diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 111295dc4..8b802bc43 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -9,7 +9,8 @@ steps: command: - "echo $$JULIA_DEPOT_PATH" - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'" - - "julia --project -e 'using Conda; Conda.add(\"scikit-learn\")'" + - "julia --project -e 'using Conda; Conda.add(\"scipy=1.8.1\")'" + - "julia --project -e 'using Conda; Conda.add(\"scikit-learn=1.1.1\")'" - "julia --project -e 'using Conda; Conda.add(\"matplotlib\")'" env: PYTHON: "" diff --git a/.github/workflows/Docs.yml b/.github/workflows/Docs.yml index 5e35cb11f..2ce37205c 100644 --- a/.github/workflows/Docs.yml +++ b/.github/workflows/Docs.yml @@ -43,7 +43,8 @@ jobs: PYTHON: "" run: | julia --color=yes --project -e 'using Pkg; Pkg.instantiate()' - julia --color=yes --project -e 'using Conda; Conda.add("scikit-learn")' + julia --project -e 'using Conda; Conda.add("scipy=1.8.1")' + julia --color=yes --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")' julia --color=yes --project=docs/ -e 'using Pkg; Pkg.instantiate()' julia --color=yes --project=docs/ -e 'using Pkg; Pkg.precompile()' - name: Build and deploy diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml index 521982ffb..3d9bfce21 100644 --- a/.github/workflows/Tests.yml +++ b/.github/workflows/Tests.yml @@ -40,7 +40,8 @@ jobs: env: PYTHON: "" run: | - julia --project -e 'using Conda; Conda.add("scikit-learn")' + julia --project -e 'using Conda; Conda.add("scipy=1.8.1")' + julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")' - name: Run Unit Tests env: @@ -92,7 +93,8 @@ jobs: env: PYTHON: "" run: | - julia --project -e 'using Conda; Conda.add("scikit-learn")' + julia --project -e 'using Conda; Conda.add("scipy=1.8.1")' + julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")' - name: Run Unit Tests env: @@ -131,7 +133,8 @@ jobs: env: PYTHON: "" run: | - julia --project -e 'using Conda; Conda.add(\"scikit-learn\")' + julia --project -e 'using Conda; Conda.add("scipy=1.8.1")' + julia --project -e 'using Conda; Conda.add(\"scikit-learn=1.1.1\")' - name: Run Unit Tests env: diff --git a/deps/build.jl b/deps/build.jl index a420e85bc..01b3cd7fe 100644 --- a/deps/build.jl +++ b/deps/build.jl @@ -7,4 +7,5 @@ if lowercase(get(ENV, "CI", "false")) == "true" Pkg.build("PyCall") end -Conda.add("scikit-learn") +Conda.add("scipy=1.8.1") +Conda.add("scikit-learn=1.1.1") diff --git a/docs/src/installation_instructions.md b/docs/src/installation_instructions.md index 421c118c7..d758efe69 100644 --- a/docs/src/installation_instructions.md +++ b/docs/src/installation_instructions.md @@ -23,11 +23,11 @@ it is easiest to set the project to use its own ``` -The `scikit-learn` package then has to be installed if using a Julia project-specific -Conda environment: +The `scikit-learn` package (along with `scipy`) then has to be installed if using a Julia project-specific Conda environment: ``` -> PYTHON="" julia --project -e 'using Conda; Conda.add("scikit-learn")' +> PYTHON="" julia --project -e 'using Conda; Conda.add("scipy=1.8.1")' +> PYTHON="" julia --project -e 'using Conda; Conda.add("scikit-learn=1.1.1")' ``` diff --git a/examples/Emulator/GaussianProcess/Manifest.toml b/examples/Emulator/GaussianProcess/Manifest.toml index 876e3de45..b9db76084 100644 --- a/examples/Emulator/GaussianProcess/Manifest.toml +++ b/examples/Emulator/GaussianProcess/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.2" +julia_version = "1.6.7" manifest_format = "2.0" [[deps.AMD]] @@ -11,9 +11,9 @@ version = "0.4.0" [[deps.AbstractFFTs]] deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" +git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.1.0" +version = "1.2.1" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] @@ -28,15 +28,15 @@ version = "0.3.4" [[deps.Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" +git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.3" +version = "3.4.0" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] -git-tree-sha1 = "5d9e09a242d4cf222080398468244389c3428ed1" +git-tree-sha1 = "d7a7dabeaef34e5106cdf6c2ac956e9e3f97f666" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.6.7" +version = "0.6.8" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -63,9 +63,9 @@ version = "1.0.1" [[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "cf6875678085aed97f52bfc493baaebeb6d40bcb" +git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.5" +version = "0.4.6" [[deps.BangBang]] deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] @@ -106,22 +106,22 @@ uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" [[deps.CalibrateEmulateSample]] -deps = ["AbstractMCMC", "AdvancedMH", "Conda", "Distributions", "DocStringExtensions", "EnsembleKalmanProcesses", "GaussianProcesses", "LinearAlgebra", "MCMCChains", "Printf", "PyCall", "Random", "ScikitLearn", "Statistics", "StatsBase"] +deps = ["AbstractMCMC", "AdvancedMH", "Conda", "Distributions", "DocStringExtensions", "EnsembleKalmanProcesses", "GaussianProcesses", "LinearAlgebra", "MCMCChains", "Pkg", "Printf", "PyCall", "Random", "ScikitLearn", "Statistics", "StatsBase"] path = "../../.." uuid = "95e48a1f-0bec-4818-9538-3db4340308e3" version = "0.1.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "9489214b993cd42d17f44c36e359bf6a7c919abf" +git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.0" +version = "1.15.3" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53" +git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.3" +version = "0.1.4" [[deps.CodecBzip2]] deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] @@ -137,15 +137,15 @@ version = "0.7.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "7297381ccb5df764549818d9a7d57e45f1057d30" +git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.18.0" +version = "3.19.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "0f4e115f6f34bbe43c19751c90a38b2f380637b9" +git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.3" +version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] @@ -167,9 +167,9 @@ 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 = "87e84b2293559571802f97dd9c94cfd6be52c5e5" +git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.44.0" +version = "3.45.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -194,15 +194,14 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" +git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.3.0" +version = "1.4.0" [[deps.Contour]] -deps = ["StaticArrays"] -git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" +git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.5.7" +version = "0.6.2" [[deps.Convex]] deps = ["AbstractTrees", "BenchmarkTools", "LDLFactorizations", "LinearAlgebra", "MathOptInterface", "OrderedCollections", "SparseArrays", "Test"] @@ -280,9 +279,9 @@ version = "0.24.18" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" +git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.6" +version = "0.9.1" [[deps.Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -296,9 +295,9 @@ version = "2.2.3+0" [[deps.ElasticArrays]] deps = ["Adapt"] -git-tree-sha1 = "a0fcc1bb3c9ceaf07e1d0529c9806ce94be6adf9" +git-tree-sha1 = "d1933fd3e53e01e2d0ae98b8f7f65784e2d5430b" uuid = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4" -version = "1.2.9" +version = "1.2.10" [[deps.ElasticPDMats]] deps = ["LinearAlgebra", "MacroTools", "PDMats"] @@ -307,10 +306,10 @@ uuid = "2904ab23-551e-5aed-883f-487f97af5226" version = "0.2.2" [[deps.EnsembleKalmanProcesses]] -deps = ["Convex", "Distributions", "DocStringExtensions", "LinearAlgebra", "Random", "SCS", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "5e7b26419a9693f8b9223b640f0d8bb08f7432b0" +deps = ["Convex", "Distributions", "DocStringExtensions", "LinearAlgebra", "Optim", "QuadGK", "Random", "SCS", "SparseArrays", "Statistics", "StatsBase", "TOML"] +git-tree-sha1 = "345b6b7fd42517ece0d91752a63f176dcecccafa" uuid = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d" -version = "0.5.3" +version = "0.9.1" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -318,6 +317,11 @@ git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" +[[deps.Extents]] +git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.1" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -325,16 +329,16 @@ 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", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.0+0" +version = "4.4.2+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "505876577b5481e50d089c1c68899dfb6faebc62" +git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.4.6" +version = "1.5.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -380,9 +384,9 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" +git-tree-sha1 = "187198a4ed8ccd7b5d99c41b69c679269ea2b2d4" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.30" +version = "0.10.32" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -402,21 +406,21 @@ 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.GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "b316fd18f5bc025fedcb708332aecb3e13b9b453" +git-tree-sha1 = "037a1ca47e8a5989cc07d19729567bb71bfabd0c" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.64.3" +version = "0.66.0" [[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 = "1e5490a51b4e9d07e8b04836f6008f46b48aaa87" +git-tree-sha1 = "c8ab731c9127cd931c93221f65d6a1008dad7256" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.64.3+0" +version = "0.66.0+0" [[deps.GaussianProcesses]] deps = ["Distances", "Distributions", "ElasticArrays", "ElasticPDMats", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "Optim", "PDMats", "Printf", "ProgressMeter", "Random", "RecipesBase", "ScikitLearnBase", "SpecialFunctions", "StaticArrays", "Statistics", "StatsFuns"] @@ -424,11 +428,17 @@ git-tree-sha1 = "9cf8ba8037e332b1be14c71e549143e68c42a22d" uuid = "891a1506-143c-57d2-908e-e1f8e92e6de9" version = "0.12.4" +[[deps.GeoInterface]] +deps = ["Extents"] +git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" +uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" +version = "1.0.1" + [[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 = "a7a97895780dab1085a97769316aa348830dc991" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.2" +version = "0.4.3" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -454,10 +464,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "f0956f8d42a92816d2bf062f8a6a6a0ad7f9b937" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.17" +version = "1.2.1" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -491,22 +501,22 @@ 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 = "64f138f9453a018c8f3562e7bae54edc059af249" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.4" [[deps.IntervalSets]] -deps = ["Dates", "Statistics"] -git-tree-sha1 = "ad841eddfb05f6d9be0bff1fa48dcae32f134a2d" +deps = ["Dates", "Random", "Statistics"] +git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.6.2" +version = "0.7.1" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "336cc738f03e069ef2cac55a104eb823455dca75" +git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.4" +version = "0.1.7" [[deps.InvertedIndices]] git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" @@ -548,9 +558,9 @@ version = "2.1.2+0" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" +git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.3" +version = "0.6.5" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -583,9 +593,9 @@ version = "1.3.0" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "46a39b9c58749eefb5f2dc1178cb8fab5332b1ab" +git-tree-sha1 = "1a43be956d433b5d0321197150c2f94e16c0aaa0" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.15" +version = "0.15.16" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -654,9 +664,9 @@ version = "2.35.0+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "c9551dd26e31ab17b86cbd00c2ede019c08758eb" +git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.3.0+1" +version = "4.4.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -671,23 +681,23 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.1.1" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637" +git-tree-sha1 = "361c2b088575b07946508f135ac556751240091c" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.15" +version = "0.3.17" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "e9437ef53c3b29a838f4635e748bb38d29d11384" +git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.8" +version = "0.4.9" [[deps.MCMCChains]] deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -703,9 +713,9 @@ version = "2022.0.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "74d7fb54c306af241c5f9d4816b735cb4051e125" +git-tree-sha1 = "16fa7c2e14aa5b3854bc77ab5f1dbe2cdc488903" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.4.2" +version = "1.6.0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -724,10 +734,10 @@ uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" version = "0.10.9" [[deps.MbedTLS]] -deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"] -git-tree-sha1 = "1c38e51c3d08ef2278062ebceade0e46cefc96fe" +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] +git-tree-sha1 = "d9ab10da9de748859a7780338e1d6566993d1f25" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.0.3" +version = "1.1.3" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -783,9 +793,9 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "9cf6b82f7f337c01eac9995be43d11483dee5d7b" +git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.0" +version = "1.12.7" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -803,9 +813,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ab05aa4cc89736e95915b01e7279e61b1bfe33b8" +git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.14+0" +version = "1.1.17+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -815,9 +825,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "7a28efc8e34d5df89fc87343318b0a8add2c4021" +git-tree-sha1 = "7351d1daa3dad1bcf67c79d1ba34dd3f6136c9aa" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.0" +version = "1.7.1" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -850,9 +860,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "1285416549ccfcdf0c50d4997a94331e88d68413" +git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.1" +version = "2.3.2" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -872,15 +882,15 @@ version = "3.0.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "bb16469fd5224100e422f0b027d26c5a25de1200" +git-tree-sha1 = "9888e59493658e476d3073f1ce24348bdc086660" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.2.0" +version = "1.3.0" [[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"] -git-tree-sha1 = "d457f881ea56bbfa18222642de51e0abf67b9027" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "a19652399f43938413340b2068e11e55caa46b65" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.29.0" +version = "1.31.7" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -955,7 +965,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.RangeArrays]] @@ -976,9 +986,9 @@ version = "1.2.1" [[deps.RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "dc1e451e15d90347a7decc4221842a022b011714" +git-tree-sha1 = "e7eac76a958f8664f2718508435d058168c7953d" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.5.2" +version = "0.6.3" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -987,9 +997,9 @@ version = "1.2.2" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "cdbd3b1338c72ce29d9584fdbe9e9b70eeb5adca" +git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "0.1.3" +version = "0.3.0" [[deps.Requires]] deps = ["UUIDs"] @@ -1023,9 +1033,9 @@ version = "2.1.4+0" [[deps.SCS_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "6cdaccb5e6a69455f960de1ae445ba1de5db9d0d" +git-tree-sha1 = "66c07568ecec96260aaac194ee1e5ee8df62f386" uuid = "f4f2fc5b-1d94-523c-97ea-2ab488bedf4b" -version = "2.1.2+1" +version = "2.1.4+0" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1049,9 +1059,9 @@ version = "0.5.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda" +git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.0" +version = "1.1.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1072,6 +1082,11 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" +[[deps.SimpleBufferStream]] +git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" +version = "1.1.0" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1087,9 +1102,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "004051c3d87ab610e1706e8a24bd0b2b635fcdf1" +git-tree-sha1 = "5d65101b2ed17a8862c4c05639c3ddc7f3d791e1" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.8.5" +version = "1.8.7" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1104,16 +1119,21 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.5.6" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "cd56bf18ed715e8b09f06ef8c6b781e6cdc49911" +deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "8803c6dea034ab8cd988abe4a91e5589d61c7416" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.4.4" +version = "1.5.4" + +[[deps.StaticArraysCore]] +git-tree-sha1 = "5b413a57dd3cea38497d745ce088ac8592fbb5be" +uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" +version = "1.1.0" [[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"] @@ -1121,15 +1141,15 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "c82aaa13b44ea00134f8c9c89819477bd3986ecd" +git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.3.0" +version = "1.5.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.16" +version = "0.33.21" [[deps.StatsFuns]] deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -1139,9 +1159,9 @@ version = "0.9.18" [[deps.StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "9abba8f8fb8458e9adf07c8a2377a070674a24f1" +git-tree-sha1 = "ec47fb6069c57f1cee2f67541bf8f23415146de7" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.8" +version = "0.6.11" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1196,9 +1216,9 @@ uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" version = "0.4.73" [[deps.URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.0" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1248,9 +1268,9 @@ version = "0.5.5" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" +git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.12+0" +version = "2.9.14+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1400,16 +1420,18 @@ git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" +[[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"] git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" - [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" @@ -1450,6 +1472,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+0" diff --git a/examples/Lorenz/Manifest.toml b/examples/Lorenz/Manifest.toml index 4eea6b6fe..7b42045df 100644 --- a/examples/Lorenz/Manifest.toml +++ b/examples/Lorenz/Manifest.toml @@ -1,1508 +1,1529 @@ # This file is machine-generated - editing it directly is not advised -[[AMD]] +julia_version = "1.6.7" +manifest_format = "2.0" + +[[deps.AMD]] deps = ["Libdl", "LinearAlgebra", "SparseArrays", "Test"] git-tree-sha1 = "fc66ffc5cff568936649445f58a55b81eaf9592c" uuid = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e" version = "0.4.0" -[[AbstractFFTs]] +[[deps.AbstractFFTs]] deps = ["LinearAlgebra"] git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" version = "0.5.0" -[[AbstractMCMC]] +[[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "db0a7ff3fbd987055c43b4e12d2fa30aaae8749c" +git-tree-sha1 = "5dfb2514d115b449127f29eb7b3272c5528d396e" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "3.2.1" +version = "3.3.1" -[[AbstractTrees]] +[[deps.AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.3.4" -[[Adapt]] +[[deps.Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" +git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.3" +version = "3.4.0" -[[AdvancedMH]] +[[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] -git-tree-sha1 = "8ad8bfddf8bb627d689ecb91599c349cbf15e971" +git-tree-sha1 = "d7a7dabeaef34e5106cdf6c2ac956e9e3f97f666" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.6.6" +version = "0.6.8" -[[ArgCheck]] -git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a" +[[deps.ArgCheck]] +git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.1.0" +version = "2.3.0" -[[ArgTools]] +[[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -[[Arpack]] +[[deps.Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra"] git-tree-sha1 = "2ff92b71ba1747c5fdd541f8fc87736d82f40ec9" uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" version = "0.4.0" -[[Arpack_jll]] +[[deps.Arpack_jll]] deps = ["Libdl", "OpenBLAS_jll", "Pkg"] git-tree-sha1 = "e214a9b9bd1b4e1b4f15b22c0994862b66af7ff7" uuid = 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