diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 4ccc2191..45a25ec2 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 @@ -46,13 +20,8 @@ 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 }} DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} - - run: | - julia --project=docs -e ' - using Documenter: DocMeta, doctest - using IntroML - DocMeta.setdocmeta!(IntroML, :DocTestSetup, :(using IntroML); recursive=true) - doctest(IntroML)' diff --git a/.github/workflows/DocsPreviewCleanup.yml b/.github/workflows/DocsPreviewCleanup.yml new file mode 100644 index 00000000..4f57bc46 --- /dev/null +++ b/.github/workflows/DocsPreviewCleanup.yml @@ -0,0 +1,26 @@ +name: DocsPreviewCleanup + +on: + pull_request: + types: [closed] + +jobs: + cleanup: + runs-on: ubuntu-latest + steps: + - name: Checkout gh-pages branch + uses: actions/checkout@v2 + with: + ref: gh-pages + - name: Delete preview and history + push changes + run: | + if [ -d "previews/PR$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 }} 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 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/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" +[[deps.AbstractPlutoDingetjes]] +deps = ["Pkg"] +git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" +uuid = "6e696c72-6542-2067-7265-42206c756150" +version = "1.1.4" + +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +[[deps.BetterFileWatching]] +deps = ["Deno_jll", "JSON"] +git-tree-sha1 = "0d7ee0a1acad90d544fa87cc3d6f463e99abb77a" +uuid = "c9fd44ac-77b5-486c-9482-9798bd063cc6" +version = "0.1.5" + +[[deps.BitFlags]] +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.7" + +[[deps.Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + +[[deps.CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.1" + +[[deps.ColorTypes]] 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["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.Pluto]] +deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "LoggingExtras", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "PrecompileTools", "REPL", "RegistryInstances", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] +git-tree-sha1 = "c4c4dac5c1332ab510e145eea59382847c51a6fb" +uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" +version = "0.19.26" + +[[deps.PlutoSliderServer]] +deps = ["AbstractPlutoDingetjes", "Base64", "BetterFileWatching", "Configurations", "Distributed", "Distributions", "FromFile", "Git", "GitHubActions", "Glob", "HTTP", "JSON", "Logging", "Markdown", "OrderedCollections", "Pkg", "Pluto", "Random", "SHA", "Sockets", "Statistics", "TOML", "TerminalLoggers", "UUIDs"] +git-tree-sha1 = "aa63b32af7e564c16ea6426213cf6bf74ab36bf1" +repo-rev = "static-export-1" +repo-url = "https://github.com/JuliaPluto/PlutoSliderServer.jl.git" +uuid = "2fc8631c-6f24-4c5b-bca7-cbb509c42db4" +version = "0.3.25" + +[[deps.PlutoUI]] +deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] +git-tree-sha1 = "436c0db5ba99a01452f52a0ab0fd8ad6664d5470" +repo-rev = "ms_nonlazy" +repo-url = "https://github.com/sethaxen/PlutoUI.jl" +uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" +version = "0.7.51" + +[[deps.PrecompileSignatures]] +git-tree-sha1 = "18ef344185f25ee9d51d80e179f8dad33dc48eb1" +uuid = "91cefc8d-f054-46dc-8f8c-26e11d7c5411" +version = "3.0.3" + +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.1.2" + +[[deps.Preferences]] +deps = ["TOML"] +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" +uuid = "21216c6a-2e73-6563-6e65-726566657250" +version = "1.4.0" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +[[deps.ProgressLogging]] +deps = ["Logging", "SHA", "UUIDs"] +git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" +uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" +version = "0.1.4" + +[[deps.QuadGK]] +deps = ["DataStructures", "LinearAlgebra"] +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" +uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" +version = "2.8.2" + [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" @@ -83,18 +511,195 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["SHA", "Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[deps.Reexport]] +git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" +uuid = "189a3867-3050-52da-a836-e630ba90ab69" +version = "1.2.2" + +[[deps.RegistryInstances]] +deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] +git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51" +uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3" +version = "0.1.0" + +[[deps.RelocatableFolders]] +deps = ["SHA", "Scratch"] +git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" +uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" +version = "1.0.0" + +[[deps.Requires]] +deps = ["UUIDs"] +git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +uuid = "ae029012-a4dd-5104-9daa-d747884805df" +version = "1.3.0" + +[[deps.Rmath]] +deps = ["Random", "Rmath_jll"] +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" +version = "0.7.1" + +[[deps.Rmath_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" +version = "0.4.0+0" + [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" + +[[deps.Scratch]] +deps = ["Dates"] +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" +uuid = "6c6a2e73-6563-6170-7368-637461726353" +version = "1.2.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +[[deps.SimpleBufferStream]] +git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" +version = "1.1.0" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" +[[deps.SortingAlgorithms]] +deps = ["DataStructures"] +git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" +uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" +version = "1.1.0" + +[[deps.SparseArrays]] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] +uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + +[[deps.SpecialFunctions]] +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +uuid = "276daf66-3868-5448-9aa4-cd146d93841b" +version = "2.2.0" + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" + + [deps.SpecialFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + +[[deps.Statistics]] +deps = ["LinearAlgebra", "SparseArrays"] +uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" + +[[deps.StatsAPI]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" +version = "1.6.0" + +[[deps.StatsBase]] +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" +uuid = 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+[[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..bbffb8f4 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,25 +1,24 @@ 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) - @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)) - return htmlpath +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, + ) + return out_path 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) -end +build_notebooks(NB_PATH, SRC_PATH) DocMeta.setdocmeta!(IntroML, :DocTestSetup, :(using IntroML); recursive=true) 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 cd7086c6..a8bdf0e5 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 @@ -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 $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) el @@ -36,16 +43,15 @@ end md""" # Supervised learning: One step at a time -This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/intro-ml). +This notebook was created for the ML ⇌ Science Colaboratory's workshop [Introduction to Machine Learning](https://mlcolab.org/resources/introml-july-2022-workshop-materials). We here focus on [supervised learning](https://en.wikipedia.org/wiki/Supervised_learning). As we progress from a simple linear regression to a first example of a neural network, we introduce the basic concepts needed to understand machine learning. !!! note This notebook is written using [Pluto](https://github.com/fonsp/Pluto.jl), a reactive notebook environment. - If you're viewing this on the web, the interactive elements will be static, and this will not be as useful. - Click "Edit or run this notebook" on the top right to find instructions for making it interactive. - Note that because we load several heavy dependencies, Binder will likely not work. + If you're viewing this on the web and the interactive elements don't work for you, click "Edit or run this notebook" on the top right to find instructions for making it fully interactive. + Note that because we load several heavy dependencies, the Binder option will likely not work. """ # ╔═╡ 31b1a0e4-216f-4c90-b16e-f542000c8aee @@ -221,7 +227,7 @@ Let's look at this vocabulary of functions: # ╔═╡ d4c08329-baa4-438a-9555-ee0ea5443e44 let - funs = vcat(one, reduce(vcat, [[x -> cospi(2j * x), x -> sinpi(2j * x)] for j in 1:4])) + funs = vcat(one, reduce(vcat, [[x -> cospi(2j * x), x -> sinpi(2j * x)] for j in 1:4])) plots = map(funs) do gj lex = latexify(gj(Symbolics.Sym{Real}(:x)); env=:raw) plot(gj, 0, 1; color=:orange, xlabel=L"x", ylabel=L"%$lex", label="") @@ -338,7 +344,7 @@ html""" border-color: #dba058; background: #f7d698; } - + pluto-output div.admonition.model .admonition-title { background: #dba058; } @@ -349,7 +355,7 @@ html""" border-color: #d7ae61; background: #7d541f; } - + pluto-output div.admonition.model .admonition-title { background: #d7ae61; } @@ -379,10 +385,10 @@ 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 +447,7 @@ 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 $(important("root-mean-squared error")): ```math E_\mathrm{RMS}(w) = \sqrt{\frac{2E(w)}{n}} @@ -492,7 +498,7 @@ For our linear regression model, with 2 degrees of freedom, we can visualize dra # ╔═╡ b0773555-44ac-4b06-a410-d25ee1f42399 md""" Interestingly, our overparametrized model has quite a wide ensemble, since many possible curves are able to almost pass through our training data. -Similarly, our underparametrized models likewise have a wider ensemble, as many linear fits have similar errors, while for ``n=3``, the ensemble is quite tight. +Similarly, our underparametrized models likewise have a wider ensemble, as many linear fits have similar errors, while for ``n=3``, the ensemble is quite tight. Bayesian models are very useful for certain problems and have distinct advantages and disadvantages. @@ -584,7 +590,7 @@ While we could use the same sum-of-squares loss on this function, it turns out t E(w) = -\sum_{i=1}^k c_i \log \hat{f}(x_i; w) + (1 - c_i) \log (1 - \hat{f}(x_i; w)) ```` -This model with this choice of loss is called [$(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 +654,8 @@ md""" 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") - 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(0:100; 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) - 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="0.1f"); # ╔═╡ cd49e0a5-4120-481a-965e-72e7bdaf867c md""" @@ -717,6 +701,12 @@ Now drag the value of ``w_0`` until you've minimized the error shown at the top ``w_0 = `` $w0_input """ +# ╔═╡ b8ff692c-2ccb-455c-87c2-590177def1b4 +w0_input2 = @bind w0_2 Scrubbable(-2:0.1:2; default=0.3, format="0.1f"); + +# ╔═╡ fa6a31d1-f1b2-489b-9fef-4f92b5542c80 +w1_input = @bind w1 Scrubbable(-1:0.1:3; default=-1, format="0.1f"); + # ╔═╡ ae5d8669-f4c4-4b55-9af9-8488e43bcb6c md""" ### A line with slope @@ -740,7 +730,7 @@ This model is an example of [$(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 @@ -748,19 +738,31 @@ 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 ``, `` $w1_input ``)`` """ -# ╔═╡ 2eb005a3-f5b2-4216-b56f-e25157b8c33c -md""" -Let's overlay the computer-generated trajectory on our manual one. +# ╔═╡ 0103f249-52e2-4403-b62e-b3ad21536d37 +g_options = [ + one => "1", + identity => "x", + (x -> x^2) => "x²", + sin => "sin(x)", + cos => "cos(x)", + tan => "tan(x)", + exp => "exp(x)", +]; -!!! question - Can you tell what strategy the computer is using to minimize the error? - What about if you show the contours of the error function? +# ╔═╡ bf50534d-1c9a-439a-9922-262f64b83c1d +let + plots = map(g_options) do (gj, _) + lex = latexify(gj(Symbolics.Sym{Real}(:x)); env=:raw) + plot(gj, 0, 1; color=:orange, xlabel=L"x", ylabel=L"%$lex", label="") + end + plot(plots...; link=:both) +end -Show error: $show_contour_input -""" +# ╔═╡ e06d0925-585f-42e9-9dea-49044625d3d8 +g_input = @bind g MultiSelect(g_options, size=5, default=Function[one]); # ╔═╡ 74290eff-781b-44c9-8a90-96bffbe040df md""" @@ -794,14 +796,8 @@ 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); # ╔═╡ ca1f0910-d417-41bc-ae2d-eebec7f3e1e9 md""" @@ -834,12 +830,38 @@ 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); + +# ╔═╡ 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 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(-3:0.1:3; 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 +874,9 @@ Let's take the simple neural architecture with a single hidden layer displayed a Number of hidden units = $nhidden1_input """ +# ╔═╡ 38b63169-2712-48a6-b8b5-66429565cc87 +nhidden2_input = @bind nhidden2 Scrubbable(0:10; default=0); + # ╔═╡ 29fb4486-5605-438f-9b1a-a24a19b20c5e md""" Sure, we could fit this data with logistic regression if we chose the right computed features. @@ -1182,7 +1207,7 @@ end # ╔═╡ 1a906880-75e1-447b-9adf-31ae44f0135f begin - f_hat_line(x) = w0 + w1 * x + f_hat_line(x) = w0_2 + w1 * x error_line = error(f_hat_line, x, y) equation_line = as_latex(f_hat_line) end; @@ -1190,17 +1215,13 @@ end; # ╔═╡ 345ae96b-92c2-4ac4-bfdf-302113627ffb let p = plot_data(x, y; f_hat=f_hat_line, show_residuals=true, equation=equation_line) - plot!(p; title=L"E(w_0{=}%$(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))", - xlabel=L"w_0", - ylabel=L"w_1", - ) + 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") end # ╔═╡ 6016a736-11da-4451-aa82-cc3045e782db @@ -1327,7 +1348,7 @@ 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 @@ -1450,33 +1471,37 @@ 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 = "1.9.1" 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 +1515,20 @@ 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 +1544,9 @@ 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 +1555,7 @@ 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 +1564,26 @@ 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 +1608,24 @@ 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 +1642,9 @@ 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 +1659,12 @@ 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 +1676,34 @@ 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 +1713,15 @@ 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 +1729,9 @@ 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 +1741,28 @@ 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 +1772,14 @@ 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 +1793,15 @@ 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 +1825,9 @@ 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 +1836,37 @@ 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 +1875,15 @@ 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 +1892,22 @@ 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 +1915,11 @@ 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 +1927,14 @@ 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 +1943,16 @@ 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 +1965,15 @@ 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 +2000,14 @@ 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 +2022,15 @@ 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 +2043,27 @@ 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 +2073,21 @@ 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 +2096,10 @@ 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 +2114,9 @@ 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 +2137,10 @@ 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 +2156,15 @@ 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 +2194,41 @@ 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 +2248,15 @@ 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 +2264,17 @@ 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 +2290,20 @@ 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 +2323,22 @@ 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 +2353,12 @@ 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 +2367,7 @@ 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 +2386,9 @@ 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 +2398,9 @@ 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 +2428,31 @@ 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 +2464,64 @@ 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 = 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"e498ddeee6f9fdb4551ce855a46f54dbd900245f" +git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.1" +version = "0.3.2" [[deps.Media]] deps = ["MacroTools", "Test"] @@ -2398,68 +2531,76 @@ version = "0.5.0" [[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 +2609,13 @@ 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 +2626,18 @@ 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 +2658,20 @@ 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 +2680,10 @@ 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 +2692,21 @@ 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 +2715,10 @@ 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 +2732,17 @@ 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 +2778,15 @@ 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 +2798,9 @@ 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 +2821,13 @@ 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 +2836,10 @@ 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 +2848,10 @@ 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 +2878,45 @@ 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 +2925,9 @@ 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 +2948,40 @@ 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 +2991,69 @@ 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 +3064,7 @@ version = "4.3.1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -2888,13 +3074,14 @@ 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 +3096,9 @@ 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 +3106,15 @@ 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 +3124,15 @@ 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 +3141,20 @@ 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 +3174,17 @@ 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 +3192,9 @@ 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 +3210,9 @@ 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 +3355,41 @@ 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 +3398,9 @@ 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 = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3207,10 +3423,12 @@ 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 +3444,9 @@ 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: @@ -3317,7 +3535,18 @@ version = "0.9.1+5" # ╠═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 +# ╠═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 +# ╠═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