From ead38cd524dfa2b91c8858bfa2bdfda08dbd967b Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Fri, 19 May 2023 01:27:56 +0200 Subject: [PATCH 01/19] Update notebook manifest to latest versions --- notebooks/supervised_learning.jl | 841 +++++++++++++++++++------------ 1 file changed, 519 insertions(+), 322 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index cd7086c6..829a6a85 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.9 +# v0.19.26 using Markdown using InteractiveUtils @@ -1450,33 +1450,37 @@ Turing = "~0.21.1" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.3" +julia_version = "1.9.0" manifest_format = "2.0" project_hash = "addb13b0aea7688f4fe00d84034f44c777be88f4" [[deps.AbstractAlgebra]] deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "dd2f52bc149ff35158827471453e2e4f1a2685a6" +git-tree-sha1 = "29e65c331f97db9189ef00a4c7aed8127c2fd2d4" uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.26.0" +version = "0.27.10" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" +deps = ["LinearAlgebra"] +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.1.0" +version = "1.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "5c26c7759412ffcaf0dd6e3172e55d783dd7610b" +git-tree-sha1 = "b4d13c741b2bbe0e1af305a92d2f105a7caa47af" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.1.3" +version = "4.2.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "DensityInterface", "Setfield", "SparseArrays"] -git-tree-sha1 = "6320752437e9fbf49639a410017d862ad64415a5" +deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] +git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.2" +version = "0.5.4" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -1490,16 +1494,20 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.3.4" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.3" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] -git-tree-sha1 = "345effa84030f273ee86fcdd706d8484ce9a1a3c" +git-tree-sha1 = "0091e2e4d0a7125da0e3ad8c7dbff9171a921461" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.3.5" +version = "0.3.6" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] @@ -1515,9 +1523,9 @@ version = "0.3.8" [[deps.AdvancedVI]] deps = ["Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "e743af305716a527cdb3a67b31a33a7c3832c41f" +git-tree-sha1 = "67fcc7d46c26250e89fc62798fbe07b5ee264c6f" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.1.5" +version = "0.1.6" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -1526,6 +1534,7 @@ version = "2.3.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[deps.ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] @@ -1534,20 +1543,26 @@ uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" version = "5.0.8" [[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "7d255eb1d2e409335835dc8624c35d97453011eb" +deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.14" +version = "0.1.29" [[deps.ArrayInterfaceStaticArraysCore]] -deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] -git-tree-sha1 = "a1e2cf6ced6505cbad2490532388683f1e88c3ed" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] +git-tree-sha1 = "01a9f8e6cfc2bfdd01d333f70b8014a04893103c" uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9" -version = "0.1.0" +version = "0.1.4" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + [[deps.AutoHashEquals]] git-tree-sha1 = "45bb6705d93be619b81451bb2006b7ee5d4e4453" uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" @@ -1572,10 +1587,24 @@ uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" version = "0.2.0" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "b15a6bc52594f5e4a3b825858d1089618871bf9d" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "54b00d1b93791f8e19e31584bd30f2cb6004614b" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.36" +version = "0.3.38" + + [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" @@ -1592,9 +1621,9 @@ version = "0.1.4" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "51c842b5a07ad64acdd6cac9e52a304b2d6605b6" +git-tree-sha1 = "1234b03e94938e6f2b14834dfd3ef45698d5e14f" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.10.2" +version = "0.10.8" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1609,12 +1638,12 @@ version = "0.4.2" [[deps.CUDA]] deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] -git-tree-sha1 = "e4e5ece72fa2f108fb20c3c5538a5fa9ef3d668a" +git-tree-sha1 = "6717cb9a3425ebb7b31ca4f832823615d175f64a" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.11.0" +version = "3.13.1" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -1626,34 +1655,34 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["ChainRulesCore", "Compat", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"] -git-tree-sha1 = "b06ed86d99c982cbe9047a45a93ac62d9605a361" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] +git-tree-sha1 = "8bae903893aeeb429cf732cf1888490b93ecf265" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.36.2" +version = "1.49.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "2dd813e5f2f7eec2d1268c57cf2373d3ee91fcea" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.1" +version = "1.16.0" [[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53" +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "f84967c4497e0e1955f9a582c232b02847c5f589" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.3" +version = "0.1.7" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.19.0" +version = "3.21.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -1663,15 +1692,15 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.12.10" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -1679,9 +1708,9 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonSolve]] -git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25" +git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.1" +version = "0.2.3" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -1691,23 +1720,28 @@ version = "0.3.0" [[deps.Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" +git-tree-sha1 = "6c0100a8cf4ed66f66e2039af7cde3357814bad2" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" +version = "3.46.2" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.0.2+0" [[deps.CompositeTypes]] -git-tree-sha1 = "d5b014b216dc891e81fea299638e4c10c657b582" +git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.2" +version = "0.1.3" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -1717,9 +1751,14 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "c096d0e321368ac23eb1be1ea405814f8b32adb3" +git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.3.1" +version = "1.5.2" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] deps = ["StaticArrays"] @@ -1733,15 +1772,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.10.0" +version = "1.15.0" [[deps.DataFrames]] deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "daa21eb85147f72e41f6352a57fccea377e310a9" +git-tree-sha1 = "db2a9cb664fcea7836da4b414c3278d71dd602d2" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.4" +version = "1.3.6" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -1765,7 +1804,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[deps.DensityInterface]] deps = ["InverseFunctions", "Test"] @@ -1774,32 +1815,37 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffResults]] -deps = ["StaticArrays"] -git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" -version = "1.0.3" +version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120" +git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.11.0" +version = "1.13.0" [[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 = "0597dffe1268516192ff4ddebdb4d8937254512d" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "5eeb2bd01e5065090ad591a205d8cad432ae6cb6" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.63" +version = "0.25.93" +weakdeps = ["ChainRulesCore", "DensityInterface"] + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "ec811a2688b3504ce5b315fe7bc86464480d5964" +git-tree-sha1 = "c0eb6f717434b3f13cd7a24b412938d952849d77" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.41" +version = "0.6.45" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -1808,14 +1854,15 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.8.6" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "StaticArrays", "Statistics"] -git-tree-sha1 = "ac425eea956013b51e7891bef3c33684b7d37029" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] +git-tree-sha1 = "988e2db482abeb69efc76ae8b6eba2e93805ee70" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.5.11" +version = "0.5.15" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" [[deps.DualNumbers]] deps = ["Calculus", "NaNMath", "SpecialFunctions"] @@ -1824,22 +1871,22 @@ uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" [[deps.DynamicPPL]] -deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "Distributions", "LinearAlgebra", "MacroTools", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "c6f574d855670c2906af3f4053e6db10224e5dda" +deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] +git-tree-sha1 = "7bc3920ba1e577ad3d7ebac75602ab42b557e28e" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.19.3" +version = "0.20.2" [[deps.DynamicPolynomials]] deps = ["DataStructures", "Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "d0fa82f39c2a5cdb3ee385ad52bc05c42cb4b9f0" +git-tree-sha1 = "8b84876e31fa39479050e2d3395c4b3b210db8b0" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.4.5" +version = "0.4.6" [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" +git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.2.3+0" +version = "2.2.4+0" [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterfaceCore", "Distributions", "Random", "Statistics"] @@ -1847,6 +1894,11 @@ git-tree-sha1 = "4cda4527e990c0cc201286e0a0bfbbce00abcfc2" uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2" version = "1.0.0" +[[deps.EnumX]] +git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" +uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" +version = "1.0.4" + [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" @@ -1854,9 +1906,14 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" [[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "0.1.9" + +[[deps.Extents]] +git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.1" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -1865,16 +1922,16 @@ 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", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "d8a578692e3077ac998b50c0217dfd67f21d1e5f" +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" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.0+0" +version = "4.4.2+2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" +git-tree-sha1 = "f9818144ce7c8c41edf5c4c179c684d92aa4d9fe" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.5.0" +version = "1.6.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1887,15 +1944,15 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" +git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.2" +version = "0.13.11" [[deps.FiniteDiff]] -deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "ee13c773ce60d9e95a6c6ea134f25605dce2eda3" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.13.0" +version = "2.17.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -1922,10 +1979,14 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.30" +version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1940,9 +2001,15 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[deps.FunctionWrappers]] -git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" +git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" -version = "1.1.2" +version = "1.1.3" + +[[deps.FunctionWrappersWrappers]] +deps = ["FunctionWrappers"] +git-tree-sha1 = "b104d487b34566608f8b4e1c39fb0b10aa279ff8" +uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" +version = "0.1.3" [[deps.Functors]] git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4" @@ -1955,27 +2022,27 @@ 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 = "51d2dfe8e590fbd74e7a842cf6d13d8a2f45dc01" +git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.6+0" +version = "3.3.8+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "73a4c9447419ce058df716925893e452ba5528ad" +git-tree-sha1 = "9ade6983c3dbbd492cf5729f865fe030d1541463" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.4.0" +version = "8.6.6" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "4078d3557ab15dd9fe6a0cf6f65e3d4937e98427" +git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.0" +version = "0.1.4" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "47f63159f7cb5d0e5e0cfd2f20454adea429bec9" +git-tree-sha1 = "19d693666a304e8c371798f4900f7435558c7cde" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.16.1" +version = "0.17.3" [[deps.GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] @@ -1985,15 +2052,21 @@ version = "0.64.4" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "3a233eeeb2ca45842fe100e0413936834215abf5" +git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.64.4+0" +version = "0.69.1+0" + +[[deps.GeoInterface]] +deps = ["Extents"] +git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab" +uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" +version = "1.3.1" [[deps.GeometryBasics]] -deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" +deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] +git-tree-sha1 = "659140c9375afa2f685e37c1a0b9c9a60ef56b40" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.2" +version = "0.4.7" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -2002,10 +2075,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+2" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2020,9 +2093,9 @@ version = "1.0.2" [[deps.Groebner]] deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random"] -git-tree-sha1 = "7ac3333b82b85f753dd22bed79b85cabcd5e7317" +git-tree-sha1 = "47f0f03eddecd7ad59c42b1dd46d5f42916aff63" uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.2.7" +version = "0.2.11" [[deps.GroupsCore]] deps = ["Markdown", "Random"] @@ -2043,10 +2116,10 @@ uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "SpecialFunctions", "Test"] -git-tree-sha1 = "cb7099a0109939f16a4d3b572ba8396b1f6c7c31" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "84204eae2dd237500835990bcade263e27674a93" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.10" +version = "0.3.16" [[deps.Hyperscript]] deps = ["Test"] @@ -2062,15 +2135,15 @@ version = "0.9.4" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.3" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "af14a478780ca78d5eb9908b263023096c2b9d64" +git-tree-sha1 = "eac00994ce3229a464c2847e956d77a2c64ad3a5" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.6" +version = "0.4.10" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -2100,41 +2173,41 @@ version = "0.1.0" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d979e54b71da82f3a65b62553da4fc3d18c9004c" +git-tree-sha1 = "0cb9352ef2e01574eeebdb102948a58740dcaf83" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2018.0.3+2" +version = "2023.1.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.Interpolations]] -deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" +deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.7" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" +git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.1" +version = "0.7.3" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.7" +version = "0.1.9" [[deps.InvertedIndices]] -git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IterTools]] git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" @@ -2154,15 +2227,15 @@ version = "1.4.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" [[deps.Juno]] deps = ["Base64", "Logging", "Media", "Profile"] @@ -2170,11 +2243,17 @@ git-tree-sha1 = "07cb43290a840908a771552911a6274bc6c072c7" uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" version = "0.8.4" +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "47be64f040a7ece575c2b5f53ca6da7b548d69f4" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.4" + [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" +git-tree-sha1 = "90442c50e202a5cdf21a7899c66b240fdef14035" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.3" +version = "0.6.7" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2190,20 +2269,20 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "e7e9184b0bf0158ac4e4aa9daf00041b5909bf1a" +git-tree-sha1 = "f044a2796a9e18e0531b9b3072b0019a61f264bc" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.14.0" +version = "4.17.1" [[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "070e4b5b65827f82c16ae0916376cb47377aa1b5" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.16+0" +version = "0.0.18+0" [[deps.LRUCache]] -git-tree-sha1 = "d64a0aff6691612ab9fb0117b0995270871c5dfc" +git-tree-sha1 = "48c10e3cc27e30de82463c27bef0b8bdbd1dc634" uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" -version = "1.3.0" +version = "1.4.1" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2223,10 +2302,22 @@ uuid = "2ee39098-c373-598a-b85f-a56591580800" version = "1.9.0" [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "46a39b9c58749eefb5f2dc1178cb8fab5332b1ab" +deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] +git-tree-sha1 = "8c57307b5d9bb3be1ff2da469063628631d4d51e" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.15" +version = "0.15.21" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + DiffEqBiologicalExt = "DiffEqBiological" + ParameterizedFunctionsExt = "DiffEqBase" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -2241,10 +2332,12 @@ version = "0.1.3" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.3" [[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" [[deps.LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -2253,6 +2346,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.10.2+0" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -2271,9 +2365,9 @@ version = "1.8.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf" +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.3.0+3" +version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2283,9 +2377,9 @@ version = "1.42.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+1" +version = "1.16.1+2" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2313,19 +2407,31 @@ version = "2.36.0+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd" +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.1.1" +version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[deps.LogDensityProblems]] +deps = ["ArgCheck", "DocStringExtensions", "Random", "Requires", "UnPack"] +git-tree-sha1 = "c3e1189191e4528b605070972d7d4e9cd91dd96b" +uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +version = "1.0.3" + [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.15" +version = "0.3.23" +weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -2337,58 +2443,64 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "0.4.9" [[deps.MCMCChains]] -deps = ["AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "8cb9b8fb081afd7728f5de25b9025bff97cb5c7a" +deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] +git-tree-sha1 = "c659f7508035a7bdd5102aef2de028ab035f289a" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.3.1" +version = "5.7.1" [[deps.MCMCDiagnosticTools]] -deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "058d08594e91ba1d98dcc3669f9421a76824aa95" +deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] +git-tree-sha1 = "8b862779314f9299cbf7bdbf2413bcbd9c8e77b2" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.1.3" +version = "0.2.6" + +[[deps.MIMEs]] +git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" +uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" +version = "0.1.4" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" +git-tree-sha1 = "2ce8695e1e699b68702c03402672a69f54b8aca9" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2022.0.0+0" +version = "2022.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "b8073fe6973dcfad5fec803dabc1d3a7f6c4ebc8" +git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.4.3" +version = "1.8.0" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" +git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" +version = "0.5.10" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = 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[[deps.Metatheory]] deps = ["AutoHashEquals", "DataStructures", "Dates", "DocStringExtensions", "Parameters", "Reexport", "TermInterface", "ThreadsX", "TimerOutputs"] -git-tree-sha1 = "a160e323d3684889e6026914576f1f4288de131d" +git-tree-sha1 = "0f39bc7f71abdff12ead4fc4a7d998fb2f3c171f" uuid = "e9d8d322-4543-424a-9be4-0cc815abe26c" -version = "1.3.4" +version = "1.3.5" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "6bb7786e4f24d44b4e29df03c69add1b63d88f01" +git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.2" +version = "0.1.4" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2022.10.11" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "393fc4d82a73c6fe0e2963dd7c882b09257be537" +git-tree-sha1 = "eaa98afe2033ffc0629f9d0d83961d66a021dfcc" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.4.6" +version = "0.4.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "4e675d6e9ec02061800d6cfb695812becbd03cdf" +git-tree-sha1 = "964cb1a7069723727025ae295408747a0b36a854" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.0.4" +version = "1.3.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" +git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.2" +version = "7.8.3" [[deps.NNlib]] -deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "1a80840bcdb73de345230328d49767ab115be6f2" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.8" +version = "0.8.20" + + [deps.NNlib.extensions] + NNlibAMDGPUExt = "AMDGPU" + + [deps.NNlib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" [[deps.NNlibCUDA]] -deps = ["CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "e161b835c6aa9e2339c1e72c3d4e39891eac7a4f" +deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] +git-tree-sha1 = "b05a082b08a3af0e5c576883bc6dfb6513e7e478" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.2.3" +version = "0.2.6" [[deps.NaNMath]] -git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" +deps = ["OpenLibm_jll"] +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.7" +version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "2fd5787125d1a93fbe30961bd841707b8a80d75b" +git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.6" +version = "0.9.8" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -2468,12 +2588,13 @@ version = "1.0.0" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.7" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2484,16 +2605,18 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.21+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" +version = "0.8.1+0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9a36165cf84cff35851809a40a928e1103702013" +git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.16+0" +version = "1.1.20+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -2514,21 +2637,20 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.0" -[[deps.PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" +[[deps.PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.42.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "ca433b9e2f5ca3a0ce6702a032fce95a3b6e1e48" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.14" +version = "0.11.17" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2537,10 +2659,10 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "a5aef8d4a6e8d81f171b2bd4be5265b01384c74c" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" +version = "2.5.10" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2549,20 +2671,21 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.40.1+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 = "1.9.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce" +git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.0.0" +version = "3.1.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "9888e59493658e476d3073f1ce24348bdc086660" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.0" +version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] @@ -2571,10 +2694,10 @@ uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.27.6" [[deps.PlutoUI]] -deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "Markdown", "Random", "Reexport", "UUIDs"] -git-tree-sha1 = "8d1f54886b9037091edf146b517989fc4a09efec" +deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] +git-tree-sha1 = "b478a748be27bd2f2c73a7690da219d0844db305" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.39" +version = "0.7.51" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -2588,11 +2711,17 @@ git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "259e206946c293698122f63e2b513a7c99a244e8" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.1.1" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] @@ -2628,15 +2757,15 @@ version = "1.7.2" [[deps.Qt5Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "c6c0f690d0cc7caddb74cef7aa847b824a16b256" +git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+1" +version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.2" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -2648,9 +2777,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "afeacaecf4ed1649555a19cb2cad3c141bbc9474" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.5.0" +version = "1.6.1" [[deps.RandomExtensions]] deps = ["Random", "SparseArrays"] @@ -2671,9 +2800,13 @@ version = "0.3.2" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" +git-tree-sha1 = "6d7bb727e76147ba18eed998700998e17b8e4911" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.3" +version = "0.4.4" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -2682,9 +2815,10 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[deps.RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.4" [[deps.RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -2693,10 +2827,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.5.2" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "ZygoteRules"] -git-tree-sha1 = "7ddd4f1ac52f9cc1b784212785f86a75602a7e4b" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"] +git-tree-sha1 = "a5ce741acddc02f0d4fc6505463ca89697d7fb23" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.31.0" +version = "2.32.3" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -2723,36 +2857,45 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" [[deps.Roots]] -deps = ["CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "30e3981751855e2340e9b524ab58c1ec85c36f33" +deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] +git-tree-sha1 = "e961f57a7d5b1d46059b62a8fb7223d6497a5bc4" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.1" +version = "2.0.15" + + [deps.Roots.extensions] + RootsForwardDiffExt = "ForwardDiff" + RootsIntervalRootFindingExt = "IntervalRootFinding" + + [deps.Roots.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "cdc1e4278e91a6ad530770ebb327f9ed83cf10c4" +git-tree-sha1 = "d7d9ebe28062161c1e314ed643097b0c6fe657d9" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.3" +version = "0.5.7" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" [[deps.SciMLBase]] -deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables", "TreeViews"] -git-tree-sha1 = "3243a883fa422a0a5cfe2d3b6ea6287fc396018f" +deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "RuntimeGeneratedFunctions", "StaticArraysCore", "Statistics", "Tables"] +git-tree-sha1 = "fe89a8113ea445bcff9ee570077830674babb534" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.42.2" +version = "1.81.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -2761,9 +2904,9 @@ version = "3.0.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.0" +version = "1.2.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -2784,30 +2927,40 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" +[[deps.SnoopPrecompile]] +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" +uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" +version = "1.0.3" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" +git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.0.1" +version = "1.1.0" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "a9e798cae4867e3a41cae2dd9eb60c047f1212db" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.6" +version = "2.2.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] -git-tree-sha1 = "39c9f91521de844bad65049efd4f9223e7ed43f9" +git-tree-sha1 = "e08a62abc517eb79667d0a29dc08a3b589516bb5" uuid = "171d559e-b47b-412a-8079-5efa626c420e" -version = "0.1.14" +version = "0.1.15" [[deps.Static]] deps = ["IfElse"] @@ -2817,58 +2970,69 @@ version = "0.6.6" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "9f8a5dc5944dc7fbbe6eb4180660935653b0a9d9" +git-tree-sha1 = "8982b3607a212b070a5e46eea83eb62b4744ae12" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.0" +version = "1.5.25" [[deps.StaticArraysCore]] -git-tree-sha1 = "66fe9eb253f910fe8cf161953880cfdaef01cdf0" +git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.0.1" +version = "1.4.0" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] -git-tree-sha1 = "271a7fea12d319f23d55b785c51f6876aadb9ac0" +git-tree-sha1 = "30b9236691858e13f167ce829490a68e1a597782" uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" -version = "3.0.0" +version = "3.2.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "2c11d7290036fe7aac9038ff312d3b3a2a5bf89e" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.4.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "48598584bacbebf7d30e20880438ed1d24b7c7d6" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.18" +version = "0.33.21" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.0.1" +version = "1.3.0" +weakdeps = ["ChainRulesCore", "InverseFunctions"] + + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "ec47fb6069c57f1cee2f67541bf8f23415146de7" +deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.11" +version = "0.6.15" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + [[deps.SymbolicUtils]] deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "Metatheory", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "TermInterface", "TimerOutputs"] -git-tree-sha1 = "92b21f756625f2ff3b2a05495c105f432be01e17" +git-tree-sha1 = "027b43d312f6d52187bb16c2d4f0588ddb8c4bb2" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "0.19.10" +version = "0.19.11" [[deps.Symbolics]] deps = ["ArrayInterface", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "Groebner", "IfElse", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "Metatheory", "NaNMath", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "TermInterface", "TreeViews"] @@ -2879,6 +3043,7 @@ version = "4.3.1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -2888,13 +3053,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -2909,9 +3075,9 @@ version = "0.2.3" [[deps.TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] -git-tree-sha1 = "62846a48a6cd70e63aa29944b8c4ef704360d72f" +git-tree-sha1 = "f133fab380933d042f6796eda4e130272ba520ca" uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed" -version = "0.1.5" +version = "0.1.7" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -2919,15 +3085,15 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.ThreadsX]] deps = ["ArgCheck", "BangBang", "ConstructionBase", "InitialValues", "MicroCollections", "Referenceables", "Setfield", "SplittablesBase", "Transducers"] -git-tree-sha1 = "d223de97c948636a4f34d1f84d92fd7602dc555b" +git-tree-sha1 = "34e6bcf36b9ed5d56489600cf9f3c16843fa2aa2" uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" -version = "0.1.10" +version = "0.1.11" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "464d64b2510a25e6efe410e7edab14fffdc333df" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.20" +version = "0.5.23" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -2937,15 +3103,15 @@ version = "0.2.20" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" +version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c76399a3bbe6f5a88faa33c8f8a65aa631d95013" +git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.73" +version = "0.4.76" [[deps.TreeViews]] deps = ["Test"] @@ -2954,20 +3120,20 @@ uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" version = "0.3.0" [[deps.Tricks]] -git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.6" +version = "0.1.7" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] -git-tree-sha1 = "05596da2440006a18f956c08cb6b827182dc254f" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "631fdfe9720d8c2e2a885b1580c8f8c18347b5da" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.21.7" +version = "0.21.13" [[deps.URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -2987,6 +3153,17 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "ead6292c02aab389cb29fe64cc9375765ab1e219" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.1" + [[deps.Unzip]] git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" @@ -2994,9 +3171,9 @@ version = "0.1.2" [[deps.Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3012,9 +3189,9 @@ version = "0.5.5" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" +git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.14+0" +version = "2.10.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -3157,24 +3334,41 @@ version = "0.9.4" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+0" [[deps.Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.5+0" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "3cfdb31b517eec4173584fba2b1aa65daad46e09" +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 = "ebac1ae9f048c669317ad48c9bed815790a468d8" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.41" +version = "0.6.61" + + [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 = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.4.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -3183,8 +3377,9 @@ 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 = "5.7.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3207,10 +3402,12 @@ version = "1.3.7+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3226,9 +3423,9 @@ 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 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+0" """ # ╔═╡ Cell order: From a6468f7fb3b8cc79f6dfdf826343b635e36b909b Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Sat, 20 May 2023 10:48:49 +0200 Subject: [PATCH 02/19] Reduce number of slider options --- notebooks/supervised_learning.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index 829a6a85..d92c5476 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -650,8 +650,8 @@ This section contains UI elements and variables they are bound to. # ╔═╡ 2cc52188-b262-4f65-b042-ad94d90523d8 begin - w0_input = @bind w0 Scrubbable(-5:0.01:5; default=0.3, format="0.2f") - w1_input = @bind w1 Scrubbable(-5:0.01:5; default=-3, format="0.2f") + w0_input = @bind w0 Scrubbable(-3:0.1:3; default=0.3, format="0.2f") + w1_input = @bind w1 Scrubbable(-3:0.1:3; default=-3, format="0.2f") g_input = @bind g MultiSelect( [ one => "1", @@ -665,10 +665,10 @@ begin size=5, default=Function[one], ) - max_order_input = @bind max_order Scrubbable(0:100; default=0) + max_order_input = @bind max_order Scrubbable(0:20; default=0) show_contour_input = @bind show_contour CheckBox(; default=false) λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g") - thresh_input = @bind thresh Scrubbable(-4:0.01:4; default=0) + thresh_input = @bind thresh Scrubbable(-4:0.1:4; default=0) nhidden1_input = @bind nhidden1 Scrubbable(0:10; default=0) nhidden2_input = @bind nhidden2 Scrubbable(0:10; default=0) end; From a26fb2af90005ffebb38e625f4e0174e196e79ff Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 10:46:27 +0200 Subject: [PATCH 03/19] Build notebook with PlutoSliderServer --- docs/Manifest.toml | 629 ++++++++++++++++++++++++++++++++++++++++++++- docs/Project.toml | 4 +- docs/make.jl | 20 +- 3 files changed, 633 insertions(+), 20 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 9f67c595..d5c2674d 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,37 +1,249 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.2" +julia_version = "1.9.1" manifest_format = "2.0" +project_hash = "e15f6fea10b993fa9946ae154fd2fe6d6534a886" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" 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+deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] +uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" + +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + +[[deps.TOML]] +deps = ["Dates"] +uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.3" + +[[deps.TableTraits]] +deps = ["IteratorInterfaceExtensions"] +git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" +uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" +version = "1.0.1" + +[[deps.Tables]] +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" +uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" +version = "1.10.1" + +[[deps.Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" + +[[deps.TerminalLoggers]] +deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] +git-tree-sha1 = "f133fab380933d042f6796eda4e130272ba520ca" +uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed" +version = "0.1.7" + [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TranscodingStreams]] +deps = ["Random", "Test"] +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.9.13" + +[[deps.Tricks]] +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.7" + +[[deps.URIs]] +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" +uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" +version = "1.4.2" + +[[deps.UUIDs]] +deps = ["Random", "SHA"] +uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" + [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" diff --git a/docs/Project.toml b/docs/Project.toml index 25ff5748..508e622a 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -2,6 +2,8 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" IntroML = "f16ed5a4-c5bd-47e9-8f9b-55da3edf7325" Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" +PlutoSliderServer = "2fc8631c-6f24-4c5b-bca7-cbb509c42db4" +PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" [compat] -Pluto = "0.18.4" +Pluto = "0.19" diff --git a/docs/make.jl b/docs/make.jl index 91ac9c26..16e70fff 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,24 +1,30 @@ using IntroML using Documenter -using Pluto +using PlutoSliderServer const DOCS_PATH = @__DIR__ const SRC_PATH = joinpath(DOCS_PATH, "src") const NB_PATH = joinpath(dirname(DOCS_PATH), "notebooks") -function build_notebook(nbpath, htmlpath) +function build_notebook(nbpath, outpath) + htmlpath = joinpath(outpath, first(splitext(nbpath)) * ".html") @info "Building notebook at $nbpath to HTML file at $htmlpath" - s = Pluto.ServerSession() - nb = Pluto.SessionActions.open(s, nbpath; run_async=false) - write(htmlpath, Pluto.generate_html(nb)) + PlutoSliderServer.export_notebook( + nbpath; + Export_output_dir=outpath, + Precompute_enabled=true, + Precompute_max_filesize_per_group=1e9, + Export_create_index=false, + ) + isfile(htmlpath) || + @warn "Failed to build notebook at $nbpath to HTML file at $htmlpath" return htmlpath end # build Pluto notebooks for fn in readdir(NB_PATH) nbpath = joinpath(NB_PATH, fn) - htmlpath = joinpath(SRC_PATH, first(splitext(fn)) * ".html") - build_notebook(nbpath, htmlpath) + build_notebook(nbpath, SRC_PATH) end DocMeta.setdocmeta!(IntroML, :DocTestSetup, :(using IntroML); recursive=true) From 55bbb6c412d6b8f7616761d0a7616aca0611dac6 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 10:46:39 +0200 Subject: [PATCH 04/19] Ignore PlutoSliderServer prebuild files --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index ae4eaa94..0920d75d 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,8 @@ *.jl.mem /Manifest.toml /docs/build/ + +# PlutoSliderServer outputs /docs/src/*.html +/docs/src/staterequest +/docs/src/bondconnections From af2a4e233379c70433b2740bbbb4fb9b2c832d9d Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 10:47:02 +0200 Subject: [PATCH 05/19] Separate bind elements to different cells --- notebooks/supervised_learning.jl | 110 ++++++++++++++++++------------- 1 file changed, 66 insertions(+), 44 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index d92c5476..83b72614 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -36,7 +36,7 @@ end md""" # Supervised learning: One step at a time -This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/intro-ml). +This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/intro-ml). We here focus on [supervised learning](https://en.wikipedia.org/wiki/Supervised_learning). As we progress from a simple linear regression to a first example of a neural network, we introduce the basic concepts needed to understand machine learning. @@ -221,7 +221,7 @@ Let's look at this vocabulary of functions: # ╔═╡ d4c08329-baa4-438a-9555-ee0ea5443e44 let - funs = vcat(one, reduce(vcat, [[x -> cospi(2j * x), x -> sinpi(2j * x)] for j in 1:4])) + funs = vcat(one, reduce(vcat, [[x -> cospi(2j * x), x -> sinpi(2j * x)] for j in 1:4])) plots = map(funs) do gj lex = latexify(gj(Symbolics.Sym{Real}(:x)); env=:raw) plot(gj, 0, 1; color=:orange, xlabel=L"x", ylabel=L"%$lex", label="") @@ -338,7 +338,7 @@ html""" border-color: #dba058; background: #f7d698; } - + pluto-output div.admonition.model .admonition-title { background: #dba058; } @@ -349,7 +349,7 @@ html""" border-color: #d7ae61; background: #7d541f; } - + pluto-output div.admonition.model .admonition-title { background: #d7ae61; } @@ -379,10 +379,10 @@ In mathematical terminology, we seek to find a function ``y=\hat{f}(x)``. In ML we call this function a $(important("model")), and our goal in ML is to devise ways to learn models automatically from the data -- or $(important("learning algorithms")). Let's explore how to build ML algorithms together! -!!! note +!!! note No plants were harmed to generate dataset ``\mathcal{D}``. Instead of measuring water amounts and plant heights, we generated ``10`` ``x_i`` values at regular intervals and used a function ``f`` (that we keep secret from you) to generate each ``y_i``: - ```math + ```math y_i = f(x_i) + \mathrm{noise}. ``` These "invented" outputs ``f(x_i)`` also received some noise to reflect measurement errors. @@ -441,7 +441,7 @@ Conversely, we say that a model $(important("overfits")) the training data if it To check this for our models, we hold out a $(important("validation set")) ``(x_\mathrm{val}, y_\mathrm{val})``, data similar to ``(x, y)`` that we only use to validate our model. -Often for validation, we use a different error function than for training. +Often for validation, we use a different error function than for training. Here, we use the $(important("root-mean-squared error")): ```math E_\mathrm{RMS}(w) = \sqrt{\frac{2E(w)}{n}} @@ -492,7 +492,7 @@ For our linear regression model, with 2 degrees of freedom, we can visualize dra # ╔═╡ b0773555-44ac-4b06-a410-d25ee1f42399 md""" Interestingly, our overparametrized model has quite a wide ensemble, since many possible curves are able to almost pass through our training data. -Similarly, our underparametrized models likewise have a wider ensemble, as many linear fits have similar errors, while for ``n=3``, the ensemble is quite tight. +Similarly, our underparametrized models likewise have a wider ensemble, as many linear fits have similar errors, while for ``n=3``, the ensemble is quite tight. Bayesian models are very useful for certain problems and have distinct advantages and disadvantages. @@ -584,7 +584,7 @@ While we could use the same sum-of-squares loss on this function, it turns out t E(w) = -\sum_{i=1}^k c_i \log \hat{f}(x_i; w) + (1 - c_i) \log (1 - \hat{f}(x_i; w)) ```` -This model with this choice of loss is called [$(important("logistic regression"))](https://en.wikipedia.org/wiki/Logistic_regression). +This model with this choice of loss is called [$(important("logistic regression"))](https://en.wikipedia.org/wiki/Logistic_regression). Below we show the results of fitting an order ``n=33`` polynomial with logistic function output to the binary labels. """ @@ -648,30 +648,8 @@ md""" This section contains UI elements and variables they are bound to. """ -# ╔═╡ 2cc52188-b262-4f65-b042-ad94d90523d8 -begin - w0_input = @bind w0 Scrubbable(-3:0.1:3; default=0.3, format="0.2f") - w1_input = @bind w1 Scrubbable(-3:0.1:3; default=-3, format="0.2f") - g_input = @bind g MultiSelect( - [ - one => "1", - identity => "x", - (x -> x^2) => "x²", - sin => "sin(x)", - cos => "cos(x)", - tan => "tan(x)", - exp => "exp(x)", - ]; - size=5, - default=Function[one], - ) - max_order_input = @bind max_order Scrubbable(0:20; default=0) - show_contour_input = @bind show_contour CheckBox(; default=false) - λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g") - thresh_input = @bind thresh Scrubbable(-4:0.1:4; default=0) - nhidden1_input = @bind nhidden1 Scrubbable(0:10; default=0) - nhidden2_input = @bind nhidden2 Scrubbable(0:10; default=0) -end; +# ╔═╡ 879e4355-d4f0-492c-9ac2-7359c794a9fd +w0_input = @bind w0 Scrubbable(-3:0.1:3; default=0.3, format="0.2f"); # ╔═╡ cd49e0a5-4120-481a-965e-72e7bdaf867c md""" @@ -717,6 +695,9 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top ``w_0 = `` $w0_input """ +# ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 +w1_input = @bind w1 Scrubbable(-3:0.1:3; default=-3, format="0.2f"); + # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" ### A line with slope @@ -751,16 +732,20 @@ So we can equivalently plot the combination of weights on a 2D grid with a reado ``w^\top = (`` $w0_input ``, `` $w1_input ``)`` """ -# ╔═╡ 2eb005a3-f5b2-4216-b56f-e25157b8c33c -md""" -Let's overlay the computer-generated trajectory on our manual one. - -!!! question - Can you tell what strategy the computer is using to minimize the error? - What about if you show the contours of the error function? - -Show error: $show_contour_input -""" +# ╔═╡ e06d0925-585f-42e9-9dea-49044625d3d8 +g_input = @bind g MultiSelect( + [ + one => "1", + identity => "x", + (x -> x^2) => "x²", + sin => "sin(x)", + cos => "cos(x)", + tan => "tan(x)", + exp => "exp(x)", + ]; + size=5, + default=Function[one], +); # ╔═╡ 74290eff-781b-44c9-8a90-96bffbe040df md""" @@ -803,6 +788,9 @@ let plot(plots...; link=:both) end +# ╔═╡ aa8c6266-0338-44a9-b14b-088f98b04db3 +max_order_input = @bind max_order Scrubbable(0:20; default=0); + # ╔═╡ ca1f0910-d417-41bc-ae2d-eebec7f3e1e9 md""" ### Systematically scaling the model by adding terms @@ -834,12 +822,35 @@ md"``n = `` $max_order_input" # ╔═╡ efb34c1a-5505-49f1-aa7f-24f6fd1fc01d md"``n = `` $max_order_input" +# ╔═╡ c6218e7c-1999-4e90-8868-a81717837fb2 +show_contour_input = @bind show_contour CheckBox(; default=false); + +# ╔═╡ 2eb005a3-f5b2-4216-b56f-e25157b8c33c +md""" +Let's overlay the computer-generated trajectory on our manual one. + +!!! question + Can you tell what strategy the computer is using to minimize the error? + What about if you show the contours of the error function? + +Show error: $show_contour_input +""" + +# ╔═╡ 186680f8-9b47-4a93-9fa0-81c0c2ea894b +λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g"); + # ╔═╡ e2890775-2e29-4244-adac-c37f8f2a8a8e md"``n = `` $max_order_input ``\quad`` ``\lambda =`` $λ_input" +# ╔═╡ fb5e7b56-66e5-45ef-9ad7-b50dd997137d +thresh_input = @bind thresh Scrubbable(-4:0.1:4; default=0); + # ╔═╡ 1e12834c-4b29-41db-ab1f-d93db62c8341 md"``t = `` $thresh_input" +# ╔═╡ 94629920-3a9a-4d50-973f-cd18d3ea50f0 +nhidden1_input = @bind nhidden1 Scrubbable(0:10; default=0); + # ╔═╡ d2e5bde1-8c65-494f-8944-b16dec6ab193 md""" ### Fitting 1D data with neural networks @@ -852,6 +863,9 @@ Let's take the simple neural architecture with a single hidden layer displayed a Number of hidden units = $nhidden1_input """ +# ╔═╡ 38b63169-2712-48a6-b8b5-66429565cc87 +nhidden2_input = @bind nhidden2 Scrubbable(0:10; default=0); + # ╔═╡ 29fb4486-5605-438f-9b1a-a24a19b20c5e md""" Sure, we could fit this data with logistic regression if we chose the right computed features. @@ -3514,7 +3528,15 @@ version = "1.4.1+0" # ╠═54ef467e-8cc2-436e-bddc-37c57b6e6980 # ╠═b176823e-b8b5-413d-87b1-90d7efa0e377 # ╟─c75744a0-3c3f-4042-a796-6cbd9ec11195 -# ╠═2cc52188-b262-4f65-b042-ad94d90523d8 +# ╠═879e4355-d4f0-492c-9ac2-7359c794a9fd +# ╠═b8ff692c-2ccb-455c-87c2-590177def1b4 +# ╠═e06d0925-585f-42e9-9dea-49044625d3d8 +# ╠═aa8c6266-0338-44a9-b14b-088f98b04db3 +# ╠═c6218e7c-1999-4e90-8868-a81717837fb2 +# ╠═186680f8-9b47-4a93-9fa0-81c0c2ea894b +# ╠═fb5e7b56-66e5-45ef-9ad7-b50dd997137d +# ╠═94629920-3a9a-4d50-973f-cd18d3ea50f0 +# ╠═38b63169-2712-48a6-b8b5-66429565cc87 # ╟─d8983a9d-1880-4dc4-9c17-23281767e0c2 # ╠═5e7bda42-0266-4498-906d-9aca8b6c4bf3 # ╠═805d2824-86cc-45bd-88b0-e6e14d9fde48 From 308c0ffa96544a1cc941aa2f85a9591c8f46f6be Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 10:48:16 +0200 Subject: [PATCH 06/19] Add DocsPreviewCleanup workflow --- .github/workflows/DocsPreviewCleanup.yml | 26 ++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 .github/workflows/DocsPreviewCleanup.yml diff --git a/.github/workflows/DocsPreviewCleanup.yml b/.github/workflows/DocsPreviewCleanup.yml new file mode 100644 index 00000000..4f57bc46 --- /dev/null +++ b/.github/workflows/DocsPreviewCleanup.yml @@ -0,0 +1,26 @@ +name: DocsPreviewCleanup + +on: + pull_request: + types: [closed] + +jobs: + cleanup: + runs-on: ubuntu-latest + steps: + - name: Checkout gh-pages branch + uses: actions/checkout@v2 + with: + ref: gh-pages + - name: Delete preview and history + push changes + run: | + if [ -d "previews/PR$PRNUM" ]; then + git config user.name "Documenter.jl" + git config user.email "documenter@juliadocs.github.io" + git rm -rf "previews/PR$PRNUM" + git commit -m "delete preview" + git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree}) + git push --force origin gh-pages-new:gh-pages + fi + env: + PRNUM: ${{ github.event.number }} From f8f00e56cb6d725d72383d7f6461ee758b32507a Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 10:51:36 +0200 Subject: [PATCH 07/19] Remove test job from CI --- .github/workflows/CI.yml | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 4ccc2191..1f268402 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -11,32 +11,6 @@ concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }} jobs: - test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - version: - - '1.6' - - 'nightly' - os: - - ubuntu-latest - arch: - - x64 - steps: - - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 - with: - version: ${{ matrix.version }} - arch: ${{ matrix.arch }} - - uses: julia-actions/cache@v1 - - uses: julia-actions/julia-buildpkg@v1 - - uses: julia-actions/julia-runtest@v1 - - uses: julia-actions/julia-processcoverage@v1 - - uses: codecov/codecov-action@v2 - with: - files: lcov.info docs: name: Documentation runs-on: ubuntu-latest From f6e50037c0a4c53a4110a8e7d5d3224ec6c5cb37 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 11:01:57 +0200 Subject: [PATCH 08/19] Instantiate before building docs --- .github/workflows/CI.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 1f268402..aa750baf 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -20,6 +20,7 @@ jobs: with: version: '1' - uses: julia-actions/julia-buildpkg@v1 + - run: julia --project=docs/ -e 'using Pkg; Pkg.instantiate()' - uses: julia-actions/julia-docdeploy@v1 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From d81c25d5fc9c99228de44546b6054e2ac2cc7dfb Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 11:02:30 +0200 Subject: [PATCH 09/19] Don't test docstrings --- .github/workflows/CI.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index aa750baf..45a25ec2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -25,9 +25,3 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} - - run: | - julia --project=docs -e ' - using Documenter: DocMeta, doctest - using IntroML - DocMeta.setdocmeta!(IntroML, :DocTestSetup, :(using IntroML); recursive=true) - doctest(IntroML)' From 8ee6eafc5bb59ecd6d63279cf544096b474a3ef0 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 14:11:38 +0200 Subject: [PATCH 10/19] Rerun notebook --- notebooks/supervised_learning.jl | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index 83b72614..c22dd2f1 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -732,6 +732,16 @@ So we can equivalently plot the combination of weights on a 2D grid with a reado ``w^\top = (`` $w0_input ``, `` $w1_input ``)`` """ +# ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 +let + scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") + plot!(; + title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))", + xlabel=L"w_0", + ylabel=L"w_1", + ) +end + # ╔═╡ e06d0925-585f-42e9-9dea-49044625d3d8 g_input = @bind g MultiSelect( [ @@ -1207,16 +1217,6 @@ let plot!(p; title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))") end -# ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 -let - scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") - plot!(; - title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))", - xlabel=L"w_0", - ylabel=L"w_1", - ) -end - # ╔═╡ 6016a736-11da-4451-aa82-cc3045e782db let obj(w) = error(x -> w[1] + w[2] * x, x, y) @@ -1464,7 +1464,7 @@ Turing = "~0.21.1" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.0" +julia_version = "1.9.1" manifest_format = "2.0" project_hash = "addb13b0aea7688f4fe00d84034f44c777be88f4" @@ -3393,7 +3393,7 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.7.0+0" +version = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] From 44a434cb7646a75a769d67925db6fa809c867862 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 14:27:14 +0200 Subject: [PATCH 11/19] Update IntroML URL --- README.md | 2 +- docs/src/index.md | 2 +- notebooks/supervised_learning.jl | 22 +++++++++++----------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 70af22a3..03a13ad0 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac) [![License: CC BY-SA 4.0](https://img.shields.io/badge/License-CC%20BY--SA%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by-sa/4.0/) -This repository contains notebooks for the [Introduction to Machine Learning workshop](https://mlcolab.org/intro-ml) with the [Machine Learning ⇌ Science Colaboratory](https://mlcolab.org). +This repository contains notebooks for the [Introduction to Machine Learning workshop](https://mlcolab.org/resources/introml-july-2022-workshop-materials) with the [Machine Learning ⇌ Science Colaboratory](https://mlcolab.org). [![notebook_preview](https://user-images.githubusercontent.com/8673634/161941600-b1c31af3-df9b-4481-bb6f-1e25a4f849d2.gif)](https://mlcolab.github.io/IntroML.jl/dev/supervised_learning.html) diff --git a/docs/src/index.md b/docs/src/index.md index f6f35ca2..02d43b0b 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -4,6 +4,6 @@ CurrentModule = IntroML # Introduction to Machine Learning -Materials for the Introduction to Machine Learning workshop with the [Machine Learning ⇌ Science Colaboratory](https://mlcolab.org/). +Materials for the [Introduction to Machine Learning](https://mlcolab.org/resources/introml-july-2022-workshop-materials) workshop with the [Machine Learning ⇌ Science Colaboratory](https://mlcolab.org/). - [Supervised Learning: One step at a time](./supervised_learning.html) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index c22dd2f1..f43b1c18 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -36,7 +36,7 @@ end md""" # Supervised learning: One step at a time -This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/intro-ml). +This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/resources/introml-july-2022-workshop-materials). We here focus on [supervised learning](https://en.wikipedia.org/wiki/Supervised_learning). As we progress from a simple linear regression to a first example of a neural network, we introduce the basic concepts needed to understand machine learning. @@ -732,16 +732,6 @@ So we can equivalently plot the combination of weights on a 2D grid with a reado ``w^\top = (`` $w0_input ``, `` $w1_input ``)`` """ -# ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 -let - scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") - plot!(; - title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))", - xlabel=L"w_0", - ylabel=L"w_1", - ) -end - # ╔═╡ e06d0925-585f-42e9-9dea-49044625d3d8 g_input = @bind g MultiSelect( [ @@ -1217,6 +1207,16 @@ let plot!(p; title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))") end +# ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 +let + scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") + plot!(; + title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))", + xlabel=L"w_0", + ylabel=L"w_1", + ) +end + # ╔═╡ 6016a736-11da-4451-aa82-cc3045e782db let obj(w) = error(x -> w[1] + w[2] * x, x, y) From 095e7b9a4e25e422327aeb3f9d7a43aad7ac67cd Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 15:20:27 +0200 Subject: [PATCH 12/19] Reduce size of groups for precomputation --- notebooks/supervised_learning.jl | 72 ++++++++++++++++++-------------- 1 file changed, 40 insertions(+), 32 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index f43b1c18..d4c1d62e 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -649,7 +649,7 @@ This section contains UI elements and variables they are bound to. """ # ╔═╡ 879e4355-d4f0-492c-9ac2-7359c794a9fd -w0_input = @bind w0 Scrubbable(-3:0.1:3; default=0.3, format="0.2f"); +w0_input = @bind w0 Scrubbable(-2:0.25:2; default=0.25, format="0.2f"); # ╔═╡ cd49e0a5-4120-481a-965e-72e7bdaf867c md""" @@ -696,7 +696,10 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top """ # ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 -w1_input = @bind w1 Scrubbable(-3:0.1:3; default=-3, format="0.2f"); +w0_input2 = @bind w0_2 Scrubbable(-2:0.25:2; default=0.25, format="0.2f"); + +# ╔═╡ fa6a31d1-f1b2-489b-9fef-4f92b5542c80 +w1_input = @bind w1 Scrubbable(-1:0.25:3; default=-1, format="0.2f"); # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" @@ -721,7 +724,7 @@ This model is an example of [$(important("linear regression"))](https://en.wikip Drag the below values to minimize the loss. How low can you get the error? -``w^\top = (`` $w0_input ``, `` $w1_input ``)`` +``w^\top = (`` $w0_input2 ``, `` $w1_input ``)`` """ # ╔═╡ b657b5fe-af35-46e9-93c7-f897e7b22ddc @@ -732,20 +735,28 @@ So we can equivalently plot the combination of weights on a 2D grid with a reado ``w^\top = (`` $w0_input ``, `` $w1_input ``)`` """ +# ╔═╡ 0103f249-52e2-4403-b62e-b3ad21536d37 +g_options = [ + one => "1", + identity => "x", + (x -> x^2) => "x²", + sin => "sin(x)", + cos => "cos(x)", + tan => "tan(x)", + exp => "exp(x)", +]; + +# ╔═╡ bf50534d-1c9a-439a-9922-262f64b83c1d +let + plots = map(g_options) do (gj, _) + lex = latexify(gj(Symbolics.Sym{Real}(:x)); env=:raw) + plot(gj, 0, 1; color=:orange, xlabel=L"x", ylabel=L"%$lex", label="") + end + plot(plots...; link=:both) +end + # ╔═╡ e06d0925-585f-42e9-9dea-49044625d3d8 -g_input = @bind g MultiSelect( - [ - one => "1", - identity => "x", - (x -> x^2) => "x²", - sin => "sin(x)", - cos => "cos(x)", - tan => "tan(x)", - exp => "exp(x)", - ]; - size=5, - default=Function[one], -); +g_input = @bind g MultiSelect(g_options, size=5, default=Function[one]); # ╔═╡ 74290eff-781b-44c9-8a90-96bffbe040df md""" @@ -779,15 +790,6 @@ Hint: ``\begin{bmatrix}1 \\ x\end{bmatrix}`` is equivalent to fitting the line w ``g(x) = `` $g_input """ -# ╔═╡ bf50534d-1c9a-439a-9922-262f64b83c1d -let - plots = map(g) do gj - lex = latexify(gj(Symbolics.Sym{Real}(:x)); env=:raw) - plot(gj, 0, 1; color=:orange, xlabel=L"x", ylabel=L"%$lex", label="") - end - plot(plots...; link=:both) -end - # ╔═╡ aa8c6266-0338-44a9-b14b-088f98b04db3 max_order_input = @bind max_order Scrubbable(0:20; default=0); @@ -822,6 +824,9 @@ md"``n = `` $max_order_input" # ╔═╡ efb34c1a-5505-49f1-aa7f-24f6fd1fc01d md"``n = `` $max_order_input" +# ╔═╡ 9b96ba97-1fe6-4d08-aa69-07a04219686b +max_order_reg_input = @bind max_order_reg Scrubbable(0:20; default=0); + # ╔═╡ c6218e7c-1999-4e90-8868-a81717837fb2 show_contour_input = @bind show_contour CheckBox(; default=false); @@ -833,17 +838,17 @@ Let's overlay the computer-generated trajectory on our manual one. Can you tell what strategy the computer is using to minimize the error? What about if you show the contours of the error function? -Show error: $show_contour_input +Show contours of error function: $show_contour_input """ # ╔═╡ 186680f8-9b47-4a93-9fa0-81c0c2ea894b λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g"); # ╔═╡ e2890775-2e29-4244-adac-c37f8f2a8a8e -md"``n = `` $max_order_input ``\quad`` ``\lambda =`` $λ_input" +md"``n = `` $max_order_reg_input ``\quad`` ``\lambda =`` $λ_input" # ╔═╡ fb5e7b56-66e5-45ef-9ad7-b50dd997137d -thresh_input = @bind thresh Scrubbable(-4:0.1:4; default=0); +thresh_input = @bind thresh Scrubbable(-3:0.1:3; default=0); # ╔═╡ 1e12834c-4b29-41db-ab1f-d93db62c8341 md"``t = `` $thresh_input" @@ -1196,7 +1201,7 @@ end # ╔═╡ 1a906880-75e1-447b-9adf-31ae44f0135f begin - f_hat_line(x) = w0 + w1 * x + f_hat_line(x) = w0_2 + w1 * x error_line = error(f_hat_line, x, y) equation_line = as_latex(f_hat_line) end; @@ -1204,14 +1209,14 @@ end; # ╔═╡ 345ae96b-92c2-4ac4-bfdf-302113627ffb let p = plot_data(x, y; f_hat=f_hat_line, show_residuals=true, equation=equation_line) - plot!(p; title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))") + plot!(p; title=L"E(w)= %$(round(error_line; digits=2))") end # ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 let scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") plot!(; - title=L"E(w_0{=}%$(w0),w_1{=}%$(w1))= %$(round(error_line; digits=2))", + title=L"E(w)= %$(round(error_line; digits=2))", xlabel=L"w_0", ylabel=L"w_1", ) @@ -1341,7 +1346,7 @@ plot_poly_compare(x, y, ytest, max_order) plot_poly_compare(xmore, ymore, ymore_test, max_order) # ╔═╡ 9ce43ec1-78f5-414f-9796-ab3159be7985 -plot_poly_compare(x, y, ytest, max_order; λ) +plot_poly_compare(x, y, ytest, max_order_reg; λ) # ╔═╡ 86e58e39-186e-470f-832a-32cd86717daa # for computational reasons, we use the QR parameterization of the regression model @@ -3530,8 +3535,11 @@ version = "1.4.1+0" # ╟─c75744a0-3c3f-4042-a796-6cbd9ec11195 # ╠═879e4355-d4f0-492c-9ac2-7359c794a9fd # ╠═b8ff692c-2ccb-455c-87c2-590177def1b4 +# ╠═fa6a31d1-f1b2-489b-9fef-4f92b5542c80 +# ╠═0103f249-52e2-4403-b62e-b3ad21536d37 # ╠═e06d0925-585f-42e9-9dea-49044625d3d8 # ╠═aa8c6266-0338-44a9-b14b-088f98b04db3 +# ╠═9b96ba97-1fe6-4d08-aa69-07a04219686b # ╠═c6218e7c-1999-4e90-8868-a81717837fb2 # ╠═186680f8-9b47-4a93-9fa0-81c0c2ea894b # ╠═fb5e7b56-66e5-45ef-9ad7-b50dd997137d From a9670a54ae2bcfe55a183052c434a5d84728c520 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 16:53:16 +0200 Subject: [PATCH 13/19] Simplify notebook building code --- docs/make.jl | 19 ++++++------------- 1 file changed, 6 insertions(+), 13 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 16e70fff..bbffb8f4 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -6,26 +6,19 @@ const DOCS_PATH = @__DIR__ const SRC_PATH = joinpath(DOCS_PATH, "src") const NB_PATH = joinpath(dirname(DOCS_PATH), "notebooks") -function build_notebook(nbpath, outpath) - htmlpath = joinpath(outpath, first(splitext(nbpath)) * ".html") - @info "Building notebook at $nbpath to HTML file at $htmlpath" - PlutoSliderServer.export_notebook( - nbpath; - Export_output_dir=outpath, +function build_notebooks(dir_path, out_path) + PlutoSliderServer.export_directory( + dir_path; + Export_output_dir=out_path, Precompute_enabled=true, Precompute_max_filesize_per_group=1e9, Export_create_index=false, ) - isfile(htmlpath) || - @warn "Failed to build notebook at $nbpath to HTML file at $htmlpath" - return htmlpath + return out_path end # build Pluto notebooks -for fn in readdir(NB_PATH) - nbpath = joinpath(NB_PATH, fn) - build_notebook(nbpath, SRC_PATH) -end +build_notebooks(NB_PATH, SRC_PATH) DocMeta.setdocmeta!(IntroML, :DocTestSetup, :(using IntroML); recursive=true) From ab102fdb926eeb4750b348fb7371bb3f6402173a Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 16:54:35 +0200 Subject: [PATCH 14/19] Fix splitting of weight groups --- notebooks/supervised_learning.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index d4c1d62e..509888ed 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -732,7 +732,7 @@ md""" Because we now have two weights, our parameter space is 2-dimensional. So we can equivalently plot the combination of weights on a 2D grid with a readout of the error and just move the values around until the error is minimized: -``w^\top = (`` $w0_input ``, `` $w1_input ``)`` +``w^\top = (`` $w0_input2 ``, `` $w1_input ``)`` """ # ╔═╡ 0103f249-52e2-4403-b62e-b3ad21536d37 @@ -1214,7 +1214,7 @@ end # ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 let - scatter([w0], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") + scatter([w0_2], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") plot!(; title=L"E(w)= %$(round(error_line; digits=2))", xlabel=L"w_0", From 5a2c02fe7c3648fde550e23be627d714da9dbbbf Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Wed, 14 Jun 2023 16:58:00 +0200 Subject: [PATCH 15/19] Run formatter --- notebooks/supervised_learning.jl | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index 509888ed..8cbfc198 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -7,7 +7,14 @@ using InteractiveUtils # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). macro bind(def, element) quote - local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local iv = try + Base.loaded_modules[Base.PkgId( + Base.UUID("6e696c72-6542-2067-7265-42206c756150"), + "AbstractPlutoDingetjes", + )].Bonds.initial_value + catch + b -> missing + end local el = $(esc(element)) global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el @@ -737,13 +744,13 @@ So we can equivalently plot the combination of weights on a 2D grid with a reado # ╔═╡ 0103f249-52e2-4403-b62e-b3ad21536d37 g_options = [ - one => "1", - identity => "x", - (x -> x^2) => "x²", - sin => "sin(x)", - cos => "cos(x)", - tan => "tan(x)", - exp => "exp(x)", + one => "1", + identity => "x", + (x -> x^2) => "x²", + sin => "sin(x)", + cos => "cos(x)", + tan => "tan(x)", + exp => "exp(x)", ]; # ╔═╡ bf50534d-1c9a-439a-9922-262f64b83c1d @@ -1215,11 +1222,7 @@ end # ╔═╡ 0d1164df-8236-494b-b8b9-71481c94c0d9 let scatter([w0_2], [w1]; xlims=(-4.1, 4.1), ylims=(-3.1, 2.1), color=:orange, label="") - plot!(; - title=L"E(w)= %$(round(error_line; digits=2))", - xlabel=L"w_0", - ylabel=L"w_1", - ) + plot!(; title=L"E(w)= %$(round(error_line; digits=2))", xlabel=L"w_0", ylabel=L"w_1") end # ╔═╡ 6016a736-11da-4451-aa82-cc3045e782db From e0802ad455ba3a4d724f024a52b272faabb48e17 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Thu, 15 Jun 2023 15:40:53 +0200 Subject: [PATCH 16/19] Update note about interactivity --- notebooks/supervised_learning.jl | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index 8cbfc198..b78a60c7 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -50,9 +50,8 @@ As we progress from a simple linear regression to a first example of a neural ne !!! note This notebook is written using [Pluto](https://github.com/fonsp/Pluto.jl), a reactive notebook environment. - If you're viewing this on the web, the interactive elements will be static, and this will not be as useful. - Click "Edit or run this notebook" on the top right to find instructions for making it interactive. - Note that because we load several heavy dependencies, Binder will likely not work. + If you're viewing this on the web and the interactive elements don't work for you, click "Edit or run this notebook" on the top right to find instructions for making it fully interactive. + Note that because we load several heavy dependencies, the Binder option will likely not work. """ # ╔═╡ 31b1a0e4-216f-4c90-b16e-f542000c8aee From 71433a96104ee0231dab9ebfc293ea5b2e19ccc7 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Thu, 15 Jun 2023 16:19:18 +0200 Subject: [PATCH 17/19] Make sliders a little finer again --- notebooks/supervised_learning.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index b78a60c7..a8bdf0e5 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -655,7 +655,7 @@ This section contains UI elements and variables they are bound to. """ # ╔═╡ 879e4355-d4f0-492c-9ac2-7359c794a9fd -w0_input = @bind w0 Scrubbable(-2:0.25:2; default=0.25, format="0.2f"); +w0_input = @bind w0 Scrubbable(-3:0.1:3; default=0.3, format="0.1f"); # ╔═╡ cd49e0a5-4120-481a-965e-72e7bdaf867c md""" @@ -702,10 +702,10 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top """ # ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 -w0_input2 = @bind w0_2 Scrubbable(-2:0.25:2; default=0.25, format="0.2f"); +w0_input2 = @bind w0_2 Scrubbable(-2:0.1:2; default=0.3, format="0.1f"); # ╔═╡ fa6a31d1-f1b2-489b-9fef-4f92b5542c80 -w1_input = @bind w1 Scrubbable(-1:0.25:3; default=-1, format="0.2f"); +w1_input = @bind w1 Scrubbable(-1:0.1:3; default=-1, format="0.1f"); # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" From 37c274b4456dd6ae84f22159d475c52155fb7b59 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 20 Jun 2023 11:31:54 +0200 Subject: [PATCH 18/19] Make bounds of bivariate plot match interactive elements --- notebooks/supervised_learning.jl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index a8bdf0e5..e6df54d7 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -702,10 +702,10 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top """ # ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 -w0_input2 = @bind w0_2 Scrubbable(-2:0.1:2; default=0.3, format="0.1f"); +w0_input2 = @bind w0_2 Scrubbable(vcat(-2, -2:0.1:2, 2); default=0.3, format="0.1f"); # ╔═╡ fa6a31d1-f1b2-489b-9fef-4f92b5542c80 -w1_input = @bind w1 Scrubbable(-1:0.1:3; default=-1, format="0.1f"); +w1_input = @bind w1 Scrubbable(vcat(-1, -1:0.1:3, 3); default=-1.1, format="0.1f"); # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" @@ -848,7 +848,7 @@ Show contours of error function: $show_contour_input """ # ╔═╡ 186680f8-9b47-4a93-9fa0-81c0c2ea894b -λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g"); +λ_input = @bind λ Scrubbable(exp10.([-Inf; -Inf; -15:1:0]); default=0, format=".1g"); # ╔═╡ e2890775-2e29-4244-adac-c37f8f2a8a8e md"``n = `` $max_order_reg_input ``\quad`` ``\lambda =`` $λ_input" @@ -1272,8 +1272,8 @@ let ) plot!( p; - xlims=(-2.1, 4.1), - ylims=(-3.1, 2.1), + xlims=(-2.1, 2.1), + ylims=(-1.1, 3.1), aspect_ratio=1, xlabel=L"w_0", ylabel=L"w_1", @@ -1416,8 +1416,8 @@ let scatter!(p, [f_hat.w[1]], [f_hat.w[2]]; color=:orange, msc=:white, msw=1.3, ms=3) plot!( p; - xlims=(-4.1, 4.1), - ylims=(-3.1, 2.1), + xlims=(-2.1, 2.1), + ylims=(-1.1, 3.1), aspect_ratio=1, xlabel=L"w_0", ylabel=L"w_1", From 8bd6a0df288ea61462b30d274955f060d6a6c88f Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Tue, 20 Jun 2023 13:00:13 +0200 Subject: [PATCH 19/19] Revert "Make bounds of bivariate plot match interactive elements" This reverts commit 37c274b4456dd6ae84f22159d475c52155fb7b59. --- notebooks/supervised_learning.jl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/notebooks/supervised_learning.jl b/notebooks/supervised_learning.jl index e6df54d7..a8bdf0e5 100644 --- a/notebooks/supervised_learning.jl +++ b/notebooks/supervised_learning.jl @@ -702,10 +702,10 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top """ # ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 -w0_input2 = @bind w0_2 Scrubbable(vcat(-2, -2:0.1:2, 2); default=0.3, format="0.1f"); +w0_input2 = @bind w0_2 Scrubbable(-2:0.1:2; default=0.3, format="0.1f"); # ╔═╡ fa6a31d1-f1b2-489b-9fef-4f92b5542c80 -w1_input = @bind w1 Scrubbable(vcat(-1, -1:0.1:3, 3); default=-1.1, format="0.1f"); +w1_input = @bind w1 Scrubbable(-1:0.1:3; default=-1, format="0.1f"); # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" @@ -848,7 +848,7 @@ Show contours of error function: $show_contour_input """ # ╔═╡ 186680f8-9b47-4a93-9fa0-81c0c2ea894b -λ_input = @bind λ Scrubbable(exp10.([-Inf; -Inf; -15:1:0]); default=0, format=".1g"); +λ_input = @bind λ Scrubbable(exp10.([-Inf; -15:1:0]); default=0, format=".1g"); # ╔═╡ e2890775-2e29-4244-adac-c37f8f2a8a8e md"``n = `` $max_order_reg_input ``\quad`` ``\lambda =`` $λ_input" @@ -1272,8 +1272,8 @@ let ) plot!( p; - xlims=(-2.1, 2.1), - ylims=(-1.1, 3.1), + xlims=(-2.1, 4.1), + ylims=(-3.1, 2.1), aspect_ratio=1, xlabel=L"w_0", ylabel=L"w_1", @@ -1416,8 +1416,8 @@ let scatter!(p, [f_hat.w[1]], [f_hat.w[2]]; color=:orange, msc=:white, msw=1.3, ms=3) plot!( p; - xlims=(-2.1, 2.1), - ylims=(-1.1, 3.1), + xlims=(-4.1, 4.1), + ylims=(-3.1, 2.1), aspect_ratio=1, xlabel=L"w_0", ylabel=L"w_1",