b1798a4a6b9aafb530f8f0c4a7b2eb5501e2f2a3" +git-tree-sha1 = "08b0e6354b21ef5dd5e49026028e41831401aca8" uuid = "51556ac3-7006-55f5-8cb3-34580c88182d" -version = "0.2.16" +version = "0.2.17" [[deps.ImageFiltering]] -deps = ["CatIndices", "ComputationalResources", "DataStructures", "FFTViews", "FFTW", "ImageBase", "ImageCore", "LinearAlgebra", "OffsetArrays", "Reexport", "SnoopPrecompile", "SparseArrays", "StaticArrays", "Statistics", "TiledIteration"] -git-tree-sha1 = "f265e53558fbbf23e0d54e4fab7106c0f2a9e576" +deps = ["CatIndices", "ComputationalResources", "DataStructures", "FFTViews", "FFTW", "ImageBase", "ImageCore", "LinearAlgebra", "OffsetArrays", "PrecompileTools", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "TiledIteration"] +git-tree-sha1 = "3447781d4c80dbe6d71d239f7cfb1f8049d4c84f" uuid = "6a3955dd-da59-5b1f-98d4-e7296123deb5" -version = "0.7.3" +version = "0.7.6" [[deps.ImageIO]] deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] -git-tree-sha1 = "342f789fd041a55166764c351da1710db97ce0e0" +git-tree-sha1 = "bca20b2f5d00c4fbc192c3212da8fa79f4688009" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.6" +version = "0.6.7" [[deps.ImageMagick]] deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils", "Libdl", "Pkg", "Random"] @@ -750,52 +952,52 @@ uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1" version = "1.2.1" [[deps.ImageMagick_jll]] -deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "124626988534986113cfd876e3093e4a03890f58" +deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "d65554bad8b16d9562050c67e7223abf91eaba2f" uuid = "c73af94c-d91f-53ed-93a7-00f77d67a9d7" -version = "6.9.12+3" +version = "6.9.13+0" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] -git-tree-sha1 = "36cbaebed194b292590cba2593da27b34763804a" +git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7" uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" -version = "0.9.8" +version = "0.9.9" [[deps.ImageMorphology]] -deps = ["ImageCore", "LinearAlgebra", "Requires", "TiledIteration"] -git-tree-sha1 = "e7c68ab3df4a75511ba33fc5d8d9098007b579a8" +deps = ["DataStructures", "ImageCore", "LinearAlgebra", "LoopVectorization", "OffsetArrays", "Requires", "TiledIteration"] +git-tree-sha1 = "6f0a801136cb9c229aebea0df296cdcd471dbcd1" uuid = "787d08f9-d448-5407-9aad-5290dd7ab264" -version = "0.3.2" +version = "0.4.5" [[deps.ImageQualityIndexes]] -deps = ["ImageContrastAdjustment", "ImageCore", "ImageDistances", "ImageFiltering", "LazyModules", "OffsetArrays", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "5985d467623f106523ed8351f255642b5141e7be" +deps = ["ImageContrastAdjustment", "ImageCore", "ImageDistances", "ImageFiltering", "LazyModules", "OffsetArrays", "PrecompileTools", "Statistics"] +git-tree-sha1 = "783b70725ed326340adf225be4889906c96b8fd1" uuid = "2996bd0c-7a13-11e9-2da2-2f5ce47296a9" -version = "0.3.4" +version = "0.3.7" [[deps.ImageSegmentation]] deps = ["Clustering", "DataStructures", "Distances", "Graphs", "ImageCore", "ImageFiltering", "ImageMorphology", "LinearAlgebra", "MetaGraphs", "RegionTrees", "SimpleWeightedGraphs", "StaticArrays", "Statistics"] -git-tree-sha1 = "fb0b597b4928e29fed0597724cfbb5940974f8ca" +git-tree-sha1 = "44664eea5408828c03e5addb84fa4f916132fc26" uuid = "80713f31-8817-5129-9cf8-209ff8fb23e1" -version = "1.8.0" +version = "1.8.1" [[deps.ImageShow]] deps = ["Base64", "ColorSchemes", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"] -git-tree-sha1 = "ce28c68c900eed3cdbfa418be66ed053e54d4f56" +git-tree-sha1 = "3b5344bcdbdc11ad58f3b1956709b5b9345355de" uuid = "4e3cecfd-b093-5904-9786-8bbb286a6a31" -version = "0.3.7" +version = "0.3.8" [[deps.ImageTransformations]] -deps = ["AxisAlgorithms", "ColorVectorSpace", "CoordinateTransformations", "ImageBase", "ImageCore", "Interpolations", "OffsetArrays", "Rotations", "StaticArrays"] -git-tree-sha1 = "8717482f4a2108c9358e5c3ca903d3a6113badc9" +deps = ["AxisAlgorithms", "CoordinateTransformations", "ImageBase", "ImageCore", "Interpolations", "OffsetArrays", "Rotations", "StaticArrays"] +git-tree-sha1 = "e0884bdf01bbbb111aea77c348368a86fb4b5ab6" uuid = "02fcd773-0e25-5acc-982a-7f6622650795" -version = "0.9.5" +version = "0.10.1" [[deps.Images]] -deps = ["Base64", "FileIO", "Graphics", "ImageAxes", "ImageBase", "ImageContrastAdjustment", "ImageCore", "ImageDistances", "ImageFiltering", "ImageIO", "ImageMagick", "ImageMetadata", "ImageMorphology", "ImageQualityIndexes", "ImageSegmentation", "ImageShow", "ImageTransformations", "IndirectArrays", "IntegralArrays", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TiledIteration"] -git-tree-sha1 = "03d1301b7ec885b266c0f816f338368c6c0b81bd" +deps = ["Base64", "FileIO", "Graphics", "ImageAxes", "ImageBase", "ImageBinarization", "ImageContrastAdjustment", "ImageCore", "ImageCorners", "ImageDistances", "ImageFiltering", "ImageIO", "ImageMagick", "ImageMetadata", "ImageMorphology", "ImageQualityIndexes", "ImageSegmentation", "ImageShow", "ImageTransformations", "IndirectArrays", "IntegralArrays", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TiledIteration"] +git-tree-sha1 = "12fdd617c7fe25dc4a6cc804d657cc4b2230302b" uuid = "916415d5-f1e6-5110-898d-aaa5f9f070e0" -version = "0.25.2" +version = "0.26.1" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -809,14 +1011,9 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" version = "1.0.0" [[deps.Inflate]] -git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" +git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.3" - -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" +version = "0.1.4" [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" @@ -836,10 +1033,10 @@ uuid = "1d092043-8f09-5a30-832f-7509e371ab51" version = "0.1.5" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2023.1.0+0" +version = "2024.1.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -853,21 +1050,24 @@ version = "0.7.0" [[deps.Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" +git-tree-sha1 = "88a101217d7cb38a7b481ccd50d21876e1d1b0e0" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.14.7" +version = "0.15.1" +weakdeps = ["Unitful"] + + [deps.Interpolations.extensions] + InterpolationsUnitfulExt = "Unitful" [[deps.IntervalSets]] -deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" +git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.4" +version = "0.7.10" +weakdeps = ["Random", "RecipesBase", "Statistics"] -[[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" -uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" + [deps.IntervalSets.extensions] + IntervalSetsRandomExt = "Random" + IntervalSetsRecipesBaseExt = "RecipesBase" + IntervalSetsStatisticsExt = "Statistics" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -880,9 +1080,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" [[deps.IterTools]] -git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.4.0" +version = "1.10.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -890,22 +1090,22 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "5ea6acdd53a51d897672edb694e3cc2912f3f8a7" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.31" +version = "0.4.46" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.5" +version = "0.1.7" [[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"] @@ -914,28 +1114,40 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.14.0" + + [deps.JSON3.extensions] + JSON3ArrowExt = ["ArrowTypes"] + + [deps.JSON3.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" [[deps.JointEnergyModels]] -deps = ["CategoricalArrays", "ChainRulesCore", "ComputationalResources", "Distributions", "Flux", "MLJFlux", "MLJModelInterface", "MLUtils", "PkgTemplates", "ProgressMeter", "Random", "StatsBase", "Tables"] +deps = ["CategoricalArrays", "ChainRulesCore", "ComputationalResources", "Distributions", "Flux", "MLJFlux", "MLJModelInterface", "MLUtils", "ProgressMeter", "Random", "StatsBase", "Tables", "Zygote"] path = ".." uuid = "48c56d24-211d-4463-bbc0-7a701b291131" -version = "0.1.0" +version = "0.1.3" [[deps.JpegTurbo]] deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] -git-tree-sha1 = "106b6aa272f294ba47e96bd3acbabdc0407b5c60" +git-tree-sha1 = "fa6d0bcff8583bac20f1ffa708c3913ca605c611" uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" -version = "0.1.2" +version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" +git-tree-sha1 = "3336abae9a713d2210bb57ab484b1e065edd7d23" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.91+0" +version = "3.0.2+0" + +[[deps.JuliaNVTXCallbacks_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "af433a10f3942e882d3c671aacb203e006a5808f" +uuid = "9c1d0b0a-7046-5b2e-a33f-ea22f176ac7e" +version = "0.2.1+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -943,16 +1155,17 @@ git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" -[[deps.JuliennedArrays]] -git-tree-sha1 = "4aeebbfcf0615641ec4b0782b73b638eeeabd62e" -uuid = "5cadff95-7770-533d-a838-a1bf817ee6e0" -version = "0.3.0" - [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "SnoopPrecompile", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "976231af02176082fb266a9f96a59da51fcacf20" +deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "ed7167240f40e62d97c1f5f7735dea6de3cc5c49" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.2" +version = "0.9.18" + + [deps.KernelAbstractions.extensions] + EnzymeExt = "EnzymeCore" + + [deps.KernelAbstractions.weakdeps] + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -967,16 +1180,31 @@ uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "3.0.0+1" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "a8960cae30b42b66dd41808beb76490519f6f9e2" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] +git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "5.0.0" +version = "6.6.3" +weakdeps = ["BFloat16s"] + + [deps.LLVM.extensions] + BFloat16sExt = "BFloat16s" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "09b7505cc0b1cee87e5d4a26eea61d2e1b0dcd35" +git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.21+0" +version = "0.0.29+0" + +[[deps.LLVMLoopInfo]] +git-tree-sha1 = "2e5c102cfc41f48ae4740c7eca7743cc7e7b75ea" +uuid = "8b046642-f1f6-4319-8d3c-209ddc03c586" +version = "1.0.0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -985,21 +1213,34 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.0" - -[[deps.LaplaceRedux]] -deps = ["Flux", "LinearAlgebra", "Parameters", "Plots", "Zygote"] -git-tree-sha1 = "a4adebbeafb96d0864b4833c254013f66dc6e0ee" -uuid = "c52c1a26-f7c5-402b-80be-ba1e638ad478" -version = "0.1.2" +version = "1.3.1" [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "98dc144f1e0b299d49e8d23e56ad68d3e4f340a5" +deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] +git-tree-sha1 = "e0b5cd21dc1b44ec6e64f351976f961e6f31d6c4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.20" +version = "0.16.3" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" + +[[deps.LayoutPointers]] +deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +uuid = "10f19ff3-798f-405d-979b-55457f8fc047" +version = "0.1.15" + +[[deps.LazilyInitializedFields]] +git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612" +uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" +version = "1.2.2" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -1010,24 +1251,35 @@ git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e" version = "0.3.1" +[[deps.LearnAPI]] +deps = ["InteractiveUtils", "Statistics"] +git-tree-sha1 = "ec695822c1faaaa64cee32d0b21505e1977b4809" +uuid = "92ad9a40-7767-427a-9ee6-6e577f1266cb" +version = "0.1.0" + [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] 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"JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "4b683b19157282f50bfd5dcaa2efe5295814ea22" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.35.0+0" +version = "2.40.0+0" [[deps.Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" uuid = 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"ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LinearAlgebra", "LossFunctions", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "ScientificTypes", "Serialization", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "e99e84c7ca1696b38e2a8823f53ac9cc775599dd" +deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LearnAPI", "LinearAlgebra", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "RecipesBase", "Reexport", "ScientificTypes", "Serialization", "StatisticalMeasuresBase", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] +git-tree-sha1 = "17d160e8f796ab5ceb4c017bc4019d21fd686a35" uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -version = "0.21.9" +version = "1.2.1" + + [deps.MLJBase.extensions] + DefaultMeasuresExt = "StatisticalMeasures" + + [deps.MLJBase.weakdeps] + StatisticalMeasures = "a19d573c-0a75-4610-95b3-7071388c7541" + +[[deps.MLJDecisionTreeInterface]] +deps = ["CategoricalArrays", "DecisionTree", "MLJModelInterface", "Random", "Tables"] +git-tree-sha1 = "90ef4d3b6cacec631c57cc034e1e61b4aa0ce511" +uuid = "c6f25543-311c-4c74-83dc-3ea6d1015661" +version = "0.4.2" [[deps.MLJFlux]] deps = ["CategoricalArrays", "ColorTypes", "ComputationalResources", "Flux", "MLJModelInterface", "Metalhead", "ProgressMeter", "Random", "Statistics", "Tables"] -git-tree-sha1 = "b27c3b96cc2a602a1e91eba36b8ca3d796f30ae0" +git-tree-sha1 = "40f9e99a6770bc795f70f1908316e1491488a7b7" uuid = "094fc8d1-fd35-5302-93ea-dabda2abf845" -version = "0.2.10" +version = "0.3.1" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "d2a45e1b5998ba3fdfb6cfe0c81096d4c7fb40e7" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" - -[[deps.MLJModels]] -deps = ["CategoricalArrays", "CategoricalDistributions", "Combinatorics", "Dates", "Distances", "Distributions", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "Markdown", "OrderedCollections", "Parameters", "Pkg", "PrettyPrinting", "REPL", "Random", "RelocatableFolders", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "21acf47dc53ccc3d68e38ac7629756cd09b599f5" -uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7" -version = "0.16.6" +version = "1.9.6" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1165,42 +1432,65 @@ uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "FoldsThreads", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "f69cdbb5b7c630c02481d81d50eac43697084fe0" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.4.1" +version = "0.4.4" + +[[deps.MPICH_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "d8a7bf80c88326ebc98b7d38437208c3a0f20725" +uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" +version = "4.2.1+0" + +[[deps.MPIPreferences]] +deps = ["Libdl", "Preferences"] +git-tree-sha1 = "8f6af051b9e8ec597fa09d8885ed79fd582f33c9" +uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.10" + +[[deps.MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "3f884417b47a96d87e7c6219f8f7b30ce67f4f2c" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.3.3+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.13" + +[[deps.ManualMemory]] +git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" +uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" +version = "0.1.8" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" - -[[deps.MarchingCubes]] -deps = ["SnoopPrecompile", "StaticArrays"] -git-tree-sha1 = "b198463d1a631e8771709bc8e011ba329da9ad38" -uuid = "299715c1-40a9-479a-aaf9-4a633d36f717" -version = "0.1.7" +version = 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= ["Artifacts", "BSON", "Flux", "Functors", "LazyArtifacts", "MLUtils", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "0e95f91cc5f23610f8f270d7397f307b21e19d2b" +deps = ["Artifacts", "BSON", "CUDA", "ChainRulesCore", "Flux", "Functors", "JLD2", "LazyArtifacts", "MLUtils", "NNlib", "PartialFunctions", "Random", "Statistics"] +git-tree-sha1 = "4bbdb628c60c5f473148292df3ecb87058ba515f" uuid = "dbeba491-748d-5e0e-a39e-b530a07fa0cc" -version = "0.7.4" +version = "0.8.3" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] @@ -1225,21 +1515,21 @@ git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" version = "0.1.4" +[[deps.MicrosoftMPI_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" +uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" +version = "10.1.4+2" + [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -[[deps.Mocking]] -deps = ["Compat", "ExprTools"] -git-tree-sha1 = "782e258e80d68a73d8c916e55f8ced1de00c2cea" -uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.7.6" - [[deps.MosaicViews]] deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] git-tree-sha1 = "7b86a5d4d70a9f5cdf2dacb3cbe6d251d1a61dbe" @@ -1248,37 +1538,31 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2023.1.10" [[deps.MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "91a48569383df24f0fd2baf789df2aade3d0ad80" +git-tree-sha1 = "68bf5103e002c44adfd71fea6bd770b3f0586843" uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.10.1" - -[[deps.Mustache]] -deps = ["Printf", "Tables"] -git-tree-sha1 = "87c371d27dbf2449a5685652ab322be163269df0" -uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.15" - -[[deps.NLSolversBase]] -deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" -uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.3" +version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" +git-tree-sha1 = "5055845dd316575ae2fc1f6dcb3545ff15fe547a" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.20" +version = "0.9.14" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] + NNlibCUDAExt = "CUDA" + NNlibEnzymeCoreExt = "EnzymeCore" -[[deps.NNlibCUDA]] -deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics", "cuDNN"] -git-tree-sha1 = "f94a9684394ff0d325cc12b06da7032d8be01aaf" -uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.2.7" + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NPZ]] deps = ["FileIO", "ZipFile"] @@ -1286,6 +1570,18 @@ git-tree-sha1 = "60a8e272fe0c5079363b28b0953831e2dd7b7e6f" uuid = "15e1cf62-19b3-5cfa-8e77-841668bca605" version = "0.4.3" +[[deps.NVTX]] +deps = ["Colors", "JuliaNVTXCallbacks_jll", "Libdl", "NVTX_jll"] +git-tree-sha1 = "53046f0483375e3ed78e49190f1154fa0a4083a1" +uuid = "5da4648a-3479-48b8-97b9-01cb529c0a1f" +version = "0.3.4" + +[[deps.NVTX_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ce3269ed42816bf18d500c9f63418d4b0d9f5a3b" +uuid = "e98f9f5b-d649-5603-91fd-7774390e6439" +version = "3.1.0+2" + [[deps.NaNMath]] deps = ["OpenLibm_jll"] git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" @@ -1298,39 +1594,30 @@ git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e" uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391" version = "0.1.5" -[[deps.NearestNeighborDescent]] -deps = ["DataStructures", "Distances", "LightGraphs", "Random", "Reexport", "SparseArrays"] -git-tree-sha1 = "8f41eced4332166c3548bda137779c38975ac4af" -uuid = "dd2c4c9e-a32f-5b2f-b342-08c2f244fce8" -version = "0.3.5" - -[[deps.NearestNeighborModels]] -deps = ["Distances", "FillArrays", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "NearestNeighbors", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "c2179f9d8de066c481b889a1426068c5831bb10b" -uuid = "636a865e-7cf4-491e-846c-de09b730eb36" -version = "0.2.2" - [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "2c3726ceb3388917602169bed973dbc97f1b51a8" +git-tree-sha1 = "ded64ff6d4fdd1cb68dfcbb818c69e144a5b2e4c" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.13" +version = "0.4.16" [[deps.Netpbm]] deps = ["FileIO", "ImageCore", "ImageMetadata"] -git-tree-sha1 = "5ae7ca23e13855b3aba94550f26146c01d259267" +git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd" uuid = "f09324ee-3d7c-5217-9330-fc30815ba969" -version = "1.1.0" +version = "1.1.1" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.OffsetArrays]] -deps = ["Adapt"] -git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" +git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.9" +version = "1.14.0" +weakdeps = ["Adapt"] + + [deps.OffsetArrays.extensions] + OffsetArraysAdaptExt = "Adapt" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1340,14 +1627,14 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "f511fca956ed9e70b80cd3417bb8c2dde4b68644" +git-tree-sha1 = "963a3f28a2e65bb87a68033ea4a616002406037d" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.3" +version = "0.2.5" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.23+4" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] @@ -1361,22 +1648,34 @@ git-tree-sha1 = "a4ca623df1ae99d09bc9868b008262d0c0ac1e4f" uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" version = "3.1.4+0" +[[deps.OpenJpeg_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "libpng_jll"] +git-tree-sha1 = "8d4c87ffaf09dbdd82bcf8c939843e94dd424df2" +uuid = "643b3616-a352-519d-856d-80112ee9badc" +version = "2.5.0+0" + [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" +version = "0.8.1+2" + +[[deps.OpenMPI_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "PMIx_jll", "TOML", "Zlib_jll", "libevent_jll", "prrte_jll"] +git-tree-sha1 = "f46caf663e069027a06942d00dced37f1eb3d8ad" +uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" +version = "5.0.2+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "5b3e170ea0724f1e3ed6018c5b006c190f80e87d" +git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.5" +version = "1.4.3" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.20+0" +version = "3.0.13+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1384,17 +1683,11 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" -[[deps.OptimBase]] -deps = ["NLSolversBase", "Printf", "Reexport"] -git-tree-sha1 = "9cb1fee807b599b5f803809e85c81b582d2009d6" -uuid = "87e2bd06-a317-5318-96d9-3ecbac512eee" -version = "2.0.2" - [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "6a01f65dd8583dee82eecc2a19b0ff21521aa749" +git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.18" +version = "0.3.3" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1403,26 +1696,38 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.0" +version = "1.6.3" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" +git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.17" +version = "0.11.31" + +[[deps.PMIx_jll]] +deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "Zlib_jll", "libevent_jll"] +git-tree-sha1 = "360f48126b5f2c2f0c833be960097f7c62705976" +uuid = "32165bc3-0280-59bc-8c0b-c33b6203efab" +version = "4.2.9+0" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] -git-tree-sha1 = "f809158b27eba0c18c269cf2a2be6ed751d3e81d" +git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd" uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" -version = "0.3.17" +version = "0.4.3" + +[[deps.PackageExtensionCompat]] +git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" +uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" +version = "1.0.2" +weakdeps = ["Requires", "TOML"] [[deps.PaddedViews]] deps = ["OffsetArrays"] @@ -1437,10 +1742,22 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.8" +version = "2.8.1" + +[[deps.PartialFunctions]] +deps = ["MacroTools"] +git-tree-sha1 = "47b49a4dbc23b76682205c646252c0f9e1eb75af" +uuid = "570af359-4316-4cb7-8c74-252c00c2016b" +version = "1.2.0" + +[[deps.PeriodicTable]] +deps = ["Base64", "Unitful"] +git-tree-sha1 = "238aa6298007565529f911b734e18addd56985e1" +uuid = "7b2266bf-644c-5ea3-82d8-af4bbd25a884" +version = "1.2.1" [[deps.Pickle]] deps = ["DataStructures", "InternedStrings", "Serialization", "SparseArrays", "Strided", "StringEncodings", "ZipFile"] @@ -1454,27 +1771,21 @@ uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" version = "1.3.0" [[deps.Pixman_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] +git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.1+0" +version = "0.42.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" - -[[deps.PkgTemplates]] -deps = ["Dates", "InteractiveUtils", "LibGit2", "Mocking", "Mustache", "Parameters", "Pkg", "REPL", "UUIDs"] -git-tree-sha1 = "b8e88d61d55607c07ac1ed9dabf474cfab8490b9" -uuid = "14b8a8f1-9102-5b29-a752-f990bacb7fe1" -version = "0.7.34" +version = "1.10.0" [[deps.PkgVersion]] deps = ["Pkg"] -git-tree-sha1 = "f6cf8e7944e50901594838951729a1861e668cb8" +git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" -version = "0.3.2" +version = "0.3.3" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1483,44 +1794,81 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.1.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.4" +version = "1.4.1" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "5434b0ee344eaf2854de251f326df8720f6a7b55" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", 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"LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.3" +version = "2.3.1" [[deps.Printf]] deps = ["Unicode"] @@ -1528,9 +1876,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[deps.ProgressBars]] deps = ["Printf"] -git-tree-sha1 = "9d84c8646109eb8bc7a006d59b157c64d5155c81" +git-tree-sha1 = "b437cdb0385ed38312d91d9c00c20f3798b30256" uuid = "49802e3a-d2f1-5c88-81d8-b72133a6f568" -version = "1.5.0" +version = "1.5.1" [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] @@ -1540,9 +1888,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.10.0" [[deps.QOI]] deps = ["ColorTypes", "FileIO", 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[[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.7.0" [[deps.RandomNumbers]] deps = ["Random", "Requires"] @@ -1595,9 +1943,13 @@ version = "0.3.2" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.3" +version = "0.4.5" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -1606,16 +1958,16 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[deps.RecipesBase]] -deps = ["SnoopPrecompile"] -git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" +deps = ["PrecompileTools"] +git-tree-sha1 = 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["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" + +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.2" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.2.0" +version = "2.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1775,16 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"StaticArraysCore"] +git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.21" +version = "1.9.3" +weakdeps = ["ChainRulesCore", "Statistics"] + + [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" + StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.2" + +[[deps.StatisticalMeasuresBase]] +deps = ["CategoricalArrays", "InteractiveUtils", "MLUtils", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "Statistics"] +git-tree-sha1 = "17dfb22e2e4ccc9cd59b487dce52883e0151b4d3" +uuid = "c062fc1d-0d66-479b-b6ac-8b44719de4cc" +version = "0.1.1" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] @@ -1795,24 +2201,33 @@ version = "3.2.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" +git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.21" +version = "0.34.3" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.0" +version = "1.3.1" + + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Strided]] deps = ["LinearAlgebra", "TupleTools"] @@ -1822,20 +2237,28 @@ version = "1.2.3" [[deps.StringEncodings]] deps = ["Libiconv_jll"] -git-tree-sha1 = "33c0da881af3248dafefb939a21694b97cfece76" +git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" -version = "0.3.6" +version = "0.3.7" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.4" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["ConstructionBase", "DataAPI", "Tables"] +git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.18" +weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] + + [deps.StructArrays.extensions] + StructArraysAdaptExt = "Adapt" + StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysSparseArraysExt = "SparseArrays" + StructArraysStaticArraysExt = "StaticArrays" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1847,10 +2270,15 @@ version = "1.10.0" deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "7.2.1+1" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1859,15 +2287,20 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.1" +version = "1.11.1" + +[[deps.TaijaBase]] +git-tree-sha1 = "f7b57ab4a5c746d83e8883a38454839d0fab8b6f" +uuid = "10284c91-9f28-4c9a-abbf-ee43576dfff6" +version = "1.0.2" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1879,17 +2312,23 @@ version = "0.1.1" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.ThreadingUtilities]] +deps = ["ManualMemory"] +git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" +uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" +version = "0.5.2" + [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "8621f5c499a8aa4aa970b1ae381aae0ef1576966" +git-tree-sha1 = "34cc045dd0aaa59b8bbe86c644679bc57f1d5bd0" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.6.4" +version = "0.6.8" [[deps.TiledIteration]] -deps = ["OffsetArrays"] -git-tree-sha1 = "5683455224ba92ef59db72d10690690f4a8dc297" +deps = ["OffsetArrays", "StaticArrayInterface"] +git-tree-sha1 = "1176cc31e867217b06928e2f140c90bd1bc88283" uuid = "06e1c1a7-607b-532d-9fad-de7d9aa2abac" -version = "0.3.1" +version = "0.5.0" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] @@ -1897,39 +2336,44 @@ git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.23" -[[deps.Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "0874c1b5de1b5529b776cfeca3ec0acfada97b1b" -uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.20" - [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "0b829474fed270a4b0ab07117dce9b9a2fa7581a" +git-tree-sha1 = 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TransducersDataFramesExt = "DataFrames" + TransducersLazyArraysExt = "LazyArrays" + TransducersOnlineStatsBaseExt = "OnlineStatsBase" + TransducersReferenceablesExt = "Referenceables" + + [deps.Transducers.weakdeps] + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" + Referenceables = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" [[deps.TupleTools]] -git-tree-sha1 = "3c712976c47707ff893cf6ba4354aa14db1d8938" +git-tree-sha1 = "41d61b1c545b06279871ef1a4b5fcb2cac2191cd" uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" -version = "1.3.0" - -[[deps.UMAP]] -deps = ["Arpack", "Distances", "LinearAlgebra", "LsqFit", "NearestNeighborDescent", "Random", "SparseArrays"] -git-tree-sha1 = "2a6991639e93fcbbdb8a0476b521a6ac9700ee97" -uuid = "c4f8c510-2410-5be4-91d7-4fbaeb39457e" -version = "0.1.9" +version = "1.5.0" [[deps.URIs]] -git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" +git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.2" +version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1949,11 +2393,31 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" -[[deps.UnicodePlots]] -deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "Printf", "Requires", "SnoopPrecompile", "SparseArrays", "StaticArrays", "StatsBase"] -git-tree-sha1 = "2825e58f6ec3cab889dfa2c824f8d89b9f7ee731" -uuid = "b8865327-cd53-5732-bb35-84acbb429228" -version = "3.5.1" +[[deps.Unitful]] +deps = ["Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" +uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.19.0" + + [deps.Unitful.extensions] + ConstructionBaseUnitfulExt = "ConstructionBase" + InverseFunctionsUnitfulExt = "InverseFunctions" + + [deps.Unitful.weakdeps] + ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + +[[deps.UnitfulAtomic]] +deps = ["Unitful"] +git-tree-sha1 = "903be579194534af1c4b4778d1ace676ca042238" +uuid = "a7773ee8-282e-5fa2-be4e-bd808c38a91a" +version = "1.0.0" + +[[deps.UnitfulLatexify]] +deps = ["LaTeXStrings", "Latexify", "Unitful"] +git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" +version = "1.6.3" [[deps.UnsafeAtomics]] git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" @@ -1962,26 +2426,38 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "ea37e6066bf194ab78f4e747f5245261f17a7175" +git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.2" +version = "0.1.3" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" version = "0.2.0" +[[deps.VectorizationBase]] +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "ac377f0a248753a1b1d58bbc92a64f5a726dfb71" +uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" +version = "0.21.66" + +[[deps.Vulkan_Loader_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] +git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" +uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c" +version = "1.3.243+0" + [[deps.Wayland_jll]] -deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" +deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "7558e29847e99bc3f04d6569e82d0f5c54460703" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.21.0+0" +version = "1.21.0+1" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" +git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.25.0+0" +version = "1.31.0+0" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] @@ -1991,9 +2467,9 @@ version = "1.4.2" [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" +git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.5" +version = "1.0.0" [[deps.WorkerUtilities]] git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" @@ -2001,10 +2477,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.12.6+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -2012,17 +2488,35 @@ git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" version = "1.1.34+0" +[[deps.XZ_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" +version = "5.4.6+0" + +[[deps.Xorg_libICE_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "e5becd4411063bdcac16be8b66fc2f9f6f1e8fe5" +uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" +version = "1.0.10+1" + +[[deps.Xorg_libSM_jll]] +deps = ["Libdl", "Pkg", "Xorg_libICE_jll"] +git-tree-sha1 = "4a9d9e4c180e1e8119b5ffc224a7b59d3a7f7e18" +uuid = "c834827a-8449-5923-a945-d239c165b7dd" +version = "1.2.3+0" + [[deps.Xorg_libX11_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.6.9+4" +version = "1.8.6+0" [[deps.Xorg_libXau_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.9+4" +version = "1.0.11+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -2031,10 +2525,10 @@ uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.3+4" +version = "1.1.4+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -2073,22 +2567,28 @@ uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" version = "0.9.10+4" [[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" +version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" +version = "1.15.0+0" [[deps.Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.0+4" +version = "1.1.2+0" + +[[deps.Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.4+0" [[deps.Xorg_xcb_util_image_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] @@ -2121,22 +2621,22 @@ uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" version = "0.4.1+1" [[deps.Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" +version = "1.4.6+0" [[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" +version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" +version = "1.5.0+0" [[deps.ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] @@ -2147,37 +2647,59 @@ version = "0.10.1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SnoopPrecompile", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "987ae5554ca90e837594a0f30325eeb5e7303d1e" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.60" +version = "0.6.69" + + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" +git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.3" +version = "0.2.5" -[[deps.cuDNN]] -deps = ["CEnum", "CUDA", "CUDNN_jll"] -git-tree-sha1 = "3aa15aba7aad5be8b9b3c1b77a9b81e3e1357280" -uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" -version = "1.0.2" +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" [[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.29.0+0" +version = "0.43.0+0" + +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+0" + +[[deps.libaec_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" +version = "1.1.2+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2192,9 +2714,21 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+1" + +[[deps.libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libevent_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll"] +git-tree-sha1 = "f04ec6d9a186115fb38f858f05c0c4e1b7fc9dcb" +uuid = "1080aeaf-3a6a-583e-a51c-c537b09f60ec" +version = "2.1.13+1" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2202,11 +2736,17 @@ git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.2+0" +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + [[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" +version = "1.6.43+1" [[deps.libsixel_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] @@ -2220,15 +2760,33 @@ git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+1" +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" + +[[deps.prrte_jll]] +deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "PMIx_jll", "libevent_jll"] +git-tree-sha1 = "5adb2d7a18a30280feb66cad6f1a1dfdca2dc7b0" +uuid = "eb928a42-fffd-568d-ab9c-3f5d54fc65b9" +version = "3.0.2+0" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2244,6 +2802,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+0" +version = "1.4.1+1" diff --git a/docs/setup_docs.jl b/docs/setup_docs.jl index 576f9fb..e635432 100644 --- a/docs/setup_docs.jl +++ b/docs/setup_docs.jl @@ -7,7 +7,7 @@ setup_docs = quote using Distributions using Flux using Flux.Data: DataLoader - using Flux: onehotbatch, onecold, @epochs, @functor, logsumexp + using Flux: onehotbatch, onecold, @functor, logsumexp using Flux.Losses: logitcrossentropy using Images using JointEnergyModels diff --git a/docs/src/_intro.qmd b/docs/src/_intro.qmd index 5cc3078..ff50352 100644 --- a/docs/src/_intro.qmd +++ b/docs/src/_intro.qmd @@ -15,7 +15,8 @@ execute: ```{julia} #| echo: false -include("docs/setup_docs.jl") + +include("$(pwd())/docs/setup_docs.jl") eval(setup_docs) ``` From dfa04674aee008fad8af8fa8d5e1ad590003f5f4 Mon Sep 17 00:00:00 2001 From: pat-alt Date: Mon, 29 Apr 2024 14:03:13 +0200 Subject: [PATCH 2/3] updated --- .../samplers/execute-results/md.json | 11 + .../mlj_flux/execute-results/md.json | 11 + .../docs/src/index/execute-results/md.json | 3 +- .../figure-commonmark/cell-3-output-1.svg | 4054 ++++---- .../figure-commonmark/cell-8-output-1.svg | 9183 +++++++++-------- .../tutorials/mnist/execute-results/md.json | 11 + .../synthetic/execute-results/md.json | 11 + _quarto.yml | 2 +- docs/Manifest.toml | 24 +- docs/Project.toml | 1 + docs/assets.jl | 2 + docs/make.jl | 2 + docs/src/LICENSE | 21 + docs/src/assets/resources-commonmark.md | 11 + docs/src/assets/resources.md | 1 + docs/src/explanation/index.md | 2 + docs/src/explanation/samplers.md | 101 + docs/src/explanation/samplers.qmd | 6 +- docs/src/how_to_guides/index.md | 2 + docs/src/how_to_guides/mlj_flux.md | 141 + docs/src/index.md | 1 + .../figure-commonmark/cell-3-output-1.svg | 4054 ++++---- .../figure-commonmark/cell-8-output-1.svg | 9183 +++++++++-------- docs/src/reference.md | 44 + docs/src/reference.qmd | 8 +- docs/src/tutorials/index.md | 2 + docs/src/tutorials/mnist.md | 132 + docs/src/tutorials/mnist.qmd | 2 +- docs/src/tutorials/synthetic.md | 131 + docs/src/tutorials/synthetic.qmd | 2 +- test/runtests.jl | 3 - 31 files changed, 13945 insertions(+), 13217 deletions(-) create mode 100644 _freeze/docs/src/explanation/samplers/execute-results/md.json create mode 100644 _freeze/docs/src/how_to_guides/mlj_flux/execute-results/md.json create mode 100644 _freeze/docs/src/tutorials/mnist/execute-results/md.json create mode 100644 _freeze/docs/src/tutorials/synthetic/execute-results/md.json create mode 100644 docs/assets.jl create mode 100644 docs/src/LICENSE create mode 100644 docs/src/assets/resources-commonmark.md create mode 100644 docs/src/explanation/index.md create mode 100644 docs/src/explanation/samplers.md create mode 100644 docs/src/how_to_guides/index.md create mode 100644 docs/src/how_to_guides/mlj_flux.md create mode 100644 docs/src/reference.md create mode 100644 docs/src/tutorials/index.md create mode 100644 docs/src/tutorials/mnist.md create mode 100644 docs/src/tutorials/synthetic.md diff --git a/_freeze/docs/src/explanation/samplers/execute-results/md.json b/_freeze/docs/src/explanation/samplers/execute-results/md.json new file mode 100644 index 0000000..3bd3b2c --- /dev/null +++ b/_freeze/docs/src/explanation/samplers/execute-results/md.json @@ -0,0 +1,11 @@ +{ + "hash": "577028b23128dbdcef11147ab874511c", + "result": { + "engine": "jupyter", + "markdown": "---\ntitle: MNIST\n---\n\n\n\n\n\n\n::: {.cell execution_count=2}\n``` {.julia .cell-code}\nusing TaijaData: load_mnist\nusing CounterfactualExplanations.Models: load_mnist_mlp, load_mnist_ensemble\n```\n:::\n\n\n::: {.cell execution_count=3}\n``` {.julia .cell-code}\nX, y = load_mnist()\nK = size(y, 1)\nD = size(X, 1)\nmlp = load_mnist_mlp().model\nf_mlp(x) = mlp(x)\nens = load_mnist_ensemble().model\nf_ens(x) = sum(map(mlp -> mlp(x), ens))/length(ens)\nbatch_size = 100\n```\n:::\n\n\n## Sampling\n\n::: {.cell execution_count=4}\n``` {.julia .cell-code}\n𝒟x = Uniform(0,1)\n𝒟y = Categorical(ones(K) ./ K)\nsampler = UnconditionalSampler(𝒟x; input_size=(D,))\nconditional_sampler = ConditionalSampler(𝒟x, 𝒟y; input_size=(D,))\nopt = ImproperSGLD()\nn_iter = 256\n```\n:::\n\n\n### Conditional Draws\n\n::: {.cell execution_count=5}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = conditional_sampler(f_mlp, opt; niter=n_iter, y=i, n_samples=neach)\n plts_i = []\n for j in 1:size(x,2)\n xj = reshape(x[:,j], (28,28))\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n::: {.cell execution_count=6}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = conditional_sampler(f_ens, opt; niter=n_iter, y=i, n_samples=neach)\n plts_i = []\n for j in 1:size(x,2)\n xj = reshape(x[:,j], (28,28))\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n### Unconditional Draws\n\n::: {.cell execution_count=7}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = sampler(f_mlp, opt; niter=n_iter, n_samples=neach)\n plts_i = []\n for j in 1:size(x,2)\n xj = reshape(x[:,j], (28,28))\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n::: {.cell execution_count=8}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = sampler(f_ens, opt; niter=n_iter, n_samples=neach)\n plts_i = []\n for j in 1:size(x,2)\n xj = reshape(x[:,j], (28,28))\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n", + "supporting": [ + "samplers_files" + ], + "filters": [] + } +} \ No newline at end of file diff --git a/_freeze/docs/src/how_to_guides/mlj_flux/execute-results/md.json b/_freeze/docs/src/how_to_guides/mlj_flux/execute-results/md.json new file mode 100644 index 0000000..a707548 --- /dev/null +++ b/_freeze/docs/src/how_to_guides/mlj_flux/execute-results/md.json @@ -0,0 +1,11 @@ +{ + "hash": "155039eb05e14711352a223bba059fae", + "result": { + "engine": "jupyter", + "markdown": "---\ntitle: Compatibility with `MLJFlux`\n---\n\n\n\n\n\n\n## Synthetic Data\n\n::: {.cell execution_count=2}\n``` {.julia .cell-code}\nnobs=2000\nX, y = make_circles(nobs, noise=0.1, factor=0.5)\nXplot = Float32.(permutedims(matrix(X)))\nX = table(permutedims(Xplot))\ndisplay(scatter(Xplot[1,:], Xplot[2,:], group=y, label=\"\"))\nbatch_size = Int(round(nobs/10))\n```\n:::\n\n\n::: {.cell execution_count=3}\n``` {.julia .cell-code}\nsampler = ConditionalSampler(X, y, batch_size=batch_size)\nclf = JointEnergyClassifier(\n sampler;\n builder=MLJFlux.MLP(hidden=(32, 32, 32,), σ=Flux.relu),\n batch_size=batch_size,\n finaliser=Flux.softmax,\n loss=Flux.Losses.crossentropy,\n jem_training_params=(α=[1.0,1.0,1e-1],verbosity=10,),\n)\n```\n:::\n\n\n::: {.cell execution_count=4}\n``` {.julia .cell-code}\nprintln(typeof(clf) <: MLJFlux.MLJFluxModel)\n```\n:::\n\n\n::: {.cell execution_count=5}\n``` {.julia .cell-code}\nmach = machine(clf, X, y)\nfit!(mach)\n```\n:::\n\n\n::: {.cell execution_count=6}\n``` {.julia .cell-code}\njem = mach.model.jem\nbatch_size = mach.model.batch_size\nX = Float32.(permutedims(matrix(X)))\ny_labels = Int.(y.refs)\ny = Flux.onehotbatch(y.refs, sort(unique(y_labels)))\n```\n:::\n\n\n::: {.cell execution_count=7}\n``` {.julia .cell-code}\nif typeof(jem.sampler) <: ConditionalSampler\n \n plts = []\n for target in 1:size(y,1)\n X̂ = generate_conditional_samples(jem, batch_size, target; niter=1000) \n ex = extrema(hcat(X,X̂), dims=2)\n xlims = ex[1]\n ylims = ex[2]\n x1 = range(1.0f0.*xlims...,length=100)\n x2 = range(1.0f0.*ylims...,length=100)\n plt = contour(\n x1, x2, (x, y) -> softmax(jem([x, y]))[target], \n fill=true, alpha=0.5, title=\"Target: $target\", cbar=false,\n xlims=xlims,\n ylims=ylims,\n )\n scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5)\n scatter!(\n X̂[1,:], X̂[2,:], \n color=repeat([target], size(X̂,2)), \n group=repeat([target], size(X̂,2)), \n shape=:star5, ms=10\n )\n push!(plts, plt)\n end\n plt = plot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400))\n display(plt)\nend\n```\n:::\n\n\n## MNIST \n\n::: {.cell execution_count=8}\n``` {.julia .cell-code}\n# Data:\nnobs = 1000\nn_digits = 28\nXtrain, ytrain, _, _, _, _ = load_mnist_data(nobs=nobs, n_digits=n_digits)\nXtrain = table(permutedims(MLUtils.flatten(Xtrain)))\nytrain = coerce(Flux.onecold(ytrain, 0:9), Multiclass)\n\n# Hyperparameters:\nD = n_digits^2 \nK = 10 \nM = 32\nlr = 1e-3 \nnum_epochs = 500\nmax_patience = 5 \nbatch_size = Int(round(nobs/10))\nα = [1.0,1.0,1e-2]\n```\n:::\n\n\n::: {.cell execution_count=9}\n``` {.julia .cell-code}\nactivation = Flux.swish\nbuilder = MLJFlux.MLP(hidden=(M,M,M,), σ=activation)\n```\n:::\n\n\n::: {.cell execution_count=10}\n``` {.julia .cell-code}\n# We initialize the full model\n𝒟x = Uniform(-1,1)\n𝒟y = Categorical(ones(K) ./ K)\nsampler = ConditionalSampler(𝒟x, 𝒟y, input_size=(D,), batch_size=10)\nclf = JointEnergyClassifier(\n sampler;\n builder=builder,\n batch_size=batch_size,\n finaliser=Flux.softmax,\n loss=Flux.Losses.crossentropy,\n jem_training_params=(α=α,verbosity=10,),\n sampling_steps=20,\n optimiser=Flux.Optimise.Adam(lr),\n)\n```\n:::\n\n\n::: {.cell execution_count=11}\n``` {.julia .cell-code}\nmach = machine(clf, Xtrain, ytrain)\nfit!(mach)\n```\n:::\n\n\n::: {.cell execution_count=12}\n``` {.julia .cell-code}\njem = mach.model.jem\nn_iter = 1000\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = jem.sampler(jem.chain, jem.sampling_rule; niter=n_iter, n_samples=neach, y=i)\n plts_i = []\n for j in 1:size(x, 2)\n xj = x[:,j]\n xj = reshape(xj, (n_digits, n_digits))\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n", + "supporting": [ + "mlj_flux_files" + ], + "filters": [] + } +} \ No newline at end of file diff --git a/_freeze/docs/src/index/execute-results/md.json b/_freeze/docs/src/index/execute-results/md.json index 2401c6b..45277e0 100644 --- a/_freeze/docs/src/index/execute-results/md.json +++ b/_freeze/docs/src/index/execute-results/md.json @@ -1,9 +1,10 @@ { "hash": "8d26f827b22cadaf45d98344b37a0051", "result": { + "engine": "jupyter", "markdown": "```@meta\nCurrentModule = JointEnergyModels\n```\n\n# `JointEnergyModels.jl`\n\nDocumentation for [JointEnergyModels.jl](https://github.com/juliatrustworthyai/JointEnergyModels.jl).\n\n---\nexecute: \n eval: false\n---\n\n*Joint Energy Models in Julia.*\n\n[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliatrustworthyai.github.io/JointEnergyModels.jl/stable)\n[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliatrustworthyai.github.io/JointEnergyModels.jl/dev)\n[![Build Status](https://github.com/juliatrustworthyai/JointEnergyModels.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/juliatrustworthyai/JointEnergyModels.jl/actions/workflows/CI.yml?query=branch%3Amain)\n[![Coverage](https://codecov.io/gh/juliatrustworthyai/JointEnergyModels.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/juliatrustworthyai/JointEnergyModels.jl)\n[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)\n[![License](https://img.shields.io/github/license/juliatrustworthyai/JointEnergyModels.jl)](LICENSE)\n[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/JointEnergyModels/)](https://pkgs.genieframework.com?packages=JointEnergyModels)\n\n\n\n`JointEnergyModels.jl` is a package for training Joint Energy Models in Julia. Joint Energy Models (JEM) are hybrid models that learn to discriminate between classes $y$ and generate input data $x$. They were introduced in @grathwohl2020your, which provides the foundation for the methodologies implemented in this package.\n\n## 🔁 Status\n\nThis package is still in its infancy and the API is subject to change. Currently, the package can be used to train JEMs for classification. It is also possible to train pure Energy-Based Models (EBMs) for the generative task only. The package is compatible with `Flux.jl`. Work on compatibility with `MLJ.jl` (through `MLJFlux.jl`) is currently under way.\n\nWe welcome contributions and feedback at this early stage. To install the development version of the package you can run the following command:\n\n```{.julia}\nusing Pkg\nPkg.add(url=\"https://github.com/juliatrustworthyai/JointEnergyModels.jl\")\n```\n\n## 🔍 Usage Example\n\nBelow we first generate some synthetic data:\n\n::: {.cell execution_count=2}\n``` {.julia .cell-code}\nnobs=2000\nX, y = make_circles(nobs, noise=0.1, factor=0.5)\nXplot = Float32.(permutedims(matrix(X)))\nX = table(permutedims(Xplot))\nplt = scatter(Xplot[1,:], Xplot[2,:], group=y, label=\"\")\nbatch_size = Int(round(nobs/10))\ndisplay(plt)\n```\n\n::: {.cell-output .cell-output-display}\n![](index_files/figure-commonmark/cell-3-output-1.svg){}\n:::\n:::\n\n\nThe `MLJ` compatible classifier can be instantiated as follows:\n\n::: {.cell execution_count=3}\n``` {.julia .cell-code}\n𝒟x = Normal()\n𝒟y = Categorical(ones(2) ./ 2)\nsampler = ConditionalSampler(𝒟x, 𝒟y, input_size=size(Xplot)[1:end-1], batch_size=batch_size)\nclf = JointEnergyClassifier(\n sampler;\n builder=MLJFlux.MLP(hidden=(32, 32, 32,), σ=Flux.relu),\n batch_size=batch_size,\n finaliser=x -> x,\n loss=Flux.Losses.logitcrossentropy,\n)\n```\n:::\n\n\nIt uses the `MLJFlux` package to build the model:\n\n::: {.cell execution_count=4}\n``` {.julia .cell-code}\nprintln(typeof(clf) <: MLJFlux.MLJFluxModel)\n```\n\n::: {.cell-output .cell-output-stdout}\n```\ntrue\n```\n:::\n:::\n\n\nThe model can be wrapped in data and trained using the `fit!` function:\n\n::: {.cell execution_count=5}\n``` {.julia .cell-code}\nmach = machine(clf, X, y)\nfit!(mach)\n```\n:::\n\n\nThe results are visualised below. The model has learned to discriminate between the two classes (as indicated by the contours) and to generate samples from each class (as indicated by the stars).\n\n\n\n::: {.cell execution_count=7}\n\n::: {.cell-output .cell-output-display}\n![](index_files/figure-commonmark/cell-8-output-1.svg){}\n:::\n:::\n\n\n## 🎓 References\n\n", "supporting": [ - "index_files/figure-commonmark" + "index_files" ], "filters": [] } diff --git a/_freeze/docs/src/index/figure-commonmark/cell-3-output-1.svg b/_freeze/docs/src/index/figure-commonmark/cell-3-output-1.svg index 623d1a1..451aa9d 100644 --- a/_freeze/docs/src/index/figure-commonmark/cell-3-output-1.svg +++ b/_freeze/docs/src/index/figure-commonmark/cell-3-output-1.svg @@ -1,2042 +1,2042 @@ - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_freeze/docs/src/tutorials/mnist/execute-results/md.json b/_freeze/docs/src/tutorials/mnist/execute-results/md.json new file mode 100644 index 0000000..c628c81 --- /dev/null +++ b/_freeze/docs/src/tutorials/mnist/execute-results/md.json @@ -0,0 +1,11 @@ +{ + "hash": "cb52ac7dbc3ba18a9dbd60671c92d906", + "result": { + "engine": "jupyter", + "markdown": "---\ntitle: Joint Energy Models\n---\n\n\n\n\n\n\n## Data\n\n::: {.cell execution_count=2}\n``` {.julia .cell-code}\nnobs = 1000\nn_digits = 28\nXtrain, ytrain, Xval, yval, Xtest, ytest = load_mnist_data(nobs=nobs, n_digits=n_digits)\n```\n:::\n\n\n## `JointEnergyModel`\n\n### Hyperparameters\n\n::: {.cell execution_count=3}\n``` {.julia .cell-code}\nD = n_digits \nK = 10 \nM = 128\nlr = 1e-3 \nnum_epochs = 100\nmax_patience = 5 \nbatchsize = Int(round(nobs/10))\n```\n:::\n\n\n### Initializing the model\n\n::: {.cell execution_count=4}\n``` {.julia .cell-code}\nactivation = relu\nmlp = Chain(\n MLUtils.flatten,\n Dense(prod((D,D)), M, activation),\n # BatchNorm(M, activation),\n # Dense(M, M),\n # BatchNorm(M, activation),\n Dense(M, K),\n)\n\n# We initialize the full model\n𝒟x = Uniform(-1,1)\n𝒟y = Categorical(ones(K) ./ K)\nsampler = ConditionalSampler(𝒟x, 𝒟y, input_size=(D,D), batch_size=10)\njem = JointEnergyModel(\n mlp, sampler;\n sampling_steps=20,\n)\n```\n:::\n\n\n### Training loop\n\n::: {.cell execution_count=5}\n``` {.julia .cell-code}\n# Initialise \nopt = Adam(lr)\nopt_state = Flux.setup(opt, jem)\ntrain_set = DataLoader((Xtrain, ytrain); batchsize=batchsize, shuffle=true)\nval_set = DataLoader((Xval, yval); batchsize=batchsize, shuffle=false)\ntest_set = DataLoader((Xtest, ytest); batchsize=batchsize, shuffle=false)\n```\n:::\n\n\n::: {.cell execution_count=6}\n``` {.julia .cell-code}\nlogs = train_model(\n jem, train_set, opt_state; num_epochs=num_epochs, val_set=val_set,\n verbosity = minimum([num_epochs, 10]),\n α = [1.0,1.0,1e-2],\n # use_class_loss=false,\n # use_gen_loss=false,\n # use_reg_loss=false,\n)\n```\n:::\n\n\n### The final evaluation\n\n::: {.cell execution_count=7}\n``` {.julia .cell-code}\nn_iter = 200\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = jem.sampler(jem.chain, jem.sampling_rule; niter=n_iter, n_samples=neach, y=i)\n plts_i = []\n for j in 1:size(x, 3)\n xj = x[:,:,j]\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n#### From Scratch\n\n::: {.cell execution_count=8}\n``` {.julia .cell-code}\nsampler = UnconditionalSampler(𝒟x; input_size=(D,D))\nconditional_sampler = ConditionalSampler(𝒟x, 𝒟y; input_size=(D,D))\nopt = ImproperSGLD(10.0,0.005)\nn_iter = 256\n```\n:::\n\n\n::: {.cell execution_count=9}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = conditional_sampler(jem.chain, opt; niter=n_iter, y=i, n_samples=neach)\n plts_i = []\n for j in 1:size(x,3)\n xj = x[:,:,j]\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n::: {.cell execution_count=10}\n``` {.julia .cell-code}\n_w = 1500\nplts = []\nneach = 10\nfor i in 1:10\n x = sampler(jem.chain, opt; niter=n_iter, y=i, n_samples=neach)\n plts_i = []\n for j in 1:size(x,3)\n xj = x[:,:,j]\n plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)]\n end\n plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10))\n plts = [plts..., plt]\nend\nplot(plts..., size=(_w,_w), layout=(10,1))\n```\n:::\n\n\n", + "supporting": [ + "mnist_files" + ], + "filters": [] + } +} \ No newline at end of file diff --git a/_freeze/docs/src/tutorials/synthetic/execute-results/md.json b/_freeze/docs/src/tutorials/synthetic/execute-results/md.json new file mode 100644 index 0000000..2a0937f --- /dev/null +++ b/_freeze/docs/src/tutorials/synthetic/execute-results/md.json @@ -0,0 +1,11 @@ +{ + "hash": "87a430414d7edb9878cb2539943aabc0", + "result": { + "engine": "jupyter", + "markdown": "---\ntitle: Synthetic Data\n---\n\n\n\n\n\n\n## Binary Classification\n\n::: {.cell execution_count=2}\n``` {.julia .cell-code}\nnobs=2000\nX, y = make_circles(nobs, noise=0.1, factor=0.5)\nX = Float32.(permutedims(matrix(X)))\ny_labels = Int.(y.refs)\ny = Flux.onehotbatch(y.refs, sort(unique(y_labels)))\ndisplay(scatter(X[1,:], X[2,:], color=vec(y_labels), label=\"\"))\nbatch_size = Int(round(nobs/10))\ntrain_set = DataLoader((X, y), batchsize=batch_size, shuffle=true)\n```\n:::\n\n\n::: {.cell execution_count=3}\n``` {.julia .cell-code}\nn_hidden = 32\nactivation = relu\nmodels = Dict(\n \"Logistic Regression\" => Chain(Dense(2, size(y,1))),\n \"MLP\" => Chain(\n Dense(2, n_hidden, activation), \n Dense(n_hidden, n_hidden, activation), \n Dense(n_hidden, n_hidden, activation), \n Dense(n_hidden, size(y,1))\n ),\n)\n```\n:::\n\n\n::: {.cell execution_count=4}\n``` {.julia .cell-code}\n_loss(y_hat, y) = Flux.Losses.logitcrossentropy(y_hat, y)\nrule = Adam()\n```\n:::\n\n\n::: {.cell execution_count=5}\n``` {.julia .cell-code}\n_lims = extrema(X, dims=2)\nx1, x2 = map(ex -> range(1.1f0.*ex..., length=100), _lims)\nn_epochs = 100\nplts = []\nfor (name, model) in models\n opt_state = Flux.setup(rule, model)\n for epoch in 1:n_epochs\n Flux.train!(model, train_set, opt_state) do m, x, y\n _loss(model(x), y)\n end\n end\n plt = contour(x1, x2, (x, y) -> softmax(model([x, y]))[1], fill=true, alpha=0.5, title=name, cbar=false)\n scatter!(X[1,:], X[2,:], color=vec(y_labels), label=\"\")\n push!(plts, plt)\nend\nplot(plts..., layout=(1, 2), size=(800, 400))\n```\n:::\n\n\n## Joint Energy Model\n\n::: {.cell execution_count=6}\n``` {.julia .cell-code}\n# We initialize the full model:\n𝒟x = Normal()\n𝒟y = Categorical(ones(2) ./ 2)\nsampler = ConditionalSampler(𝒟x, 𝒟y, input_size=size(X)[1:end-1], batch_size=batch_size)\njem = JointEnergyModel(\n models[\"MLP\"], \n sampler;\n sampling_rule=ImproperSGLD(),\n sampling_steps=10\n)\n# Initialise training:\nopt = Adam(1e-3)\nopt_state = Flux.setup(opt, jem)\nnum_epochs = 100\n```\n:::\n\n\n::: {.cell execution_count=7}\n``` {.julia .cell-code}\nlogs = JointEnergyModels.train_model(\n jem, train_set, opt_state; \n num_epochs=num_epochs,\n α=[1.0,1.0,1e-1],\n verbosity=minimum([num_epochs, 50]),\n # use_class_loss=false,\n # use_gen_loss=false,\n # use_reg_loss=false,\n)\n```\n:::\n\n\n::: {.cell execution_count=8}\n``` {.julia .cell-code}\nplts = []\nfor target in 1:size(y,1)\n plt = contour(x1, x2, (x, y) -> softmax(jem([x, y]))[target], fill=true, alpha=0.5, title=\"Target: $target\", cbar=false)\n scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels))\n push!(plts, plt)\nend\nplot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400))\n```\n:::\n\n\n::: {.cell execution_count=9}\n``` {.julia .cell-code}\nX̂ = generate_samples(jem, 1000; niter=1000)\nŷ = onecold(softmax(jem(X̂)))\nscatter(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5)\nscatter!(X̂[1,:], X̂[2,:], color=vec(ŷ), group=vec(ŷ), title=\"Generated Samples\", shape=:star5)\n```\n:::\n\n\n::: {.cell execution_count=10}\n``` {.julia .cell-code}\nif typeof(jem.sampler) <: ConditionalSampler\n \n plts = []\n for target in 1:size(y,1)\n X̂ = generate_conditional_samples(jem, batch_size, target; niter=1000) \n ex = extrema(hcat(X,X̂), dims=2)\n xlims = ex[1]\n ylims = ex[2]\n x1 = range(1.0f0.*xlims...,length=100)\n x2 = range(1.0f0.*ylims...,length=100)\n plt = contour(\n x1, x2, (x, y) -> softmax(jem([x, y]))[target], \n fill=true, alpha=0.5, title=\"Target: $target\", cbar=false,\n xlims=xlims,\n ylims=ylims,\n )\n scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5)\n scatter!(\n X̂[1,:], X̂[2,:], \n color=repeat([target], size(X̂,2)), \n group=repeat([target], size(X̂,2)), \n shape=:star5, ms=10\n )\n push!(plts, plt)\n end\n plot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400))\nend\n```\n:::\n\n\n", + "supporting": [ + "synthetic_files" + ], + "filters": [] + } +} \ No newline at end of file diff --git a/_quarto.yml b/_quarto.yml index d49920d..a8ac075 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -12,4 +12,4 @@ execute: echo: true output: false -jupyter: julia-1.8 \ No newline at end of file +jupyter: julia-1.10 \ No newline at end of file diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 15977cb..d66f584 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.2" manifest_format = "2.0" -project_hash = "fa1661325a4c5d26fc571a0abf72240342ef1bdf" +project_hash = "4022d4cae6a493bff6b60ac345b69e61a5a7563d" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -343,6 +343,11 @@ git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.12.10" +[[deps.Combinatorics]] +git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" +uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" +version = "1.0.2" + [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" @@ -1426,6 +1431,12 @@ git-tree-sha1 = "d2a45e1b5998ba3fdfb6cfe0c81096d4c7fb40e7" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" version = "1.9.6" +[[deps.MLJModels]] +deps = ["CategoricalArrays", "CategoricalDistributions", "Combinatorics", "Dates", "Distances", "Distributions", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "Markdown", "OrderedCollections", "Parameters", "Pkg", "PrettyPrinting", "REPL", "Random", "RelocatableFolders", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] +git-tree-sha1 = "410da88e0e6ece5467293d2c76b51b7c6df7d072" +uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7" +version = "0.16.17" + [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" @@ -1864,6 +1875,11 @@ git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" uuid = "8162dcfd-2161-5ef2-ae6c-7681170c5f98" version = "0.2.0" +[[deps.PrettyPrinting]] +git-tree-sha1 = "142ee93724a9c5d04d78df7006670a93ed1b244e" +uuid = "54e16d92-306c-5ea0-a30b-337be88ac337" +version = "0.4.2" + [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" @@ -2297,6 +2313,12 @@ git-tree-sha1 = "f7b57ab4a5c746d83e8883a38454839d0fab8b6f" uuid = "10284c91-9f28-4c9a-abbf-ee43576dfff6" version = "1.0.2" +[[deps.TaijaData]] +deps = ["CSV", "CounterfactualExplanations", "DataAPI", "DataFrames", "Flux", "LazyArtifacts", "MLDatasets", "MLJBase", "MLJModels", "Random", "StatsBase"] +git-tree-sha1 = "04fed01efa65478c9f55a35c27c12add47ffe49e" +uuid = "9d524318-b4e6-4a65-86d2-b2b72d07866c" +version = "1.0.0" + [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" diff --git a/docs/Project.toml b/docs/Project.toml index b2cae88..ff24f68 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -15,4 +15,5 @@ ProgressBars = "49802e3a-d2f1-5c88-81d8-b72133a6f568" ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +TaijaData = "9d524318-b4e6-4a65-86d2-b2b72d07866c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/docs/assets.jl b/docs/assets.jl new file mode 100644 index 0000000..7fbd20e --- /dev/null +++ b/docs/assets.jl @@ -0,0 +1,2 @@ +# Since Documenter.jl cannot handle links to anything outside the docs/src directory, we need to copy the LICENSE and CHANGELOG.md files to the src/assets directory: https://discourse.julialang.org/t/make-documenter-jl-understand-where-to-search-local-markdown-links/84012/6?u=pat-alt +cp(joinpath(@__DIR__, "..", "LICENSE"), joinpath(@__DIR__, "src/LICENSE"); force=true) \ No newline at end of file diff --git a/docs/make.jl b/docs/make.jl index 53ba205..d325e1d 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -3,6 +3,8 @@ using Documenter include("setup_docs.jl") +include("assets.jl") + DocMeta.setdocmeta!(JointEnergyModels, :DocTestSetup, :(setup_docs); recursive=true) makedocs(; diff --git a/docs/src/LICENSE b/docs/src/LICENSE new file mode 100644 index 0000000..2a6837c --- /dev/null +++ b/docs/src/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 Patrick Altmeyer + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/docs/src/assets/resources-commonmark.md b/docs/src/assets/resources-commonmark.md new file mode 100644 index 0000000..fb1e260 --- /dev/null +++ b/docs/src/assets/resources-commonmark.md @@ -0,0 +1,11 @@ + + +# Further Resources + +## JuliaCon 2022 + +Slides: [link](juliacon22/presentation.html) + +## JuliaCon Proceedings Paper + +TBD diff --git a/docs/src/assets/resources.md b/docs/src/assets/resources.md index cce357a..fb1e260 100644 --- a/docs/src/assets/resources.md +++ b/docs/src/assets/resources.md @@ -1,4 +1,5 @@ + # Further Resources ## JuliaCon 2022 diff --git a/docs/src/explanation/index.md b/docs/src/explanation/index.md new file mode 100644 index 0000000..139597f --- /dev/null +++ b/docs/src/explanation/index.md @@ -0,0 +1,2 @@ + + diff --git a/docs/src/explanation/samplers.md b/docs/src/explanation/samplers.md new file mode 100644 index 0000000..f3e6e48 --- /dev/null +++ b/docs/src/explanation/samplers.md @@ -0,0 +1,101 @@ +# MNIST + + +``` julia +using TaijaData: load_mnist +using CounterfactualExplanations.Models: load_mnist_mlp, load_mnist_ensemble +``` + +``` julia +X, y = load_mnist() +K = size(y, 1) +D = size(X, 1) +mlp = load_mnist_mlp().model +f_mlp(x) = mlp(x) +ens = load_mnist_ensemble().model +f_ens(x) = sum(map(mlp -> mlp(x), ens))/length(ens) +batch_size = 100 +``` + +## Sampling + +``` julia +𝒟x = Uniform(0,1) +𝒟y = Categorical(ones(K) ./ K) +sampler = UnconditionalSampler(𝒟x; input_size=(D,)) +conditional_sampler = ConditionalSampler(𝒟x, 𝒟y; input_size=(D,)) +opt = ImproperSGLD() +n_iter = 256 +``` + +### Conditional Draws + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = conditional_sampler(f_mlp, opt; niter=n_iter, y=i, n_samples=neach) + plts_i = [] + for j in 1:size(x,2) + xj = reshape(x[:,j], (28,28)) + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = conditional_sampler(f_ens, opt; niter=n_iter, y=i, n_samples=neach) + plts_i = [] + for j in 1:size(x,2) + xj = reshape(x[:,j], (28,28)) + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` + +### Unconditional Draws + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = sampler(f_mlp, opt; niter=n_iter, n_samples=neach) + plts_i = [] + for j in 1:size(x,2) + xj = reshape(x[:,j], (28,28)) + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = sampler(f_ens, opt; niter=n_iter, n_samples=neach) + plts_i = [] + for j in 1:size(x,2) + xj = reshape(x[:,j], (28,28)) + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` diff --git a/docs/src/explanation/samplers.qmd b/docs/src/explanation/samplers.qmd index de19bc0..bbe6eb6 100644 --- a/docs/src/explanation/samplers.qmd +++ b/docs/src/explanation/samplers.qmd @@ -2,19 +2,19 @@ ```{julia} #| echo: false -include("docs/setup_docs.jl") +include("$(pwd())/docs/setup_docs.jl") eval(setup_docs) ``` ```{julia} -using CounterfactualExplanations.Data: load_mnist +using TaijaData: load_mnist using CounterfactualExplanations.Models: load_mnist_mlp, load_mnist_ensemble ``` ```{julia} -X, y = load_mnist().X, load_mnist().y +X, y = load_mnist() K = size(y, 1) D = size(X, 1) mlp = load_mnist_mlp().model diff --git a/docs/src/how_to_guides/index.md b/docs/src/how_to_guides/index.md new file mode 100644 index 0000000..139597f --- /dev/null +++ b/docs/src/how_to_guides/index.md @@ -0,0 +1,2 @@ + + diff --git a/docs/src/how_to_guides/mlj_flux.md b/docs/src/how_to_guides/mlj_flux.md new file mode 100644 index 0000000..5a4a1ec --- /dev/null +++ b/docs/src/how_to_guides/mlj_flux.md @@ -0,0 +1,141 @@ +# Compatibility with `MLJFlux` + + +## Synthetic Data + +``` julia +nobs=2000 +X, y = make_circles(nobs, noise=0.1, factor=0.5) +Xplot = Float32.(permutedims(matrix(X))) +X = table(permutedims(Xplot)) +display(scatter(Xplot[1,:], Xplot[2,:], group=y, label="")) +batch_size = Int(round(nobs/10)) +``` + +``` julia +sampler = ConditionalSampler(X, y, batch_size=batch_size) +clf = JointEnergyClassifier( + sampler; + builder=MLJFlux.MLP(hidden=(32, 32, 32,), σ=Flux.relu), + batch_size=batch_size, + finaliser=Flux.softmax, + loss=Flux.Losses.crossentropy, + jem_training_params=(α=[1.0,1.0,1e-1],verbosity=10,), +) +``` + +``` julia +println(typeof(clf) <: MLJFlux.MLJFluxModel) +``` + +``` julia +mach = machine(clf, X, y) +fit!(mach) +``` + +``` julia +jem = mach.model.jem +batch_size = mach.model.batch_size +X = Float32.(permutedims(matrix(X))) +y_labels = Int.(y.refs) +y = Flux.onehotbatch(y.refs, sort(unique(y_labels))) +``` + +``` julia +if typeof(jem.sampler) <: ConditionalSampler + + plts = [] + for target in 1:size(y,1) + X̂ = generate_conditional_samples(jem, batch_size, target; niter=1000) + ex = extrema(hcat(X,X̂), dims=2) + xlims = ex[1] + ylims = ex[2] + x1 = range(1.0f0.*xlims...,length=100) + x2 = range(1.0f0.*ylims...,length=100) + plt = contour( + x1, x2, (x, y) -> softmax(jem([x, y]))[target], + fill=true, alpha=0.5, title="Target: $target", cbar=false, + xlims=xlims, + ylims=ylims, + ) + scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5) + scatter!( + X̂[1,:], X̂[2,:], + color=repeat([target], size(X̂,2)), + group=repeat([target], size(X̂,2)), + shape=:star5, ms=10 + ) + push!(plts, plt) + end + plt = plot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400)) + display(plt) +end +``` + +## MNIST + +``` julia +# Data: +nobs = 1000 +n_digits = 28 +Xtrain, ytrain, _, _, _, _ = load_mnist_data(nobs=nobs, n_digits=n_digits) +Xtrain = table(permutedims(MLUtils.flatten(Xtrain))) +ytrain = coerce(Flux.onecold(ytrain, 0:9), Multiclass) + +# Hyperparameters: +D = n_digits^2 +K = 10 +M = 32 +lr = 1e-3 +num_epochs = 500 +max_patience = 5 +batch_size = Int(round(nobs/10)) +α = [1.0,1.0,1e-2] +``` + +``` julia +activation = Flux.swish +builder = MLJFlux.MLP(hidden=(M,M,M,), σ=activation) +``` + +``` julia +# We initialize the full model +𝒟x = Uniform(-1,1) +𝒟y = Categorical(ones(K) ./ K) +sampler = ConditionalSampler(𝒟x, 𝒟y, input_size=(D,), batch_size=10) +clf = JointEnergyClassifier( + sampler; + builder=builder, + batch_size=batch_size, + finaliser=Flux.softmax, + loss=Flux.Losses.crossentropy, + jem_training_params=(α=α,verbosity=10,), + sampling_steps=20, + optimiser=Flux.Optimise.Adam(lr), +) +``` + +``` julia +mach = machine(clf, Xtrain, ytrain) +fit!(mach) +``` + +``` julia +jem = mach.model.jem +n_iter = 1000 +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = jem.sampler(jem.chain, jem.sampling_rule; niter=n_iter, n_samples=neach, y=i) + plts_i = [] + for j in 1:size(x, 2) + xj = x[:,j] + xj = reshape(xj, (n_digits, n_digits)) + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` diff --git a/docs/src/index.md b/docs/src/index.md index c778546..752fc77 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,4 +1,5 @@ + ``` @meta CurrentModule = JointEnergyModels ``` diff --git a/docs/src/index_files/figure-commonmark/cell-3-output-1.svg b/docs/src/index_files/figure-commonmark/cell-3-output-1.svg index 623d1a1..451aa9d 100644 --- a/docs/src/index_files/figure-commonmark/cell-3-output-1.svg +++ b/docs/src/index_files/figure-commonmark/cell-3-output-1.svg @@ -1,2042 +1,2042 @@ - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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+ + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/src/reference.md b/docs/src/reference.md new file mode 100644 index 0000000..05469bf --- /dev/null +++ b/docs/src/reference.md @@ -0,0 +1,44 @@ + + +``` @meta +CurrentModule = JointEnergyModels +``` + +# Reference + +In this reference, you will find a detailed overview of the package API. + +> Reference guides are technical descriptions of the machinery and how to operate it. Reference material is information-oriented. +> +> — [Diátaxis](https://diataxis.fr/reference/) + +In other words, you come here because you want to take a very close look at the code 🧐. + +## Content + +``` @contents +Pages = ["reference.md"] +Depth = 3 +``` + +## Exported functions + +``` @autodocs +Modules = [ + JointEnergyModels, + JointEnergyModels.Samplers, + JointEnergyModels.Optimisers, +] +Private = false +``` + +## Internal functions + +``` @autodocs +Modules = [ + JointEnergyModels, + JointEnergyModels.Samplers, + JointEnergyModels.Optimisers, +] +Public = false +``` diff --git a/docs/src/reference.qmd b/docs/src/reference.qmd index f7c4d9e..ec74fa1 100644 --- a/docs/src/reference.qmd +++ b/docs/src/reference.qmd @@ -22,7 +22,9 @@ Depth = 3 ```@autodocs Modules = [ - JointEnergyModels + JointEnergyModels, + JointEnergyModels.Samplers, + JointEnergyModels.Optimisers, ] Private = false ``` @@ -31,7 +33,9 @@ Private = false ```@autodocs Modules = [ - JointEnergyModels + JointEnergyModels, + JointEnergyModels.Samplers, + JointEnergyModels.Optimisers, ] Public = false ``` \ No newline at end of file diff --git a/docs/src/tutorials/index.md b/docs/src/tutorials/index.md new file mode 100644 index 0000000..139597f --- /dev/null +++ b/docs/src/tutorials/index.md @@ -0,0 +1,2 @@ + + diff --git a/docs/src/tutorials/mnist.md b/docs/src/tutorials/mnist.md new file mode 100644 index 0000000..1710c5a --- /dev/null +++ b/docs/src/tutorials/mnist.md @@ -0,0 +1,132 @@ +# Joint Energy Models + + +## Data + +``` julia +nobs = 1000 +n_digits = 28 +Xtrain, ytrain, Xval, yval, Xtest, ytest = load_mnist_data(nobs=nobs, n_digits=n_digits) +``` + +## `JointEnergyModel` + +### Hyperparameters + +``` julia +D = n_digits +K = 10 +M = 128 +lr = 1e-3 +num_epochs = 100 +max_patience = 5 +batchsize = Int(round(nobs/10)) +``` + +### Initializing the model + +``` julia +activation = relu +mlp = Chain( + MLUtils.flatten, + Dense(prod((D,D)), M, activation), + # BatchNorm(M, activation), + # Dense(M, M), + # BatchNorm(M, activation), + Dense(M, K), +) + +# We initialize the full model +𝒟x = Uniform(-1,1) +𝒟y = Categorical(ones(K) ./ K) +sampler = ConditionalSampler(𝒟x, 𝒟y, input_size=(D,D), batch_size=10) +jem = JointEnergyModel( + mlp, sampler; + sampling_steps=20, +) +``` + +### Training loop + +``` julia +# Initialise +opt = Adam(lr) +opt_state = Flux.setup(opt, jem) +train_set = DataLoader((Xtrain, ytrain); batchsize=batchsize, shuffle=true) +val_set = DataLoader((Xval, yval); batchsize=batchsize, shuffle=false) +test_set = DataLoader((Xtest, ytest); batchsize=batchsize, shuffle=false) +``` + +``` julia +logs = train_model( + jem, train_set, opt_state; num_epochs=num_epochs, val_set=val_set, + verbosity = minimum([num_epochs, 10]), + α = [1.0,1.0,1e-2], + # use_class_loss=false, + # use_gen_loss=false, + # use_reg_loss=false, +) +``` + +### The final evaluation + +``` julia +n_iter = 200 +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = jem.sampler(jem.chain, jem.sampling_rule; niter=n_iter, n_samples=neach, y=i) + plts_i = [] + for j in 1:size(x, 3) + xj = x[:,:,j] + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` + +#### From Scratch + +``` julia +sampler = UnconditionalSampler(𝒟x; input_size=(D,D)) +conditional_sampler = ConditionalSampler(𝒟x, 𝒟y; input_size=(D,D)) +opt = ImproperSGLD(10.0,0.005) +n_iter = 256 +``` + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = conditional_sampler(jem.chain, opt; niter=n_iter, y=i, n_samples=neach) + plts_i = [] + for j in 1:size(x,3) + xj = x[:,:,j] + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` + +``` julia +_w = 1500 +plts = [] +neach = 10 +for i in 1:10 + x = sampler(jem.chain, opt; niter=n_iter, y=i, n_samples=neach) + plts_i = [] + for j in 1:size(x,3) + xj = x[:,:,j] + plts_i = [plts_i..., heatmap(rotl90(xj), axis=nothing, cb=false)] + end + plt = plot(plts_i..., size=(_w,0.10*_w), layout=(1,10)) + plts = [plts..., plt] +end +plot(plts..., size=(_w,_w), layout=(10,1)) +``` diff --git a/docs/src/tutorials/mnist.qmd b/docs/src/tutorials/mnist.qmd index d72a136..b51e803 100644 --- a/docs/src/tutorials/mnist.qmd +++ b/docs/src/tutorials/mnist.qmd @@ -3,7 +3,7 @@ ```{julia} #| echo: false -include("docs/setup_docs.jl") +include("$(pwd())/docs/setup_docs.jl") eval(setup_docs) ``` diff --git a/docs/src/tutorials/synthetic.md b/docs/src/tutorials/synthetic.md new file mode 100644 index 0000000..91f7d05 --- /dev/null +++ b/docs/src/tutorials/synthetic.md @@ -0,0 +1,131 @@ +# Synthetic Data + + +## Binary Classification + +``` julia +nobs=2000 +X, y = make_circles(nobs, noise=0.1, factor=0.5) +X = Float32.(permutedims(matrix(X))) +y_labels = Int.(y.refs) +y = Flux.onehotbatch(y.refs, sort(unique(y_labels))) +display(scatter(X[1,:], X[2,:], color=vec(y_labels), label="")) +batch_size = Int(round(nobs/10)) +train_set = DataLoader((X, y), batchsize=batch_size, shuffle=true) +``` + +``` julia +n_hidden = 32 +activation = relu +models = Dict( + "Logistic Regression" => Chain(Dense(2, size(y,1))), + "MLP" => Chain( + Dense(2, n_hidden, activation), + Dense(n_hidden, n_hidden, activation), + Dense(n_hidden, n_hidden, activation), + Dense(n_hidden, size(y,1)) + ), +) +``` + +``` julia +_loss(y_hat, y) = Flux.Losses.logitcrossentropy(y_hat, y) +rule = Adam() +``` + +``` julia +_lims = extrema(X, dims=2) +x1, x2 = map(ex -> range(1.1f0.*ex..., length=100), _lims) +n_epochs = 100 +plts = [] +for (name, model) in models + opt_state = Flux.setup(rule, model) + for epoch in 1:n_epochs + Flux.train!(model, train_set, opt_state) do m, x, y + _loss(model(x), y) + end + end + plt = contour(x1, x2, (x, y) -> softmax(model([x, y]))[1], fill=true, alpha=0.5, title=name, cbar=false) + scatter!(X[1,:], X[2,:], color=vec(y_labels), label="") + push!(plts, plt) +end +plot(plts..., layout=(1, 2), size=(800, 400)) +``` + +## Joint Energy Model + +``` julia +# We initialize the full model: +𝒟x = Normal() +𝒟y = Categorical(ones(2) ./ 2) +sampler = ConditionalSampler(𝒟x, 𝒟y, input_size=size(X)[1:end-1], batch_size=batch_size) +jem = JointEnergyModel( + models["MLP"], + sampler; + sampling_rule=ImproperSGLD(), + sampling_steps=10 +) +# Initialise training: +opt = Adam(1e-3) +opt_state = Flux.setup(opt, jem) +num_epochs = 100 +``` + +``` julia +logs = JointEnergyModels.train_model( + jem, train_set, opt_state; + num_epochs=num_epochs, + α=[1.0,1.0,1e-1], + verbosity=minimum([num_epochs, 50]), + # use_class_loss=false, + # use_gen_loss=false, + # use_reg_loss=false, +) +``` + +``` julia +plts = [] +for target in 1:size(y,1) + plt = contour(x1, x2, (x, y) -> softmax(jem([x, y]))[target], fill=true, alpha=0.5, title="Target: $target", cbar=false) + scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels)) + push!(plts, plt) +end +plot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400)) +``` + +``` julia +X̂ = generate_samples(jem, 1000; niter=1000) +ŷ = onecold(softmax(jem(X̂))) +scatter(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5) +scatter!(X̂[1,:], X̂[2,:], color=vec(ŷ), group=vec(ŷ), title="Generated Samples", shape=:star5) +``` + +``` julia +if typeof(jem.sampler) <: ConditionalSampler + + plts = [] + for target in 1:size(y,1) + X̂ = generate_conditional_samples(jem, batch_size, target; niter=1000) + ex = extrema(hcat(X,X̂), dims=2) + xlims = ex[1] + ylims = ex[2] + x1 = range(1.0f0.*xlims...,length=100) + x2 = range(1.0f0.*ylims...,length=100) + plt = contour( + x1, x2, (x, y) -> softmax(jem([x, y]))[target], + fill=true, alpha=0.5, title="Target: $target", cbar=false, + xlims=xlims, + ylims=ylims, + ) + scatter!(X[1,:], X[2,:], color=vec(y_labels), group=vec(y_labels), alpha=0.5) + scatter!( + X̂[1,:], X̂[2,:], + color=repeat([target], size(X̂,2)), + group=repeat([target], size(X̂,2)), + shape=:star5, ms=10 + ) + push!(plts, plt) + end + plot(plts..., layout=(1, size(y,1)), size=(size(y,1)*400, 400)) +end +``` diff --git a/docs/src/tutorials/synthetic.qmd b/docs/src/tutorials/synthetic.qmd index 485190a..5f9343d 100644 --- a/docs/src/tutorials/synthetic.qmd +++ b/docs/src/tutorials/synthetic.qmd @@ -2,7 +2,7 @@ ```{julia} #| echo: false -include("docs/setup_docs.jl") +include("$(pwd())/docs/setup_docs.jl") eval(setup_docs) ``` diff --git a/test/runtests.jl b/test/runtests.jl index b9a039a..481a03c 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -5,9 +5,6 @@ using MLJBase using MLJFlux using Test -import CompatHelperLocal as CHL -CHL.@check() - include("utils.jl") @testset "JointEnergyModels.jl" begin From 19202e02c5ac57da993b7dcdacdb25ca0427805f Mon Sep 17 00:00:00 2001 From: pat-alt Date: Mon, 29 Apr 2024 14:17:02 +0200 Subject: [PATCH 3/3] final things --- .github/workflows/CI.yml | 2 +- Project.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 07c618e..4db9c86 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -21,7 +21,7 @@ jobs: - '1.7' - '1.8' - '1.9' - - 'nightly' + - '1.10' os: - ubuntu-latest arch: diff --git a/Project.toml b/Project.toml index 15b22fe..308d338 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "JointEnergyModels" uuid = "48c56d24-211d-4463-bbc0-7a701b291131" authors = ["Patrick Altmeyer"] -version = "0.1.3" +version = "0.1.4" [deps] CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"