diff --git a/.buildkite/launch_benchmarks.yml.signature b/.buildkite/launch_benchmarks.yml.signature index b1d2dae2c..220d613b1 100644 --- a/.buildkite/launch_benchmarks.yml.signature +++ b/.buildkite/launch_benchmarks.yml.signature @@ -1,2 +1,3 @@ -Salted__�c? �ު��DwL�J�/���)��|p��5 +c��\~o�.�� RR�hAZR�� -$'���� 6���!�m�^����S�j�Y����� \ No newline at end of file +Salted__�c? +�ު��DwL�J�/���)��|p��5 +c��\~o�.�� RR�hAZR�� +$'���� 6���!�m�^����S�j�Y����� \ No newline at end of file diff --git a/.buildkite/run_benchmark.yml b/.buildkite/run_benchmark.yml index d104b044d..a5fa7c416 100644 --- a/.buildkite/run_benchmark.yml +++ b/.buildkite/run_benchmark.yml @@ -19,8 +19,8 @@ steps: - JuliaCI/julia#v1: version: "1.10" - staticfloat/sandbox: - rootfs_url: "https://github.com/thazhemadam/openmodelica-rootfs-image/releases/download/v1.23.0/rootfs-openmodelica-v1.23.0.amd64.tar.gz" - rootfs_treehash: "82970243dc4f188e599a976abc20951f4aba2912" + rootfs_url: "https://github.com/thazhemadam/ScimlBenchmarks-rootfs-image/releases/download/rootfs-image/rootfs-script.amd64.tar.gz" + rootfs_treehash: "943bde824554f0afad5a939341f05e3bdb393051" uid: 1000 gid: 1000 workspaces: diff --git a/benchmarks/AstroChem/Manifest.toml b/benchmarks/AstroChem/Manifest.toml index 71c54843a..692170702 100644 --- a/benchmarks/AstroChem/Manifest.toml +++ b/benchmarks/AstroChem/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.5" +julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "8702bd396dbf00bab17774defca37a9a55f9bfee" +project_hash = "81a84463ee3fb40ec2e360f288f69699605fb501" [[deps.ADTypes]] -git-tree-sha1 = "99a6f5d0ce1c7c6afdb759daa30226f71c54f6b0" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.7.1" +version = "1.9.0" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -20,31 +20,35 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.37" +version = "0.1.38" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" AccessorsIntervalSetsExt = "IntervalSets" AccessorsStaticArraysExt = "StaticArrays" AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.0.4" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -68,15 +72,16 @@ version = "0.4.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "3640d077b6dafd64ceb8fd5c1ec76f7ca53bcf76" +git-tree-sha1 = "d60a1922358aa203019b7857a2c8c37329b8736c" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.16.0" +version = "7.17.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" @@ -90,6 +95,7 @@ version = "7.16.0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" @@ -98,9 +104,9 @@ version = "7.16.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.3" +version = "1.10.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -136,9 +142,9 @@ version = "0.1.6" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "5c0ffe1dff8cb7112de075f1b1cb32191675fcba" +git-tree-sha1 = "d434647f798823bcae510aee0bc0401927f64391" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "1.1.0" +version = "1.1.1" [deps.BlockArrays.extensions] BlockArraysBandedMatricesExt = "BandedMatrices" @@ -146,11 +152,21 @@ version = "1.1.0" [deps.BlockArrays.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" +[[deps.BracketingNonlinearSolve]] +deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "95cb19c37ea427617e9795655667712f03058d98" +uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" +version = "1.1.0" +weakdeps = ["ForwardDiff"] + + [deps.BracketingNonlinearSolve.extensions] + BracketingNonlinearSolveForwardDiffExt = "ForwardDiff" + [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -171,9 +187,14 @@ version = "3.4.3" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.2+1" + +[[deps.Cassette]] +git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" +uuid = "7057c7e9-c182-5462-911a-8362d720325c" +version = "0.3.14" [[deps.Catalyst]] deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] @@ -197,9 +218,9 @@ version = "14.4.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -219,21 +240,27 @@ version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.26.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" +git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.5" +version = "0.12.0" + + [deps.ColorTypes.extensions] + StyledStringsExt = "StyledStrings" + + [deps.ColorTypes.weakdeps] + StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "a1f44953f2382ebb937d60dafbe2deea4bd23249" +git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.10.0" +version = "0.11.0" weakdeps = ["SpecialFunctions"] [deps.ColorVectorSpace.extensions] @@ -241,9 +268,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.11" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -251,10 +278,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] -git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" +deps = ["Crayons", "PrecompileTools"] +git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.12" +version = "0.8.15" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -372,10 +399,10 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "d7d43a1cc11dc4e4e5378816ae720fccd75a77c8" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "f8eefbb7e910f59087c4bb09ce670f235758ee4a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.155.0" +version = "6.158.3" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -406,17 +433,16 @@ version = "6.155.0" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "19dbd44d18bbfdfcf5e56c99cea9b0ed23df350a" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.9.1" -weakdeps = ["OrdinaryDiffEq", "OrdinaryDiffEqCore", "Sundials"] +version = "4.1.0" [[deps.DiffEqDevTools]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] -git-tree-sha1 = "35f51dc83977ca2cc45f9a0abd55ed9efd54eff7" +git-tree-sha1 = "167a3a413b954aca9e64d785f8ea096e23e5afb8" uuid = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" -version = "2.45.0" +version = "2.45.1" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -443,10 +469,10 @@ uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" [[deps.DifferentiationInterface]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.17" +version = "0.6.22" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -456,10 +482,13 @@ version = "0.5.17" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" - DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -471,18 +500,21 @@ version = "0.5.17" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "c2acd1de2c4c357928f9fb6b60b402d914621378" +git-tree-sha1 = "453df2ce2aef7de59c69a56d31dcd2ec3384dd77" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.14" +version = "0.4.17" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -491,9 +523,9 @@ weakdeps = ["ChainRulesCore", "EnzymeCore"] [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -506,9 +538,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.111" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -550,10 +582,10 @@ uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" version = "0.6.0" [[deps.DynamicQuantities]] -deps = ["Compat", "DispatchDoctor", "PackageExtensionCompat", "TestItems", "Tricks"] -git-tree-sha1 = "317430fb3dcfb17831eb0e4bcd852358a48a4e7a" +deps = ["DispatchDoctor", "TestItems", "Tricks"] +git-tree-sha1 = "192f34efd3912f4020b225e01d896f567f5f03e8" uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" -version = "1.0.0" +version = "1.3.0" [deps.DynamicQuantities.extensions] DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" @@ -573,9 +605,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" +git-tree-sha1 = "04c777af6ef65530a96ab68f0a81a4608113aa1d" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.8" +version = "0.8.5" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -618,9 +650,9 @@ version = "0.8.5" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -645,6 +677,27 @@ git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "2.0.4" +[[deps.FastPower]] +git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" +uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" +version = "1.1.1" + + [deps.FastPower.extensions] + FastPowerEnzymeExt = "Enzyme" + FastPowerForwardDiffExt = "ForwardDiff" + FastPowerMeasurementsExt = "Measurements" + FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" + FastPowerReverseDiffExt = "ReverseDiff" + FastPowerTrackerExt = "Tracker" + + [deps.FastPower.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -666,19 +719,21 @@ uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224" version = "1.4.1" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] -git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.24.0" +version = "2.26.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -700,9 +755,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -720,6 +775,12 @@ git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.14+0" +[[deps.FunctionProperties]] +deps = ["Cassette", "DiffRules"] +git-tree-sha1 = "bf7c740307eb0ee80e05d8aafbd0c5a901578398" +uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc" +version = "0.1.2" + [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" @@ -755,15 +816,21 @@ version = "0.1.6" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" +git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.7" +version = "0.73.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.7+0" +version = "0.73.8+0" + +[[deps.GenericLinearAlgebra]] +deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] +git-tree-sha1 = "c4f9c87b74aedf20920034bd4db81d0bffc527d2" +uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" +version = "0.3.14" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -779,9 +846,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.80.5+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -796,9 +863,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.2" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -807,9 +874,9 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.10" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] @@ -825,9 +892,9 @@ version = "0.1.17" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.24" +version = "0.3.25" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -866,9 +933,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -893,9 +960,9 @@ version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -905,21 +972,21 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.0.4+0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"] -git-tree-sha1 = "bb4696471330275adfd6c78c6173f276e8c067aa" +git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.60" +version = "1.0.62" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "6e0fb267f2c869df59b6bf9f8cb0f2794f2d85e9" +git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.13.7" +version = "9.14.0" weakdeps = ["FastBroadcast"] [[deps.KLU]] @@ -930,9 +997,9 @@ version = "0.6.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.6" +version = "0.9.8" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -941,16 +1008,16 @@ uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "17.0.6+0" +version = "18.1.7+0" [[deps.LSODA]] deps = ["Compat", "DiffEqBase", "LSODA_jll", "LinearAlgebra", "Parameters", "Printf", "SciMLBase"] @@ -966,19 +1033,14 @@ version = "0.1.2+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LambertW]] -git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" -uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" -version = "0.4.6" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] @@ -1059,9 +1121,9 @@ version = "3.2.2+1" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -1071,15 +1133,15 @@ version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1089,9 +1151,9 @@ version = "2.40.1+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1099,6 +1161,16 @@ git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.40.1+0" +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" + [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" @@ -1111,17 +1183,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "6c5e4555ac2bc449a28604e184f759d18fc08420" +git-tree-sha1 = "591de175461afd8323aa24b7686062574527aa3a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.34.0" +version = "2.36.2" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -1135,7 +1207,6 @@ version = "2.34.0" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -1167,9 +1238,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1244,21 +1315,23 @@ version = "1.2.0" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "f87f07e0471323694ff5d9f52ff763e2e4ffacfe" +deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "b96b0749d6d9c8d6480641dcfcc02a265cf6d9e7" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.39.0" +version = "9.50.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" + MTKHomotopyContinuationExt = "HomotopyContinuation" MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] @@ -1272,15 +1345,15 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "5c1d1d9361e1417e5a065e1f84dc3686cbdaea21" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.6" +version = "0.5.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "d0a6b1096b584a2b88efb70a92f8cb8c881eb38a" +git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.6" +version = "1.5.2" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1305,36 +1378,78 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "bcd8812e751326ff1d4b2dd50764b93df51f143b" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 = "22f3efdd47bd18d8a26bd559fff254e6b21000fd" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.14.0" +version = "4.1.0" [deps.NonlinearSolve.extensions] - NonlinearSolveBandedMatricesExt = "BandedMatrices" NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" NonlinearSolveMINPACKExt = "MINPACK" NonlinearSolveNLSolversExt = "NLSolvers" - NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"] + NonlinearSolvePETScExt = ["PETSc", "MPI"] NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" + NonlinearSolveSundialsExt = "Sundials" [deps.NonlinearSolve.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" + +[[deps.NonlinearSolveBase]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "1589ef8aac99a21d132adf1ec5cbe6ef651760ff" +uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" +version = "1.3.1" + + [deps.NonlinearSolveBase.extensions] + NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" + NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase" + NonlinearSolveBaseForwardDiffExt = "ForwardDiff" + NonlinearSolveBaseLineSearchExt = "LineSearch" + NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseSparseArraysExt = "SparseArrays" + NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + + [deps.NonlinearSolveBase.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LineSearch = "87fe0de2-c867-4266-b59a-2f0a94fc965b" + LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + +[[deps.NonlinearSolveFirstOrder]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "dc8535cecb0f9d978019e44b7144b9e84ab85424" +uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" +version = "1.0.0" + +[[deps.NonlinearSolveQuasiNewton]] +deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] +git-tree-sha1 = "066d4940938f4bb5fd1ce146e61a373f40b89d31" +uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" +version = "1.0.0" + +[[deps.NonlinearSolveSpectralMethods]] +deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "cc97c44e396ab820401c8c404bc1fd18d4c884bd" +uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" +version = "1.0.0" [[deps.ODEInterface]] deps = ["Dates", "Libdl", "LinearAlgebra", "Markdown", "ODEInterface_jll", "Unicode"] @@ -1344,9 +1459,9 @@ version = "0.5.0" [[deps.ODEInterfaceDiffEq]] deps = ["Compat", "DataStructures", "DiffEqBase", "FunctionWrappers", "LinearAlgebra", "ODEInterface", "Reexport", "SciMLBase"] -git-tree-sha1 = "a4816454042d72e4bae37d13e592591381356a17" +git-tree-sha1 = "598df5118c036a8ac8a53c5d158921eba5fc0d32" uuid = "09606e27-ecf5-54fc-bb29-004bd9f985bf" -version = "3.13.3" +version = "3.13.4" [[deps.ODEInterface_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1387,9 +1502,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1b35263570443fdd9e76c76b7062116e2f374ab8" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1422,9 +1537,9 @@ version = "1.6.3" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "cd892f12371c287dc50d6ad3af075b088b6f2d48" +git-tree-sha1 = "aa3897f89be34bdfd86472f5345d5f1f6576bcc5" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.89.0" +version = "6.90.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1439,10 +1554,10 @@ uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" version = "1.1.2" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] -git-tree-sha1 = "35fdf60f6b5e283ea2292d3f1c57abce6175c406" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "5e8c500a80674850543394ce3c745b73ad51fea0" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.5.1" +version = "1.10.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -1456,9 +1571,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "e63ec633b1efa99e3caa2e26a01faaa88ba6cef9" +git-tree-sha1 = "8977f283a7d89c5d5c06c933467ed4af0a99f2f7" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -1473,16 +1588,16 @@ uuid = "e0540318-69ee-4070-8777-9e2de6de23de" version = "1.1.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["DiffEqBase", "FastBroadcast", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "fea595528a160ed5cade9eee217a9691b1d97714" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "048bcccc8f59c20d5b4ad268eef4d7d21c005a94" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.1.0" +version = "1.2.1" [[deps.OrdinaryDiffEqFIRK]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLOperators"] -git-tree-sha1 = "795221c662698851328cb7787965ab4a180d9468" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "GenericLinearAlgebra", "GenericSchur", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polynomials", "RecursiveArrayTools", "Reexport", "RootedTrees", "SciMLOperators", "Symbolics"] +git-tree-sha1 = "5735f4c094dff311f5064d1a351da9669e4647e3" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.1.1" +version = "1.2.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1528,9 +1643,9 @@ version = "1.2.1" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "a2a4119f3e35f7982f78e17beea7b12485d179e9" +git-tree-sha1 = "5e1b316555fa95892edc13f6a429ac784d0be4dd" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.2.1" +version = "1.2.4" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1564,9 +1679,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "96b47cdd12cb4ce8f70d701b49f855271a462bd4" +git-tree-sha1 = "56cbbdc43bd0e88083fcef3efa296501b5a435da" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -1663,15 +1778,15 @@ version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.2.0" +version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.3" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] @@ -1711,6 +1826,24 @@ git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.2" +[[deps.Polynomials]] +deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736" +uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" +version = "4.0.11" + + [deps.Polynomials.extensions] + PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsFFTWExt = "FFTW" + PolynomialsMakieCoreExt = "MakieCore" + PolynomialsMutableArithmeticsExt = "MutableArithmetics" + + [deps.Polynomials.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" + MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" + [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" @@ -1786,9 +1919,9 @@ version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.0" +version = "2.11.1" [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -1830,9 +1963,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" +git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.27.0" +version = "3.27.3" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1885,15 +2018,15 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.3+0" +version = "0.5.1+0" [[deps.RootedTrees]] deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] @@ -1927,10 +2060,10 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "952e09c65264fe2a8155dd6aad60c188a0b83f69" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "7527b9adb22904f0f51d8ab85d826f81ebb6f78d" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.53.0" +version = "2.59.2" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1951,11 +2084,17 @@ version = "2.53.0" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" + [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "e39c5f217f9aca640c8e27ab21acf557a3967db5" +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.10" +version = "0.3.12" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -1994,27 +2133,27 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "4d7a7c177bcb4c6dc465f09db91bfdb28c578919" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "f7e2042e0b68c6bb19a0a1594839792737f51d84" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.0" +version = "2.0.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" SimpleNonlinearSolveTrackerExt = "Tracker" - SimpleNonlinearSolveZygoteExt = "Zygote" [deps.SimpleNonlinearSolve.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2042,10 +2181,10 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.20.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2062,10 +2201,14 @@ version = "2.20.0" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "996dff77d814c45c3f2342fa0113e4ad31e712e8" +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "670f2c8109e87d79788baef47880b946e529f1a2" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.0" +version = "0.4.9" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2083,6 +2226,12 @@ weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" @@ -2102,9 +2251,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.7" +version = "1.9.8" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2135,9 +2284,9 @@ version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2174,9 +2323,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "82304990120934137261aa085e0d05a412fe0825" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.25.0" +version = "4.26.1" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2186,9 +2335,9 @@ version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "988e04b34a4c3b824fb656f542473df99a4f610d" +git-tree-sha1 = "20cf607cafb31f922bce84d60379203e7a126911" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.30" +version = "0.3.34" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -2198,9 +2347,9 @@ version = "0.2.2" [[deps.SymbolicUtils]] deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] -git-tree-sha1 = "9d983078d9e99421fcca44c373e4304b8421fdde" +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "3.6.0" +version = "3.7.2" [deps.SymbolicUtils.extensions] SymbolicUtilsLabelledArraysExt = "LabelledArrays" @@ -2211,10 +2360,10 @@ version = "3.6.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "2226d810512c678d2ec9c2a9b2e227c2ebc43573" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "0caef7687abf7094132fa3112bf5514c36a99226" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "6.11.0" +version = "6.18.3" [deps.Symbolics.extensions] SymbolicsForwardDiffExt = "ForwardDiff" @@ -2282,9 +2431,9 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.24" +version = "0.5.25" [[deps.Tokenize]] git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" @@ -2292,9 +2441,9 @@ uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" version = "0.5.29" [[deps.TranscodingStreams]] -git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.2" +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] @@ -2366,9 +2515,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.70" +version = "0.21.71" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -2396,9 +2545,9 @@ version = "1.31.0+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" +git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.3+0" +version = "2.13.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] @@ -2408,9 +2557,9 @@ version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.6.3+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2563,9 +2712,9 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.6+1" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] @@ -2628,9 +2777,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] diff --git a/benchmarks/AstroChem/Project.toml b/benchmarks/AstroChem/Project.toml index 38b0ff0a2..5da665d4b 100644 --- a/benchmarks/AstroChem/Project.toml +++ b/benchmarks/AstroChem/Project.toml @@ -10,5 +10,22 @@ ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + +[compat] +BenchmarkTools = "1" +Catalyst = "14" +DiffEqDevTools = "2" +LSODA = "0.7" +LinearSolve = "3" +NaNMath = "1" +ODEInterface = "0.5" +ODEInterfaceDiffEq = "3" +OrdinaryDiffEq = "6.89" +OrdinaryDiffEqCore = "1.9" +Plots = "1" +RecursiveFactorization = "0.2.23" +Sundials = "4" +Symbolics = "6" diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index f2180def2..954544630 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -10,6 +10,7 @@ using Plots using Symbolics using DiffEqDevTools using Sundials, ODEInterface, ODEInterfaceDiffEq, LSODA +using RecursiveFactorization ``` ## Without Temperature Dynamics @@ -383,8 +384,6 @@ refsol = solve(oprob, Rodas5P(), abstol=1e-14, reltol=1e-14) ```julia refsol = solve(oprob, Rodas5P(), abstol=1e-13, reltol=1e-13) -solve(oprob, RadauIIA9(), abstol=1e-9, reltol=1e-9) - # Run Benchmark abstols = 1.0 ./ 10.0 .^ (9:10) @@ -393,17 +392,15 @@ reltols = 1.0 ./ 10.0 .^ (9:10) setups = [ Dict(:alg=>FBDF()), Dict(:alg=>QNDF()), - #Dict(:alg=>Rodas4P()), Dict(:alg=>CVODE_BDF()), #Dict(:alg=>ddebdf()), - #Dict(:alg=>Rodas4()), Dict(:alg=>Rodas5P()), Dict(:alg=>KenCarp4()), Dict(:alg=>KenCarp47()), - Dict(:alg=>RadauIIA9()), + #Dict(:alg=>RadauIIA9()), #Dict(:alg=>rodas()), #Dict(:alg=>radau()), - #Dict(:alg=>lsoda()), + Dict(:alg=>lsoda()), #Dict(:alg=>ImplicitEulerExtrapolation(min_order = 5, init_order = 3,threading = OrdinaryDiffEqCore.PolyesterThreads())), #Dict(:alg=>ImplicitEulerExtrapolation(min_order = 5, init_order = 3,threading = false)), #Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 5, threading = OrdinaryDiffEqCore.PolyesterThreads())), diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index 8b2226157..78d7a4e8a 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -1,6 +1,6 @@ --- title: Nelson Work-Precision Diagrams -author: Stella Offner and Chris Rackauckas +author: Nina De La Torre (Advised by Stella Offner) and Chris Rackauckas --- ```julia @@ -8,147 +8,180 @@ using OrdinaryDiffEq using DiffEqDevTools, Plots using Sundials, LSODA using ODEInterface, ODEInterfaceDiffEq +using RecursiveFactorization ``` -```julia -T = 10 -Av = 2 # This is what depotic uses for visual extinction -Go = 1.7 # I think despotic uses 1.7 -n_H = 611 -shield = 1 - -function Nelson_ODE(du,u,p,t) - # 1: H2 - #= du[1] = -1.2e-17 * u[1] + - n_H * (1.9e-6 * u[2] * u[3]) / (T^0.54) - - n_H * 4e-16 * u[1] * u[12] - - n_H * 7e-15 * u[1] * u[5] + - n_H * 1.7e-9 * u[10] * u[2] + - n_H * 2e-9 * u[2] * u[6] + - n_H * 2e-9 * u[2] * u[14] + - n_H * 8e-10 * u[2] * u[8] =# - du[1] = 0 - - # 2: H3+ - du[2] = 1.2e-17 * u[1] + - n_H * (-1.9e-6 * u[3] * u[2]) / (T^0.54) - - n_H * 1.7e-9 * u[10] * u[2] - - n_H * 2e-9 * u[2] * u[6] - - n_H * 2e-9 * u[2] * u[14] - - n_H * 8e-10 * u[2] * u[8] - - # 3: e - du[3] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - - n_H * (3.3e-5 * u[11] * u[3]) / T + - 1.2e-17 * u[1] - - n_H * (1.9e-6 * u[3] * u[2]) / (T^0.54) + - 6.8e-18 * u[4] - - n_H * (9e-11 * u[3] * u[5]) / (T^0.64) + - 3e-10 * Go * exp(-3 * Av) * u[6] + - n_H * 2e-9 * u[2] * u[13] ## CHECK I added this extra term from a CR ionization reaction - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction - - - # 4: He - du[4] = n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - - 6.8e-18 * u[4] + - n_H * 7e-15 * u[1] * u[5] + - n_H * 1.6e-9 * u[10] * u[5] - #du[4] = 0 - - # 5: He+ 6.8e-18 or 1.1 - du[5] = 6.8e-18 * u[4] - - n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - - n_H * 7e-15 * u[1] * u[5] - - n_H * 1.6e-9 * u[10] * u[5] - #u[5] = 0 - - # 6: C - du[6] = n_H * (1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * 2e-9 * u[2] * u[6] - - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] + - 1e-9 * Go * exp(-1.5 * Av) * u[7] - - 3e-10 * Go * exp(-3 * Av) * u[6] + - 1e-10 * Go * exp(-3 * Av) * u[10] * shield - - # 7: CHx - du[7] = n_H * (-2e-10) * u[7] * u[8] + - n_H * 4e-16 * u[1] * u[12] + - n_H * 2e-9 * u[2] * u[6] - - 1e-9 * Go * u[7] * exp(-1.5 * Av) - - # 8: O - du[8] = n_H * (-2e-10) * u[7] * u[8] + - n_H * 1.6e-9 * u[10] * u[5] - - n_H * 8e-10 * u[2] * u[8] + - 5e-10 * Go * exp(-1.7 * Av) * u[9] + - 1e-10 * Go * exp(-3 * Av) * u[10] * shield - - # 9: OHx - du[9] = n_H * (-1e-9) * u[9] * u[12] + - n_H * 8e-10 * u[2] * u[8] - - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - - 5e-10 * Go * exp(-1.7 * Av) * u[9] - - # 10: CO - du[10] = n_H * (3.3e-5 * u[11] * u[3]) / T + - n_H * 2e-10 * u[7] * u[8] - - n_H * 1.7e-9 * u[10] * u[2] - - n_H * 1.6e-9 * u[10] * u[5] + - n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - - 1e-10 * Go * exp(-3 * Av) * u[10] + - 1.5e-10 * Go * exp(-2.5 * Av) * u[11] * shield - - # 11: HCO+ - du[11] = n_H * (-3.3e-5 * u[11] * u[3]) / T + - n_H * 1e-9 * u[9] * u[12] + - n_H * 1.7e-9 * u[10] * u[2] - - 1.5e-10 * Go * exp(-2.5 * Av) * u[11] - - # 12: C+ - du[12] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - - n_H * 4e-16 * u[1] * u[12] - - n_H * 1e-9 * u[9] * u[12] + - n_H * 1.6e-9 * u[10] * u[5] + - 3e-10 * Go * exp(-3 * Av) * u[6] - - # 13: M+ - du[13] = n_H * (-3.8e-10 * u[13] * u[3]) / (T^0.65) + - n_H * 2e-9 * u[2] * u[14] - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction - - # 14: M - du[14] = n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - - n_H * 2e-9 * u[2] * u[14] - - 2.0e-10 * Go * exp(-1.9 * Av) * u[14] # this term was added as part of the skipped photoreaction +The ODE function defined below models the reduced carbon-oxygen +chemistry network of Nelson & Langer (1999, ApJ, 524, 923). -end +This Julia ODE function was written by Nina De La Torre advised by Dr. Stella Offner. +The solution was compared with results derived by DESPOTIC, (Mark Krumholz, 2013) +a code to Derive the Energetics and Spectra of Optically Thick Insterstellar Clouds. +DESPOTIC has pre-defined networks, one of them coming from the Nelson & Langer paper, +so the initial conditions and parameters were meant to mimic those from DESPOTIC. +Note: The composite hydrocarbon radical CHx represents both CH and CH2, +the composite oxygen species OHx represents OH, H2O, O2 and their ions, +and M represents the low ionization potential metals Mg, Fe, Ca, and Na. -u0 = [0.5 ; # 1: H2 yep? - 9.059e-9 ; # 2: H3+ yep - 2.0e-4 ; # 3: e yep - 0.1 ; # 4: He SEE lines 535 NL99 - 7.866e-7 ; # 5: He+ yep? should be 2.622e-5 - 0.0 ; # 6: C yep - 0.0 ; # 7: CHx yep - 0.0004 ; # 8: O yep - 0.0 ; # 9: OHx yep - 0.0 ; # 10: CO yep - 0.0 ; # 11: HCO+ yep - 0.0002 ; # 12: C+ yep - 2.0e-7 ; # 13: M+ yep - 2.0e-7 ] # 14: M yep + Parameter definitions: + T = 10 --> Temperature (Kelvin) + Av = 2 --> V-Band Extinction + G₀ = 1.7 --> Go; "a factor that determines the flux of FUV radiation relative to the standard interstellar value (G₀ = 1) as reported by Habing (1968)." + n_H = 611 --> Hydrogen Number Density + shield = 1 --> "CO self-shielding factor of van Dishoeck & Black (1988), taken from Bergin et al. (1995)" +```julia +function Nelson!(du,u,p,t) + T, Av, Go, n_H, shield = p + + # 1: H2 + du[1] = -1.2e-17 * u[1] + + n_H * (1.9e-6 * u[2] * u[3]) / (T^0.54) - + n_H * 4e-16 * u[1] * u[12] - + n_H * 7e-15 * u[1] * u[5] + + n_H * 1.7e-9 * u[10] * u[2] + + n_H * 2e-9 * u[2] * u[6] + + n_H * 2e-9 * u[2] * u[14] + + n_H * 8e-10 * u[2] * u[8] + + # 2: H3+ + du[2] = 1.2e-17 * u[1] + + n_H * (-1.9e-6 * u[3] * u[2]) / (T^0.54) - + n_H * 1.7e-9 * u[10] * u[2] - + n_H * 2e-9 * u[2] * u[6] - + n_H * 2e-9 * u[2] * u[14] - + n_H * 8e-10 * u[2] * u[8] + + # 3: e + du[3] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - + n_H * (3.3e-5 * u[11] * u[3]) / T + + 1.2e-17 * u[1] - + n_H * (1.9e-6 * u[3] * u[2]) / (T^0.54) + + 6.8e-18 * u[4] - + n_H * (9e-11 * u[3] * u[5]) / (T^0.64) + + 3e-10 * Go * exp(-3 * Av) * u[6] + + n_H * 2e-9 * u[2] * u[13] + + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] + + # 4: He + du[4] = n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - + 6.8e-18 * u[4] + + n_H * 7e-15 * u[1] * u[5] + + n_H * 1.6e-9 * u[10] * u[5] + + # 5: He+ + du[5] = 6.8e-18 * u[4] - + n_H * (9e-11 * u[3] * u[5]) / (T^0.64) - + n_H * 7e-15 * u[1] * u[5] - + n_H * 1.6e-9 * u[10] * u[5] + + # 6: C + du[6] = n_H * (1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * 2e-9 * u[2] * u[6] - + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] + + 1e-9 * Go * exp(-1.5 * Av) * u[7] - + 3e-10 * Go * exp(-3 * Av) * u[6] + + 1e-10 * Go * exp(-3 * Av) * u[10] * shield + + # 7: CHx + du[7] = n_H * (-2e-10) * u[7] * u[8] + + n_H * 4e-16 * u[1] * u[12] + + n_H * 2e-9 * u[2] * u[6] - + 1e-9 * Go * u[7] * exp(-1.5 * Av) + + # 8: O + du[8] = n_H * (-2e-10) * u[7] * u[8] + + n_H * 1.6e-9 * u[10] * u[5] - + n_H * 8e-10 * u[2] * u[8] + + 5e-10 * Go * exp(-1.7 * Av) * u[9] + + 1e-10 * Go * exp(-3 * Av) * u[10] * shield + + # 9: OHx + du[9] = n_H * (-1e-9) * u[9] * u[12] + + n_H * 8e-10 * u[2] * u[8] - + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - + 5e-10 * Go * exp(-1.7 * Av) * u[9] + + # 10: CO + du[10] = n_H * (3.3e-5 * u[11] * u[3]) / T + + n_H * 2e-10 * u[7] * u[8] - + n_H * 1.7e-9 * u[10] * u[2] - + n_H * 1.6e-9 * u[10] * u[5] + + n_H * 5.8e-12 * (T^0.5) * u[9] * u[6] - + 1e-10 * Go * exp(-3 * Av) * u[10] + + 1.5e-10 * Go * exp(-2.5 * Av) * u[11] * shield + + # 11: HCO+ + du[11] = n_H * (-3.3e-5 * u[11] * u[3]) / T + + n_H * 1e-9 * u[9] * u[12] + + n_H * 1.7e-9 * u[10] * u[2] - + 1.5e-10 * Go * exp(-2.5 * Av) * u[11] + + # 12: C+ + du[12] = n_H * (-1.4e-10 * u[3] * u[12]) / (T^0.61) - + n_H * 4e-16 * u[1] * u[12] - + n_H * 1e-9 * u[9] * u[12] + + n_H * 1.6e-9 * u[10] * u[5] + + 3e-10 * Go * exp(-3 * Av) * u[6] + + # 13: M+ + du[13] = n_H * (-3.8e-10 * u[13] * u[3]) / (T^0.65) + + n_H * 2e-9 * u[2] * u[14] + + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] + + # 14: M + du[14] = n_H * (3.8e-10 * u[13] * u[3]) / (T^0.65) - + n_H * 2e-9 * u[2] * u[14] - + 2.0e-10 * Go * exp(-1.9 * Av) * u[14] -tspan = (0.0, 30 * 3.16e10) # ~30 thousand yrs +end -prob = ODEProblem(Nelson_ODE, u0, tspan) +# Set the Timespan, Parameters, and Initial Conditions +seconds_per_year = 3600 * 24 * 365 +tspan = (0.0, 30000 * seconds_per_year) # ~30 thousand yrs + +params = (10, # T + 2, # Av + 1.7, # Go + 611, # n_H + 1) # shield + +u0 = [0.5, # 1: H2 + 9.059e-9, # 2: H3+ + 2.0e-4, # 3: e + 0.1, # 4: He + 7.866e-7, # 5: He+ + 0.0, # 6: C + 0.0, # 7: CHx + 0.0004, # 8: O + 0.0, # 9: OHx + 0.0, # 10: CO + 0.0, # 11: HCO+ + 0.0002, # 12: C+ + 2.0e-7, # 13: M+ + 2.0e-7] # 14: M + +prob = ODEProblem(Nelson!, u0, tspan, params) refsol = solve(prob, Vern9(), abstol=1e-14, reltol=1e-14) +sol1 = solve(prob, Rodas5P()) +sol2 = solve(prob, FBDF()) +sol3 = solve(prob, lsoda()) +sol4 = solve(prob, lsoda(), saveat = 1e10) +``` +## Validation Plot + +```julia using Plots -plot(sol; yscale=:log10, idxs = (0,5)) +colors = palette(:acton, 5) +p1 = plot(sol1, vars = (0,11), lc=colors[1], legend = false, titlefontsize = 12, lw = 3, title = "Rodas5") +p2 = plot(sol2, vars = (0,11), lc=colors[2], legend = false, titlefontsize = 12, lw = 3, title = "FBDF") +p3 = plot(sol3, vars = (0,11), lc=colors[3], legend = false, titlefontsize = 12, lw = 3, title = "lsoda") +p4 = plot(sol4, vars = (0,11), lc=colors[4], legend = false, titlefontsize = 12, lw = 3, title = "lsoda with saveat") + +combined_plot = plot(p1, p2, p3, p4, layout=(4, 1), dpi = 600, pallete=:acton) ``` ## Run Benchmark @@ -157,8 +190,6 @@ plot(sol; yscale=:log10, idxs = (0,5)) abstols = 1.0 ./ 10.0 .^ (8:10) reltols = 1.0 ./ 10.0 .^ (8:10) -sol = solve(prob, CVODE_BDF(), abstol=1e-14, reltol=1e-14) - setups = [ Dict(:alg=>FBDF()), Dict(:alg=>QNDF()), @@ -182,4 +213,4 @@ setups = [ wp = WorkPrecisionSet(prob,abstols,reltols,setups;appxsol=refsol,save_everystep=false, print_names = true) plot(wp) -``` \ No newline at end of file +``` diff --git a/benchmarks/Bio/BCR.jmd b/benchmarks/Bio/BCR.jmd index 9b2780c8a..9aab1beaa 100644 --- a/benchmarks/Bio/BCR.jmd +++ b/benchmarks/Bio/BCR.jmd @@ -17,7 +17,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() datadir = joinpath(dirname(pathof(ReactionNetworkImporters)),"../data/bcr") @@ -27,10 +27,10 @@ tf = 100000.0 # generate ModelingToolkit ODEs @timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(datadir, "bcr.net")) show(to) -rn = prnbng.rn +rn = complete(prnbng.rn) obs = [eq.lhs for eq in observed(rn)] -@timeit to "Create ODESys" osys = convert(ODESystem, rn) +@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn)) show(to) tspan = (0.,tf) @@ -56,12 +56,12 @@ As compiling the ODE derivative functions has in the past taken longer than running a simulation, we first force compilation by evaluating these functions one time. ```julia -u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn)) +u = oprob.u0 du = copy(u) -p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn)) +p = oprob.p @timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.) -@timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.) -sparsejacprob.f(du,u,p,0.) +@timeit to "ODE rhs spjac Eval1" sparsejacprob.f(du,u,p,0.) +show(to) ``` We also time the ODE rhs function with BenchmarkTools as it is more accurate @@ -99,18 +99,6 @@ test_sol = TestSolution(sol); default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5) ``` -#### Declares a plotting helper function - -```julia -function plot_settings(wp) - times = vcat(map(wp -> wp.times, wp.wps)...) - errors = vcat(map(wp -> wp.errors, wp.wps)...) - xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors)))) - ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times)))) - return xlimit,ylimit -end -``` - #### Declare pre-conditioners ```julia using IncompleteLU, LinearAlgebra @@ -189,8 +177,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups; saveat=tf/10000.,appxsol=[test_sol,test_sol,test_sol],maxiters=Int(1e6),numruns=1) names = ["lsoda" "CVODE_BDF" "CVODE_BDF (LapackDense)" "CVODE_BDF (GMRES)" "CVODE_BDF (GMRES, iLU)" "CVODE_BDF (KLU, sparse jac)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Work-Precision Diagrams (various Julia solvers) @@ -213,8 +200,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1) names = ["TRBDF2" "QNDF" "FBDF" "KenCarp4"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using GMRES linear solver). @@ -235,8 +221,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1) names = ["TRBDF2 (GMRES)" "QNDF (GMRES)" "FBDF (GMRES)" "KenCarp4 (GMRES)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using GMRES linear solver, with pre-conditioner). @@ -257,8 +242,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1) names = ["TRBDF2 (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "KenCarp4 (GMRES, iLU)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using sparse jacobian) @@ -282,8 +266,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1) names = ["TRBDF2 (KLU, sparse jac)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Summary of results @@ -312,9 +295,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups; names = ["CVODE_BDF (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"] colors = [:green :deepskyblue1 :dodgerblue2 :royalblue2 :slateblue3 :lightskyblue] markershapes = [:octagon :hexagon :rtriangle :pentagon :ltriangle :star5] -xlimit,ylimit = plot_settings(wp) -xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95]; -plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) +plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) ``` ```julia, echo = false diff --git a/benchmarks/Bio/Bidkhori2012.jmd b/benchmarks/Bio/Bidkhori2012.jmd index c9c3eda19..8f9a460a3 100644 --- a/benchmarks/Bio/Bidkhori2012.jmd +++ b/benchmarks/Bio/Bidkhori2012.jmd @@ -13,7 +13,8 @@ and the model was parsed to Julia are finally to ODEs using [ModelingToolkit](ht ```julia using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, - LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2 + LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2, + RecursiveFactorization gr() @@ -720,14 +721,6 @@ const to = TimerOutput() show(to) ``` - -```julia -@show numspecies(sys) # Number of ODEs -@show numreactions(sys) # Apprx. number of terms in the ODE -@show length(parameters(sys)) # Number of Parameters -``` - - ## Picture of the solution ```julia diff --git a/benchmarks/Bio/Manifest.toml b/benchmarks/Bio/Manifest.toml index 1f2515550..d783ceff8 100644 --- a/benchmarks/Bio/Manifest.toml +++ b/benchmarks/Bio/Manifest.toml @@ -1,56 +1,92 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.1" +julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "5ae0a598f3f9685f74ae28e389bc1c288dc36069" +project_hash = "9369fd634569cdb6d6ee43acaa4c552a88a1af3f" [[deps.ADTypes]] -git-tree-sha1 = "a4c8e0f8c09d4aa708289c1a5fc23e2d1970017a" +git-tree-sha1 = "30bb95a372787af850addf28ac937f1be7b79173" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.1" +version = "1.10.0" +weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] -[[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "41b45260ad00b666558c16f7cd9db0e8af408ea1" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.31.1" + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" + ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.AbstractTrees]] -git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.4" +version = "0.4.5" + +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.38" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" + AccessorsUnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = 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"4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.11" +version = "7.17.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -58,15 +94,24 @@ version = "7.4.11" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -[[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" -uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.29" +[[deps.ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra"] +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "1.10.4" +weakdeps = ["SparseArrays"] + + [deps.ArrayLayouts.extensions] + ArrayLayoutsSparseArraysExt = "SparseArrays" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -76,102 +121,147 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", 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= "0f109fa4-8a5d-4b75-95aa-f515264e7665" + CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" + GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" [[deps.ChainRulesCore]] -deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" +deps = ["Compat", "LinearAlgebra"] +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.16.0" +version = "1.25.0" +weakdeps = ["SparseArrays"] + + [deps.ChainRulesCore.extensions] + ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.2" +version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "d9a8f86737b665e15a9641ecbac64deef9ce6724" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.23.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.12.0" + + [deps.ColorTypes.extensions] + StyledStringsExt = "StyledStrings" + + [deps.ColorTypes.weakdeps] + StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "a1f44953f2382ebb937d60dafbe2deea4bd23249" +git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.10.0" +version = "0.11.0" weakdeps = ["SpecialFunctions"] [deps.ColorVectorSpace.extensions] @@ -179,9 +269,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -189,10 +279,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] -git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" +deps = ["Crayons", "PrecompileTools"] +git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.12" +version = "0.8.15" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -200,16 +290,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] -deps = ["UUIDs"] -git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.9.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -218,40 +313,54 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.1.1+0" [[deps.CompositeTypes]] -git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" +git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.3" +version = "0.1.4" + +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcreteStructs]] +git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" +uuid = "2569d6c7-a4a2-43d3-a901-331e8e4be471" +version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "5372dbbf8f0bdb8c700db5367132925c0771ef7e" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.2.1" +version = "2.4.2" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "8c86e48c0db1564a1d49548d3515ced5d604c408" +git-tree-sha1 = "b19db3927f0db4151cb86d073689f2428e524576" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.9.1" +version = "1.10.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" [[deps.CpuId]] deps = ["Markdown"] @@ -265,15 +374,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.15.0" +version = "1.16.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.15" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -284,6 +393,12 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DelimitedFiles]] deps = ["Mmap"] git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" @@ -291,51 +406,56 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "df8638dbfa03d1b336c410e23a9dfbf89cb53937" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "b7dbeaa770bad0980ddddf606de814cff2acb3bc" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.128.2" +version = "6.160.0" [deps.DiffEqBase.extensions] + DiffEqBaseCUDAExt = "CUDA" + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "9c7d3a84264d935f6981504388b202a770113faa" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "5458b607a6639b0e9c587d5afffc5d41a8f9cfb7" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.29.1" -weakdeps = ["OrdinaryDiffEq", "Sundials"] +version = "4.2.0" [[deps.DiffEqDevTools]] -deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics"] -git-tree-sha1 = "9fe41ca501ce654f1876735206816dca7fcd2c88" +deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] +git-tree-sha1 = "167a3a413b954aca9e64d785f8ea096e23e5afb8" uuid = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" -version = "2.35.0" +version = "2.45.1" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "6b02e9c9d0d4cacf2b20f36c33710b8b415c5194" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.18.0" +version = "5.23.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -355,14 +475,68 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" +[[deps.DifferentiationInterface]] +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" +uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +version = "0.6.22" + + [deps.DifferentiationInterface.extensions] + DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" + DifferentiationInterfaceDiffractorExt = "Diffractor" + DifferentiationInterfaceEnzymeExt = "Enzyme" + DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" + DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" + DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" + DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" + DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" + DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.DispatchDoctor]] +deps = ["MacroTools", "Preferences"] +git-tree-sha1 = "453df2ce2aef7de59c69a56d31dcd2ec3384dd77" +uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" +version = "0.4.17" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.DispatchDoctor.extensions] + DispatchDoctorChainRulesCoreExt = "ChainRulesCore" + DispatchDoctorEnzymeCoreExt = "EnzymeCore" + [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.9" -weakdeps = ["SparseArrays"] +version = "0.10.12" +weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] + DistancesChainRulesCoreExt = "ChainRulesCore" DistancesSparseArraysExt = "SparseArrays" [[deps.Distributed]] @@ -370,18 +544,20 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "938fe2981db009f531b6332e31c58e9584a2f9bd" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.100" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" DistributionsDensityInterfaceExt = "DensityInterface" + DistributionsTestExt = "Test" [deps.Distributions.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -390,73 +566,112 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = 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"Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "d73afa4a2bb9de56077242d98cf763074ab9a970" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.9" +version = "0.73.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "1596bab77f4f073a14c62424283e7ebff3072eca" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.9+1" +version = "0.73.8+0" + +[[deps.GenericLinearAlgebra]] +deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] +git-tree-sha1 = "c4f9c87b74aedf20920034bd4db81d0bffc527d2" +uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" +version = "0.3.14" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.3" +version = "0.5.4" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -598,21 +859,21 @@ version = "0.21.0+0" [[deps.Git]] deps = ["Git_jll"] -git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d" +git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e" uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" -version = "1.3.0" +version = "1.3.1" [[deps.Git_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "d8be4aab0f4e043cc40984e9097417307cce4c03" +git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.36.1+2" +version = "2.46.2+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.80.5+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -627,62 +888,50 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.8.0" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.Groebner]] -deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random", "SIMD", "SnoopPrecompile"] -git-tree-sha1 = "17c81e8dd04cc8f70bccf8c50aa2d39f5ff2a3ec" -uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.4.2" - -[[deps.GroupsCore]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "9e1a5e9f3b81ad6a5c613d181664a0efc6fe6dd7" -uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" -version = "0.4.0" - [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "cb56ccdd481c0dd7f975ad2b3b62d9eda088f7e2" +git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.9.14" +version = "1.10.10" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.3.1+0" [[deps.Highlights]] deps = ["DocStringExtensions", "InteractiveUtils", "REPL"] -git-tree-sha1 = "0341077e8a6b9fc1c2ea5edc1e93a956d2aec0c7" +git-tree-sha1 = "9e13b8d8b1367d9692a90ea4711b4278e4755c32" uuid = "eafb193a-b7ab-5a9e-9068-77385905fa72" -version = "0.5.2" +version = "0.5.3" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.25" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" +git-tree-sha1 = "1b1299f7d6617291f3d260e9f5b0250afdaac8c0" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.2" +version = "1.26.0" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -696,29 +945,46 @@ uuid = "40713840-3770-5561-ab4c-a76e7d0d7895" version = "0.2.1" [[deps.Inflate]] -git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.3" +version = "0.1.5" [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" version = "0.1.2" +[[deps.IntelOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" +uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" +version = "2024.2.1+0" + [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.IntervalSets]] -deps = ["Dates", "Random"] -git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6" +git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.7" -weakdeps = ["Statistics"] +version = "0.7.10" +weakdeps = ["Random", "RecipesBase", "Statistics"] [deps.IntervalSets.extensions] + IntervalSetsRandomExt = "Random" + IntervalSetsRecipesBaseExt = "RecipesBase" IntervalSetsStatisticsExt = "Statistics" +[[deps.InverseFunctions]] +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.17" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" @@ -730,22 +996,22 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "aa6ffef1fd85657f4999030c52eaeec22a279738" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"] +git-tree-sha1 = "ce5737c0d4490b0e0040b5dc77fbb6a351ddf188" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.33" +version = "0.5.8" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.5" +version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -755,57 +1021,58 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.91+0" +version = "3.0.4+0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "680fb31c8b8e2cf482f48e55d8fa01ccc4469e04" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"] +git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.35" +version = "1.0.62" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "add0bfe9091a0148a358dc8c52d5ac60806da76c" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.7.2" +version = "9.14.0" +weakdeps = ["FastBroadcast"] [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "764164ed65c30738750965d55652db9c94c59bfe" +git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.0" +version = 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"Libdl", "Pkg"] -git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.4+0" +version = "18.1.7+0" [[deps.LSODA]] deps = ["Compat", "DiffEqBase", "LSODA_jll", "LinearAlgebra", "Parameters", "Printf", "SciMLBase"] -git-tree-sha1 = "96a6ff0be7ebda67e35af1e6937a68141dd59e70" +git-tree-sha1 = "49c00ced68a8033b30fb1009b8dea7871aa9e928" uuid = "7f56f5a3-f504-529b-bc02-0b1fe5e64312" -version = "0.7.4" +version = "0.7.5" [[deps.LSODA_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -814,71 +1081,83 @@ uuid = "aae0fff6-70f8-51e1-979a-8150c7cc74bd" version = "0.1.2+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = 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"InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.1" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.14" +version = "0.1.17" -[[deps.Lazy]] -deps = ["MacroTools"] -git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" -uuid = 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-version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -890,10 +1169,10 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -902,74 +1181,96 @@ uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" version = "1.6.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = 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[[deps.LinearSolve]] -deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "69cbd612e6e67ba2f8121bc8725bc9d04d803599" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6b79df6e803fb62b79a364b86c790e7e21bd38ce" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.5.1" +version = "2.37.0" [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" + LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" + LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" - LinearSolveMKLExt = "MKL_jll" LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" + KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" - MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" +git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.26" +version = "0.3.28" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -986,21 +1287,27 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.1" +version = "1.1.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "c88a4afe1703d731b1c4fdf4e3c7e77e3b176ea2" +deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.165" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] SpecialFunctionsExt = "SpecialFunctions" +[[deps.MKL_jll]] +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" +uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" +version = "2024.2.0+0" + [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" @@ -1008,9 +1315,9 @@ version = "0.4.17" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.11" +version = "0.5.13" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1021,16 +1328,26 @@ version = "0.1.8" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MaybeInplace]] +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" +uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" + [[deps.MbedTLS]] -deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] +git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.7" +version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1039,28 +1356,36 @@ version = "0.3.2" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "a27885c84dbd221772bf52c151a0b83d45f74beb" +deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "b96b0749d6d9c8d6480641dcfcc02a265cf6d9e7" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.65.0" +version = "9.50.0" [deps.ModelingToolkit.extensions] + MTKBifurcationKitExt = "BifurcationKit" + MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" + MTKHomotopyContinuationExt = "HomotopyContinuation" + MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] + BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MuladdMacro]] git-tree-sha1 = 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"FiniteDiff", "ForwardDiff"] @@ -1108,10 +1433,78 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "ee53089df81a6bdf3c06c17cf674e90931b10a73" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 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"PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] +git-tree-sha1 = "7dbe4ac56f930df5e9abd003cedb54e25cbbea86" +uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" +version = "1.2.0" + +[[deps.OrdinaryDiffEqStabilizedIRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "StaticArrays"] +git-tree-sha1 = "348fd6def9a88518715425025eadd58517017325" +uuid = "e3e12d00-db14-5390-b879-ac3dd2ef6296" +version = "1.1.0" + +[[deps.OrdinaryDiffEqStabilizedRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "StaticArrays"] +git-tree-sha1 = "1b0d894c880e25f7d0b022d7257638cf8ce5b311" +uuid = "358294b1-0aab-51c3-aafe-ad5ab194a2ad" +version = "1.1.0" + +[[deps.OrdinaryDiffEqSymplecticRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "4e8b8c8b81df3df17e2eb4603115db3b30a88235" +uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" +version = "1.1.0" + +[[deps.OrdinaryDiffEqTsit5]] +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "96552f7d4619fabab4038a29ed37dd55e9eb513a" +uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" +version = "1.1.0" + +[[deps.OrdinaryDiffEqVerner]] +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "81d7841e73e385b9925d5c8e4427f2adcdda55db" +uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" +version = "1.1.1" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+0" +version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" +git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.17" +version = "0.11.31" [[deps.PackageExtensionCompat]] -git-tree-sha1 = "f9b1e033c2b1205cf30fd119f4e50881316c1923" +git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" -version = "1.0.1" +version = "1.0.2" weakdeps = ["Requires", "TOML"] +[[deps.Pango_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +uuid = "36c8627f-9965-5494-a995-c6b170f724f3" +version = "1.54.1+0" + [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" 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-version = "1.9.0" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.1.0" +version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.5" +version = "1.4.3" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.39.0" +version = "1.40.9" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1278,16 +1870,34 @@ uuid = 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+version = "0.2.2" + +[[deps.Polynomials]] +deps = ["LinearAlgebra", "OrderedCollections", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "adc25dbd4d13f148f3256b6d4743fe7e63a71c4a" +uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" +version = "4.0.12" + + [deps.Polynomials.extensions] + PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsFFTWExt = "FFTW" + PolynomialsMakieCoreExt = "MakieCore" + PolynomialsMutableArithmeticsExt = "MutableArithmetics" + + [deps.Polynomials.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" + MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1296,10 +1906,10 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] -git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" +deps = ["Adapt", "ArrayInterface", "ForwardDiff"] +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.12" +version = "0.4.24" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -1309,21 +1919,21 @@ version = "0.4.12" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.2.0" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.0" +version = "1.4.3" [[deps.Primes]] deps = ["IntegerMathUtils"] -git-tree-sha1 = "4c9f306e5d6603ae203c2000dd460d81a5251489" +git-tree-sha1 = 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"OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.4.2+3" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", 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"0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "3.27.3" [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" + RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] + FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "2b6d4a40339aa02655b1743f4cd7c03109f520c1" +git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.20" +version = "0.2.23" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1418,9 +2061,9 @@ version = "1.2.2" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" +git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "1.0.0" +version = "1.0.1" [[deps.Requires]] deps = ["UUIDs"] @@ -1436,21 +2079,21 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.5.1+0" [[deps.RootedTrees]] -deps = ["Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] -git-tree-sha1 = "dc172b0f145b0921a25b9cd48a56559f72170f10" +deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] +git-tree-sha1 = "c0c464d3063e46e4128d21fd677ca575ace44fdc" uuid = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c" -version = "2.19.2" +version = "2.23.1" weakdeps = ["Plots"] [deps.RootedTrees.extensions] @@ -1458,20 +2101,14 @@ weakdeps = ["Plots"] [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "0e270732477b9e551d884e6b07e23bb2ec947790" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.5" - [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1479,20 +2116,33 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "4b8586aece42bee682399c4c4aee95446aa5cd19" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.39" +version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "a1e295a85fd6fae9a7b2072dd4577001210f512d" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "cacc7bc54bab8749b1fc1032c4911fe80cffb959" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.95.0" +version = "2.61.0" [deps.SciMLBase.extensions] - ZygoteExt = "Zygote" + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLBenchmarks]] @@ -1501,23 +2151,34 @@ git-tree-sha1 = "f4076dd5a103010d48bb6c4e50c5526f6622fa96" uuid = "31c91b34-3c75-11e9-0341-95557aab0344" version = "0.1.3" -[[deps.SciMLNLSolve]] -deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "9dfc8e9e3d58c0c74f1a821c762b5349da13eccf" -uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.8" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "65c2e6ced6f62ea796af251eb292a0e131a3613b" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.6" +version = "0.3.12" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" + +[[deps.SciMLStructures]] +deps = ["ArrayInterface"] +git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.5.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.0" +version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1539,21 +2200,27 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "20aa9831d654bab67ed561e78917047143ecb9bf" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "f7e2042e0b68c6bb19a0a1594839792737f51d84" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.19" +version = "2.0.0" [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveNNlibExt = "NNlib" + SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" + SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" + SimpleNonlinearSolveTrackerExt = "Tracker" [deps.SimpleNonlinearSolve.weakdeps] - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1566,12 +2233,6 @@ git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" version = "1.1.0" -[[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" @@ -1583,30 +2244,45 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" +git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.1" +version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "e080a6eea9dce295161cd31af829ebe252524c25" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.5.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" + SparseDiffToolsPolyesterExt = "Polyester" + SparseDiffToolsPolyesterForwardDiffExt = "PolyesterForwardDiff" SparseDiffToolsSymbolicsExt = "Symbolics" SparseDiffToolsZygoteExt = "Zygote" [deps.SparseDiffTools.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SparseMatrixColorings]] +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9" +uuid = "0a514795-09f3-496d-8182-132a7b665d35" +version = "0.4.10" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1615,25 +2291,31 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "f295e0a1da4ca425659c57441bcb59abb035a4bc" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.8" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.1" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1641,56 +2323,54 @@ weakdeps = ["OffsetArrays", "StaticArrays"] StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" -weakdeps = ["Statistics"] +version = "1.9.8" +weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4" +git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.0" +version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.0" +version = "1.3.2" +weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.StrideArraysCore]] -deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "f02eb61eb5c97b48c153861c72fbbfdddc607e06" +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.17" +version = "0.5.7" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1698,49 +2378,86 @@ git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" version = "0.3.7" +[[deps.StructArrays]] +deps = ["ConstructionBase", "DataAPI", "Tables"] +git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" +version = "0.6.18" +weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] + + [deps.StructArrays.extensions] + StructArraysAdaptExt = "Adapt" + StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysSparseArraysExt = "SparseArrays" + StructArraysStaticArraysExt = "StaticArrays" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] -deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "4931f9013c53128337ce8df54a2d38c79fe58d4c" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.19.3" +version = "4.26.1" [[deps.Sundials_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] -git-tree-sha1 = "04777432d74ec5bc91ca047c9e0e0fd7f81acdb6" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] +git-tree-sha1 = "ba4d38faeb62de7ef47155ed321dce40a549c305" uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" -version = "5.2.1+0" +version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] -deps = ["DocStringExtensions"] -git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "6c6761e08bf5a270905cdd065be633abfa1b155b" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" +version = "0.3.35" + +[[deps.SymbolicLimits]] +deps = ["SymbolicUtils"] +git-tree-sha1 = "fabf4650afe966a2ba646cabd924c3fd43577fc3" +uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3" version = "0.2.2" [[deps.SymbolicUtils]] -deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "TimerOutputs", "Unityper"] -git-tree-sha1 = "9704a1d0ecbbf5d65700418dcf1bb4c680c790bb" +deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "1.2.0" +version = "3.7.2" + + [deps.SymbolicUtils.extensions] + SymbolicUtilsLabelledArraysExt = "LabelledArrays" + SymbolicUtilsReverseDiffExt = "ReverseDiff" + + [deps.SymbolicUtils.weakdeps] + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ArrayInterface", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "Markdown", "NaNMath", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "TreeViews"] -git-tree-sha1 = "f1d43a0dbb553890195e49fb599ea51d0e97a5ef" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "d5c0ea92aa7b14b0ffca575e07af48ecb9e83f7b" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.5.1" +version = "6.21.0" [deps.Symbolics.extensions] + SymbolicsForwardDiffExt = "ForwardDiff" + SymbolicsGroebnerExt = "Groebner" + SymbolicsLuxExt = "Lux" + SymbolicsNemoExt = "Nemo" + SymbolicsPreallocationToolsExt = ["PreallocationTools", "ForwardDiff"] SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" + Lux = "b2108857-7c20-44ae-9111-449ecde12c47" + Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a" + PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" [[deps.TOML]] @@ -1755,10 +2472,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1771,10 +2488,20 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" +[[deps.TermInterface]] +git-tree-sha1 = "d673e0aca9e46a2f63720201f55cc7b3e7169b16" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "2.0.0" + [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TestItems]] +git-tree-sha1 = "42fd9023fef18b9b78c8343a4e2f3813ffbcefcb" +uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe" +version = "1.0.0" + [[deps.ThreadingUtilities]] deps = ["ManualMemory"] git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" @@ -1783,37 +2510,30 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.25" [[deps.Tokenize]] -git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5" +git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.25" +version = "0.5.29" [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.13" - -[[deps.TreeViews]] -deps = ["Test"] -git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" -uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" -version = "0.3.0" +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "31eedbc0b6d07c08a700e26d31298ac27ef330eb" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.19" +version = "0.2.1" [[deps.Tricks]] -git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.7" +version = "0.1.9" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -1822,9 +2542,9 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.URIs]] -git-tree-sha1 = "b7a5e99f24892b6824a954199a45e9ffcc1c70f0" +git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.5.0" +version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1846,29 +2566,26 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.17.0" +version = "1.21.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.Unityper]] deps = ["ConstructionBase"] -git-tree-sha1 = "21c8fc7cd598ef49f11bc9e94871f5d7740e34b9" +git-tree-sha1 = "25008b734a03736c41e2a7dc314ecb95bd6bbdb0" uuid = "a7c27f48-0311-42f6-a7f8-2c11e75eb415" -version = "0.1.5" +version = "0.1.6" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1877,9 +2594,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "b182207d4af54ac64cbc71797765068fdeff475d" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.64" +version = "0.21.71" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -1892,17 +2609,23 @@ git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" version = "0.2.0" +[[deps.Vulkan_Loader_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] +git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" +uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c" +version = "1.3.243+0" + [[deps.Wayland_jll]] -deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" +deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "7558e29847e99bc3f04d6569e82d0f5c54460703" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.21.0+0" +version = "1.21.0+1" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" +git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.25.0+0" +version = "1.31.0+0" [[deps.Weave]] deps = ["Base64", "Dates", "Highlights", "JSON", "Markdown", "Mustache", "Pkg", "Printf", "REPL", "RelocatableFolders", "Requires", "Serialization", "YAML"] @@ -1911,22 +2634,34 @@ uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9" version = "0.10.12" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.13.5+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cf2c7de82431ca6f39250d2fc4aacd0daa1675c0" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.4+0" +version = "5.6.3+0" + +[[deps.Xorg_libICE_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" +uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" +version = "1.1.1+0" + +[[deps.Xorg_libSM_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" +uuid = "c834827a-8449-5923-a945-d239c165b7dd" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -1953,10 +2688,10 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -1983,10 +2718,10 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1996,9 +2731,9 @@ version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+0" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -2006,6 +2741,12 @@ git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" version = "1.1.2+0" +[[deps.Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.4+0" + [[deps.Xorg_xcb_util_image_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" @@ -2056,95 +2797,131 @@ version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" +git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.9" +version = "0.4.12" [[deps.ZMQ]] -deps = ["FileWatching", "Sockets", "ZeroMQ_jll"] -git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77" +deps = ["FileWatching", "PrecompileTools", "Sockets", "ZeroMQ_jll"] +git-tree-sha1 = "18cfd00df3cbbebf8ea4ec7ea6bbceb3af716bd0" uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1" -version = "1.2.2" +version = "1.3.0" [[deps.ZeroMQ_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "libsodium_jll"] -git-tree-sha1 = "fe5c65a526f066fb3000da137d5785d9649a8a47" +deps = ["Artifacts", "JLLWrappers", "Libdl", "libsodium_jll"] +git-tree-sha1 = "f02ce8f0fda1ed40f4d0d59a2ad05e35e8ac9b0e" uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568" -version = "4.3.4+0" +version = "4.3.5+1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+1" -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.3" +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" [[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.29.0+0" +version = "0.53.0+0" -[[deps.libaom_jll]] +[[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" +version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" +version = "5.11.0+0" -[[deps.libfdk_aac_jll]] +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" + +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" [[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" +version = "1.6.44+0" [[deps.libsodium_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e" +git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+0" +version = "1.0.20+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2160,6 +2937,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+0" +version = "1.4.1+1" diff --git a/benchmarks/Bio/Project.toml b/benchmarks/Bio/Project.toml index d96099c0f..4a502e021 100644 --- a/benchmarks/Bio/Project.toml +++ b/benchmarks/Bio/Project.toml @@ -12,6 +12,7 @@ ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" ReactionNetworkImporters = "b4db0fb7-de2a-5028-82bf-5021f5cfa881" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -19,19 +20,20 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" [compat] BenchmarkTools = "1.2" -Catalyst = "13" +Catalyst = "14" DiffEqBase = "6.100" DiffEqDevTools = "2.35" IncompleteLU = "0.2" JLD2 = "0.4, 0.5" LSODA = "0.7" -LinearSolve = "1, 2" -ModelingToolkit = "8" +LinearSolve = "3" +ModelingToolkit = "9" ODEInterface = "0.5" ODEInterfaceDiffEq = "3.8" OrdinaryDiffEq = "6" Plots = "1.10" -ReactionNetworkImporters = "0.14" +ReactionNetworkImporters = "0.15" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4.4" TimerOutputs = "0.5" diff --git a/benchmarks/Bio/egfr_net.jmd b/benchmarks/Bio/egfr_net.jmd index 9e73a4fdf..b9d604448 100644 --- a/benchmarks/Bio/egfr_net.jmd +++ b/benchmarks/Bio/egfr_net.jmd @@ -18,7 +18,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() @@ -26,12 +26,12 @@ tf = 10.0 # generate ModelingToolkit ODEs @timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Models/egfr_net.net")) -show(to) -rn = prnbng.rn +show(to) +rn = complete(prnbng.rn) obs = [eq.lhs for eq in observed(rn)] -@timeit to "Create ODESys" osys = convert(ODESystem, rn) -show(to) +@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn)) +show(to) tspan = (0.,tf) @timeit to "ODEProb No Jac" oprob = ODEProblem{true, SciMLBase.FullSpecialize}(osys, Float64[], tspan, Float64[]) @@ -55,9 +55,9 @@ As compiling the ODE derivative functions has in the past taken longer than running a simulation, we first force compilation by evaluating these functions one time. ```julia -u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn)) +u = oprob.u0 du = copy(u) -p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn)) +p = oprob.p @timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.) @timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.) sparsejacprob.f(du,u,p,0.) @@ -93,18 +93,6 @@ test_sol = TestSolution(sol); default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5) ``` -#### Declares a plotting helper function - -```julia -function plot_settings(wp) - times = vcat(map(wp -> wp.times, wp.wps)...) - errors = vcat(map(wp -> wp.errors, wp.wps)...) - xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors)))) - ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times)))) - return xlimit,ylimit -end -``` - #### Sets tolerances ```julia @@ -124,7 +112,7 @@ setups = [ Dict(:alg=>lsoda()), Dict(:alg=>CVODE_BDF()), Dict(:alg=>CVODE_BDF(linear_solver=:LapackDense)), - Dict(:alg=>CVODE_Adams()), + Dict(:alg=>CVODE_Adams()), Dict(:alg=>TRBDF2()), Dict(:alg=>QNDF()), Dict(:alg=>FBDF()), @@ -144,8 +132,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=100) names = ["lsoda" "CVODE_BDF" "CVODE_BDF (Lapack Dense)" "CVODE_Adams" "TRBDF2" "QNDF" "FBDF" "KenCarp4" "Rosenbrock23" "Rodas4" "Rodas5P"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using GMRES linear solver) @@ -174,8 +161,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=100) names = ["lsoda" "CVODE_BDF (GMRES)" "TRBDF2 (GMRES)" "QNDF (GMRES)" "FBDF (GMRES)" "KenCarp4 (GMRES)" "Rosenbrock23 (GMRES)" "Rodas4 (GMRES)" "Rodas5P (GMRES)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using sparse jacobian) @@ -203,8 +189,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=100) names = ["CVODE_BDF (KLU, sparse jac)" "TRBDF2 (KLU, sparse jac)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)" "Rosenbrock23 (KLU, sparse jac)" "Rodas4 (KLU, sparse jac)" "Rodas5P (KLU, sparse jac)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Explicit Work-Precision Diagram @@ -216,14 +201,14 @@ Benchmarks for explicit solvers. We designate the solvers we wish to use, this also includes lsoda and CVODE. ```julia setups = [ - Dict(:alg=>lsoda()), - Dict(:alg=>CVODE_Adams()), - Dict(:alg=>Tsit5()), - Dict(:alg=>BS5()), - Dict(:alg=>VCABM()), - Dict(:alg=>Vern6()), - Dict(:alg=>Vern7()), - Dict(:alg=>Vern8()), + Dict(:alg=>lsoda()), + Dict(:alg=>CVODE_Adams()), + Dict(:alg=>Tsit5()), + Dict(:alg=>BS5()), + Dict(:alg=>VCABM()), + Dict(:alg=>Vern6()), + Dict(:alg=>Vern7()), + Dict(:alg=>Vern8()), Dict(:alg=>Vern9()), Dict(:alg=>ROCK4()) ]; @@ -236,8 +221,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["lsoda" "CVODE_Adams" "Tsit5" "BS5" "VCABM" "Vern6" "Vern7" "Vern8" "Vern9" "ROCK4"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Additional explicit solvers @@ -247,8 +231,7 @@ setups = [Dict(:alg=>ROCK2())]; wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["ROCK2"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Summary of results @@ -262,8 +245,8 @@ setups = [ Dict(:alg=>CVODE_BDF(linear_solver=:GMRES), :prob_choice => 1), Dict(:alg=>QNDF(linsolve=KrylovJL_GMRES()), :prob_choice => 2), Dict(:alg=>QNDF(linsolve=KLUFactorization()), :prob_choice => 2), - Dict(:alg=>BS5(), :prob_choice => 1), - Dict(:alg=>Vern6(), :prob_choice => 1), + Dict(:alg=>BS5(), :prob_choice => 1), + Dict(:alg=>Vern6(), :prob_choice => 1), Dict(:alg=>ROCK4(), :prob_choice => 1) ]; ``` @@ -278,9 +261,7 @@ wp = WorkPrecisionSet([oprob,sparsejacprob],abstols,reltols,setups;error_estimat names = ["lsoda" "CVODE_BDF (GMRES)" "QNDF (GMRES)" "QNDF (KLU)" "BS5" "Vern6" "ROCK4"] colors = [:seagreen1 :darkgreen :deepskyblue1 :deepskyblue4 :thistle2 :lightslateblue :purple4] markershapes = [:star4 :rect :hexagon :octagon :star8 :rtriangle :square] -xlimit,ylimit = plot_settings(wp) -xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95]; -plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) +plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) ``` diff --git a/benchmarks/Bio/fceri_gamma2.jmd b/benchmarks/Bio/fceri_gamma2.jmd index df6ae6d37..1e9bc1fd6 100644 --- a/benchmarks/Bio/fceri_gamma2.jmd +++ b/benchmarks/Bio/fceri_gamma2.jmd @@ -17,7 +17,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() @@ -26,10 +26,10 @@ tf = 150.0 # generate ModelingToolkit ODEs @timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Models/fceri_gamma2.net")) show(to) -rn = prnbng.rn +rn = complete(prnbng.rn) obs = [eq.lhs for eq in observed(rn)] -@timeit to "Create ODESys" osys = convert(ODESystem, rn) +@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn)) show(to) tspan = (0.,tf) @@ -51,9 +51,9 @@ As compiling the ODE derivative functions has in the past taken longer than running a simulation, we first force compilation by evaluating these functions one time. ```julia -u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn)) +u = oprob.u0 du = copy(u) -p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn)) +p = oprob.p @timeit to "ODE rhs Eval1" sparsejacprob.f(du,u,p,0.) sparsejacprob.f(du,u,p,0.) ``` @@ -89,18 +89,6 @@ test_sol = TestSolution(sol); default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5) ``` -#### Declares a plotting helper function - -```julia -function plot_settings(wp) - times = vcat(map(wp -> wp.times, wp.wps)...) - errors = vcat(map(wp -> wp.errors, wp.wps)...) - xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors)))) - ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times)))) - return xlimit,ylimit -end -``` - #### Declare pre-conditioners ```julia using IncompleteLU, LinearAlgebra @@ -169,8 +157,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups; saveat=tf/10000.,appxsol=[test_sol,test_sol,test_sol],maxiters=Int(1e9),numruns=10) names = ["lsoda" "CVODE_BDF" "CVODE_BDF (LapackDense)" "CVODE_BDF (GMRES)" "CVODE_BDF (GMRES, iLU)" "CVODE_BDF (KLU, sparse jac)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Work-Precision Diagrams (various Julia solvers) @@ -193,8 +180,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=10) names = ["TRBDF2" "QNDF" "FBDF" "KenCarp4"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using GMRES linear solver). @@ -215,8 +201,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=10) names = ["TRBDF2 (GMRES)" "QNDF (GMRES)" "FBDF (GMRES)" "KenCarp4 (GMRES)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using GMRES linear solver, with pre-conditioner). @@ -237,8 +222,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=10) names = ["TRBDF2 (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "KenCarp4 (GMRES, iLU)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Declare solvers (using sparse jacobian) @@ -262,8 +246,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=10) names = ["TRBDF2 (KLU, sparse jac)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Explicit Work-Precision Diagram @@ -293,8 +276,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=10) names = ["CVODE_Adams" "Tsit5" "BS5" "Vern6" "Vern7" "Vern8" "Vern9"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Summary of results @@ -322,9 +304,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups; names = ["CVODE_BDF (GMRES)" "CVODE_BDF (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "Tsit5"] colors = [:darkgreen :green :deepskyblue1 :dodgerblue2 :orchid2] markershapes = [:rect :octagon :hexagon :rtriangle :ltriangle] -xlimit,ylimit = plot_settings(wp) -xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95]; -plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2,1e-1],yticks=[1e-1,1e0,1e1,1e2],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) +plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2,1e-1],yticks=[1e-1,1e0,1e1,1e2],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) ``` ```julia diff --git a/benchmarks/Bio/multisite2.jmd b/benchmarks/Bio/multisite2.jmd index a1a94a989..0dd7c3599 100644 --- a/benchmarks/Bio/multisite2.jmd +++ b/benchmarks/Bio/multisite2.jmd @@ -16,7 +16,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() @@ -24,12 +24,12 @@ tf = 2.0 # generate ModelingToolkit ODEs @timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Models/multisite2.net")) -show(to) -rn = prnbng.rn +show(to) +rn = complete(prnbng.rn) obs = [eq.lhs for eq in observed(rn)] -@timeit to "Create ODESys" osys = convert(ODESystem, rn) -show(to) +@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn)) +show(to) tspan = (0.,tf) @timeit to "ODEProb No Jac" oprob = ODEProblem{true, SciMLBase.FullSpecialize}(osys, Float64[], tspan, Float64[]) @@ -53,9 +53,9 @@ As compiling the ODE derivative functions has in the past taken longer than running a simulation, we first force compilation by evaluating these functions one time. ```julia -u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn)) +u = oprob.u0 du = copy(u) -p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn)) +p = oprob.p @timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.) @timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.) sparsejacprob.f(du,u,p,0.) @@ -92,18 +92,6 @@ test_sol = TestSolution(sol); default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5) ``` -#### Declares a plotting helper function - -```julia -function plot_settings(wp) - times = vcat(map(wp -> wp.times, wp.wps)...) - errors = vcat(map(wp -> wp.errors, wp.wps)...) - xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors)))) - ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times)))) - return xlimit,ylimit -end -``` - #### Sets tolerances ```julia @@ -134,8 +122,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["lsoda" "CVODE_BDF" "CVODE_BDF (LapackDense)" "CVODE_BDF (GMRES)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Implicit Work-Precision Diagram @@ -166,8 +153,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=200) names = ["TRBDF2" "QNDF" "FBDF" "KenCarp4" "Rosenbrock23" "Rodas4" "Rodas5P"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` Implicit methods doing poorly suggests it's non-stiff. @@ -181,14 +167,14 @@ Benchmarks for explicit solvers. We designate the solvers we wish to use, this also includes lsoda and CVODE. ```julia setups = [ - Dict(:alg=>lsoda()), - Dict(:alg=>CVODE_Adams()), - Dict(:alg=>Tsit5()), - Dict(:alg=>BS5()), - Dict(:alg=>VCABM()), - Dict(:alg=>Vern6()), - Dict(:alg=>Vern7()), - Dict(:alg=>Vern8()), + Dict(:alg=>lsoda()), + Dict(:alg=>CVODE_Adams()), + Dict(:alg=>Tsit5()), + Dict(:alg=>BS5()), + Dict(:alg=>VCABM()), + Dict(:alg=>Vern6()), + Dict(:alg=>Vern7()), + Dict(:alg=>Vern8()), Dict(:alg=>Vern9()), Dict(:alg=>ROCK4()) ]; @@ -201,8 +187,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["lsoda" "CVODE_Adams" "Tsit5" "BS5" "VCABM" "Vern6" "Vern7" "Vern8" "Vern9" "ROCK4"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Additional explicit solvers @@ -212,8 +197,7 @@ setups = [Dict(:alg=>ROCK2())]; wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["ROCK2"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Summary of results @@ -228,10 +212,10 @@ setups = [ Dict(:alg=>QNDF()), Dict(:alg=>FBDF()), Dict(:alg=>Rodas5P()), - Dict(:alg=>BS5()), - Dict(:alg=>VCABM()), + Dict(:alg=>BS5()), + Dict(:alg=>VCABM()), Dict(:alg=>Vern6()), - Dict(:alg=>ROCK4()) + Dict(:alg=>ROCK4()) ]; ``` @@ -245,9 +229,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, names = ["lsoda" "CVODE_BDF (GMRES)" "QNDF" "FBDF" "Rodas5P" "BS5" "VCABM" "Vern6" "ROCK4"] colors = [:seagreen1 :darkgreen :deepskyblue1 :dodgerblue2 :blue :thistle2 :lightsteelblue2 :lightslateblue :purple4] markershapes = [:star4 :rect :hexagon :rtriangle :heptagon :star8 :heptagon :rtriangle :square] -xlimit,ylimit = plot_settings(wp) -xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95]; -plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-10,1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3],yticks=[1e-3,1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) +plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-10,1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3],yticks=[1e-3,1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) ``` diff --git a/benchmarks/Bio/multistate.jmd b/benchmarks/Bio/multistate.jmd index cff93a1d2..3d2a05c64 100644 --- a/benchmarks/Bio/multistate.jmd +++ b/benchmarks/Bio/multistate.jmd @@ -15,7 +15,8 @@ Catalyst network model to ODEs. ```julia using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, - LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools + LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, + RecursiveFactorization gr() const to = TimerOutput() @@ -23,12 +24,12 @@ tf = 20.0 # generate ModelingToolkit ODEs @timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Models/multistate.net")) -show(to) -rn = prnbng.rn +show(to) +rn = complete(prnbng.rn) obs = [eq.lhs for eq in observed(rn)] -@timeit to "Create ODESys" osys = convert(ODESystem, rn) -show(to) +@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn)) +show(to) tspan = (0.,tf) @timeit to "ODEProb No Jac" oprob = ODEProblem{true, SciMLBase.FullSpecialize}(osys, Float64[], tspan, Float64[]) @@ -52,9 +53,9 @@ As compiling the ODE derivative functions has in the past taken longer than running a simulation, we first force compilation by evaluating these functions one time. ```julia -u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn)) +u = oprob.u0 du = copy(u) -p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn)) +p = oprob.p @timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.) @timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.) sparsejacprob.f(du,u,p,0.) @@ -91,18 +92,6 @@ test_sol = TestSolution(sol); default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5) ``` -#### Declares a plotting helper function - -```julia -function plot_settings(wp) - times = vcat(map(wp -> wp.times, wp.wps)...) - errors = vcat(map(wp -> wp.errors, wp.wps)...) - xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors)))) - ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times)))) - return xlimit,ylimit -end -``` - #### Sets tolerances ```julia @@ -133,8 +122,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["lsoda" "CVODE_BDF" "CVODE_BDF (LapackDense)" "CVODE_BDF (GMRES)"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Implicit Work-Precision Diagram @@ -165,8 +153,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e12),dtmin=1e-18,numruns=200) names = ["TRBDF2" "QNDF" "FBDF" "KenCarp4" "Rosenbrock23" "Rodas4" "Rodas5P"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` Implicit methods doing poorly suggests it's non-stiff. @@ -180,13 +167,13 @@ Benchmarks for explicit solvers. We designate the solvers we wish to use, this also includes lsoda and CVODE. ```julia setups = [ - Dict(:alg=>lsoda()), - Dict(:alg=>Tsit5()), - Dict(:alg=>BS5()), - Dict(:alg=>VCABM()), - Dict(:alg=>Vern6()), - Dict(:alg=>Vern7()), - Dict(:alg=>Vern8()), + Dict(:alg=>lsoda()), + Dict(:alg=>Tsit5()), + Dict(:alg=>BS5()), + Dict(:alg=>VCABM()), + Dict(:alg=>Vern6()), + Dict(:alg=>Vern7()), + Dict(:alg=>Vern8()), Dict(:alg=>Vern9()), Dict(:alg=>ROCK4()) ]; @@ -199,8 +186,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["lsoda" "Tsit5" "BS5" "VCABM" "Vern6" "Vern7" "Vern8" "Vern9" "ROCK4"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` #### Additional explicit solvers @@ -210,8 +196,7 @@ setups = [Dict(:alg=>CVODE_Adams()), Dict(:alg=>ROCK2())]; wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e9),numruns=200) names = ["CVODE_Adams" "ROCK2"] -xlimit,ylimit = plot_settings(wp) -plot(wp;label=names,xlimit=xlimit,ylimit=ylimit) +plot(wp;label=names) ``` ## Summary of results @@ -226,9 +211,9 @@ setups = [ Dict(:alg=>QNDF()), Dict(:alg=>KenCarp4()), Dict(:alg=>Rodas5P()), - Dict(:alg=>Tsit5()), - Dict(:alg=>BS5()), - Dict(:alg=>VCABM()), + Dict(:alg=>Tsit5()), + Dict(:alg=>BS5()), + Dict(:alg=>VCABM()), Dict(:alg=>Vern7()) ]; ``` @@ -243,9 +228,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2, names = ["lsoda" "CVODE_BDF" "QNDF" "KenCarp4" "Rodas5P" "Tsit5" "BS5" "VCABM" "Vern7"] colors = [:seagreen1 :chartreuse1 :deepskyblue1 :lightskyblue :blue :orchid2 :thistle2 :lightsteelblue2 :mediumpurple1] markershapes = [:star4 :circle :hexagon :star5 :heptagon :ltriangle :star8 :heptagon :star6] -xlimit,ylimit = plot_settings(wp) -xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95]; -plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-12,1e-11,1e-10,1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-3,1e-2],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) +plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-12,1e-11,1e-10,1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-3,1e-2],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000)) ``` ```julia, echo = false diff --git a/benchmarks/ComplicatedPDE/Filament.jmd b/benchmarks/ComplicatedPDE/Filament.jmd index 08883b727..7c85a6cd5 100644 --- a/benchmarks/ComplicatedPDE/Filament.jmd +++ b/benchmarks/ComplicatedPDE/Filament.jmd @@ -15,7 +15,7 @@ The model is thus defined as follows: ```julia using OrdinaryDiffEq, ODEInterfaceDiffEq, Sundials, DiffEqDevTools, LSODA, LinearSolve -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots gr() ``` diff --git a/benchmarks/ComplicatedPDE/Project.toml b/benchmarks/ComplicatedPDE/Project.toml index 51f93964e..62ee3335b 100644 --- a/benchmarks/ComplicatedPDE/Project.toml +++ b/benchmarks/ComplicatedPDE/Project.toml @@ -8,6 +8,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -17,12 +18,13 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" DiffEqDevTools = "2" GaussianRandomFields = "2" LSODA = "0.7" -LinearSolve = "2" +LinearSolve = "3" ModelingToolkit = "8" -NonlinearSolve = "1, 2" +NonlinearSolve = "1, 2, 4" ODEInterfaceDiffEq = "3" OrdinaryDiffEq = "6" Plots = "1" +RecursiveFactorization = "0.2.23" StableRNGs = "1" Sundials = "4" Symbolics = "5, 6" diff --git a/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd b/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd index c2490db5f..dcc536039 100644 --- a/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd +++ b/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd @@ -8,7 +8,7 @@ using OrdinaryDiffEq, Symbolics, ModelingToolkit, Sundials, LinearSolve, SparseA using NonlinearSolve using GaussianRandomFields using StableRNGs -using DiffEqDevTools +using DiffEqDevTools, RecursiveFactorization using Plots; gr() diff --git a/benchmarks/DynamicalODE/Henon-Heiles_energy_conservation_benchmark.jmd b/benchmarks/DynamicalODE/Henon-Heiles_energy_conservation_benchmark.jmd index c39664b80..56268b595 100644 --- a/benchmarks/DynamicalODE/Henon-Heiles_energy_conservation_benchmark.jmd +++ b/benchmarks/DynamicalODE/Henon-Heiles_energy_conservation_benchmark.jmd @@ -52,7 +52,7 @@ end const oop_q0 = @SVector [0.1, 0.] const oop_p0 = @SVector [0., 0.5] -function hamilton(du,u,p,t) +function hamilton(du, u, p, t) dq, q = @views u[3:4], du[3:4] dp, p = @views u[1:2], du[1:2] @@ -64,11 +64,11 @@ function hamilton(du,u,p,t) end function g(resid, u, p) - resid[1] = H([u[1],u[2]], [u[3],u[4]], nothing) - E + resid[1] = H([u[1], u[2]], [u[3], u[4]], nothing) - E resid[2:4] .= 0 end -const cb = ManifoldProjection(g, nlopts=Dict(:ftol=>1e-13)) +const cb = ManifoldProjection(g, nlopts=Dict(:ftol => 1e-13)) const E = H(iip_p0, iip_q0, nothing) ``` @@ -76,8 +76,8 @@ const E = H(iip_p0, iip_q0, nothing) For the comparison we will use the following function ```julia -energy_err(sol) = map(i->H([sol[1,i], sol[2,i]], [sol[3,i], sol[4,i]], nothing)-E, 1:length(sol.u)) -abs_energy_err(sol) = [abs.(H([sol[1,j], sol[2,j]], [sol[3,j], sol[4,j]], nothing) - E) for j=1:length(sol.u)] +energy_err(sol) = map(i -> H([sol[1, i], sol[2, i]], [sol[3, i], sol[4, i]], nothing) - E, 1:length(sol.u)) +abs_energy_err(sol) = [abs.(H([sol[1, j], sol[2, j]], [sol[3, j], sol[4, j]], nothing) - E) for j=1:length(sol.u)] function compare(mode=:inplace, all=true, plt=nothing; tmax=1e2) if mode == :inplace @@ -100,23 +100,21 @@ function compare(mode=:inplace, all=true, plt=nothing; tmax=1e2) GC.gc() (mode == :inplace && all) && @time sol6 = solve(prob_linear, TaylorMethod(50), abstol=1e-20) - (mode == :inplace && all) && println("Vern9 + ManifoldProjection max energy error:\t"* - "$(maximum(abs_energy_err(sol1)))\tin\t$(length(sol1.u))\tsteps.") + (mode == :inplace && all) && println("Vern9 + ManifoldProjection max energy error:\t" * "$(maximum(abs_energy_err(sol1)))\tin\t$(length(sol1.u))\tsteps.") println("KahanLi8 max energy error:\t\t\t$(maximum(abs_energy_err(sol2)))\tin\t$(length(sol2.u))\tsteps.") println("SofSpa10 max energy error:\t\t\t$(maximum(abs_energy_err(sol3)))\tin\t$(length(sol3.u))\tsteps.") println("Vern9 max energy error:\t\t\t\t$(maximum(abs_energy_err(sol4)))\tin\t$(length(sol4.u))\tsteps.") println("DPRKN12 max energy error:\t\t\t$(maximum(abs_energy_err(sol5)))\tin\t$(length(sol5.u))\tsteps.") - (mode == :inplace && all) && println("TaylorMethod max energy error:\t\t\t$(maximum(abs_energy_err(sol6)))"* - "\tin\t$(length(sol6.u))\tsteps.") + (mode == :inplace && all) && println("TaylorMethod max energy error:\t\t\t$(maximum(abs_energy_err(sol6)))\tin\t$(length(sol6.u))\tsteps.") if plt === nothing plt = plot(xlabel="t", ylabel="Energy error") end (mode == :inplace && all) && plot!(sol1.t, energy_err(sol1), label="Vern9 + ManifoldProjection") - plot!(sol2.t, energy_err(sol2), label="KahanLi8", ls=mode==:inplace ? :solid : :dash) - plot!(sol3.t, energy_err(sol3), label="SofSpa10", ls=mode==:inplace ? :solid : :dash) - plot!(sol4.t, energy_err(sol4), label="Vern9", ls=mode==:inplace ? :solid : :dash) - plot!(sol5.t, energy_err(sol5), label="DPRKN12", ls=mode==:inplace ? :solid : :dash) + plot!(sol2.t, energy_err(sol2), label="KahanLi8", ls=mode == :inplace ? :solid : :dash) + plot!(sol3.t, energy_err(sol3), label="SofSpa10", ls=mode == :inplace ? :solid : :dash) + plot!(sol4.t, energy_err(sol4), label="Vern9", ls=mode == :inplace ? :solid : :dash) + plot!(sol5.t, energy_err(sol5), label="DPRKN12", ls=mode == :inplace ? :solid : :dash) (mode == :inplace && all) && plot!(sol6.t, energy_err(sol6), label="TaylorMethod") return plt @@ -205,4 +203,4 @@ The benchmarks were performed on a machine with ```julia, echo = false using SciMLBenchmarks SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) -``` +``` \ No newline at end of file diff --git a/benchmarks/DynamicalODE/single_pendulums.jmd b/benchmarks/DynamicalODE/single_pendulums.jmd index 318c5d9eb..fe6302af9 100644 --- a/benchmarks/DynamicalODE/single_pendulums.jmd +++ b/benchmarks/DynamicalODE/single_pendulums.jmd @@ -48,107 +48,116 @@ sol2tqp(sol) = (sol.t, sol2q(sol), sol2p(sol)) # sn(u, k) = Jacobi.sn(u, k^2) # the Jacobian sn function -# Use PyPlot. +# Use Plot. # -using PyPlot +using Plots +# Define the color list colorlist = [ "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf", ] cc(k) = colorlist[mod1(k, length(colorlist))] -# plot the sulution of a Hamiltonian problem -# +# Function to plot the solution of a Hamiltonian problem function plotsol(sol::ODESolution) local t, q, p t, q, p = sol2tqp(sol) local d = size(q)[2] + p1 = plot(title="Solution", xlabel="t", grid=:on) for j in 1:d j_str = d > 1 ? "[$j]" : "" - plot(t, q[:,j], color=cc(2j-1), label="q$(j_str)", lw=1) - plot(t, p[:,j], color=cc(2j), label="p$(j_str)", lw=1, ls="--") + plot!(p1, t, q[:, j], color=cc(2j-1), label="q$(j_str)", linewidth=1) + plot!(p1, t, p[:, j], color=cc(2j), label="p$(j_str)", linewidth=1, linestyle=:dash) end - grid(ls=":") - xlabel("t") - legend() + return p1 end -# plot the solution of a Hamiltonian problem on the 2D phase space -# +# Function to plot the solution on the 2D phase space function plotsol2(sol::ODESolution) local t, q, p t, q, p = sol2tqp(sol) local d = size(q)[2] + p2 = plot(title="Phase Space", xlabel="q", ylabel="p", grid=:on) for j in 1:d j_str = d > 1 ? "[$j]" : "" - plot(q[:,j], p[:,j], color=cc(j), label="(q$(j_str),p$(j_str))", lw=1) + plot!(p2, q[:, j], p[:, j], color=cc(j), label="(q$(j_str), p$(j_str))", linewidth=1) end - grid(ls=":") - xlabel("q") - ylabel("p") - legend() + return p2 end -# plot the energy of a Hamiltonian problem -# +# Function to plot the energy of a Hamiltonian problem function plotenergy(H, sol::ODESolution) local t, q, p t, q, p = sol2tqp(sol) local energy = [H(q[i,:], p[i,:], nothing) for i in 1:size(q)[1]] - plot(t, energy, label="energy", color="red", lw=1) - grid(ls=":") - xlabel("t") - legend() - local stdenergy_str = @sprintf("%.3e", std(energy)) - title(" std(energy) = $stdenergy_str", fontsize=10) + p3 = plot(t, energy, label="energy", color="red", linewidth=1, xlabel="t", title="Energy", grid=:on) + stdenergy_str = @sprintf("%.3e", std(energy)) + title!("std(energy) = $stdenergy_str", fontsize=10) + return p3 end -# plot the numerical and exact solutions of a single pendulum -# -# Warning: Assume q(0) = 0, p(0) = 2k. (for the sake of laziness) -# +# Function to compare the numerical and exact solutions of a single pendulum function plotcomparison(k, sol::ODESolution) local t, q, p t, q, p = sol2tqp(sol) - local y = sin.(q/2) - local y_exact = k*sn.(t, k) # the exact solution - - plot(t, y, label="numerical", lw=1) - plot(t, y_exact, label="exact", lw=1, ls="--") - grid(ls=":") - xlabel("t") - ylabel("y = sin(q(t)/2)") - legend() - local error_str = @sprintf("%.3e", maximum(abs.(y - y_exact))) - title("maximum(abs(numerical - exact)) = $error_str", fontsize=10) + local y = sin.(q / 2) + local y_exact = k * sn.(t, k) # the exact solution + + p4 = plot(t, y, label="numerical", linewidth=1, grid=:on, xlabel="t", ylabel="y = sin(q(t)/2)", title="Comparison") + plot!(p4, t, y_exact, label="exact", linewidth=1, linestyle=:dash) + error_str = @sprintf("%.3e", maximum(abs.(y - y_exact))) + title!("maximum(abs(numerical - exact)) = $error_str", fontsize=10) + return p4 end -# plot solution and energy -# +# Plot solution and energy function plotsolenergy(H, integrator, Δt, sol::ODESolution) - local integrator_str = replace("$integrator", r"^[^.]*\." => "") + integrator_str = replace("$integrator", r"^[^.]*\\." => "") - figure(figsize=(10,8)) + p1 = plotsol(sol) + p2 = plotsol2(sol) + p3 = plotenergy(H, sol) - subplot2grid((21,20), ( 1, 0), rowspan=10, colspan=10) - plotsol(sol) + suptitle = "===== $integrator_str, Δt = $Δt =====" + plot(p1, p2, p3, layout=(3, 1), title=suptitle) +end - subplot2grid((21,20), ( 1,10), rowspan=10, colspan=10) - plotsol2(sol) +# Solve a single pendulum +function singlependulum(k, integrator, Δt; t0 = 0.0, t1 = 100.0) + H(p, q, params) = p[1]^2 / 2 - cos(q[1]) + 1 + q0 = [0.0] + p0 = [2k] + prob = HamiltonianProblem(H, p0, q0, (t0, t1)) - subplot2grid((21,20), (11, 0), rowspan=10, colspan=10) - plotenergy(H, sol) + integrator_str = replace("$integrator", r"^[^.]*\\." => "") + @printf("%-25s", "$integrator_str:") + sol = solve(prob, integrator, dt=Δt) + @time sol = solve(prob, integrator, dt=Δt) - suptitle("===== $integrator_str, Δt = $Δt =====") + sleep(0.1) + + p1 = plotsol(sol) + p2 = plotsol2(sol) + p3 = plotenergy(H, sol) + p4 = plotcomparison(k, sol) + + suptitle = "===== $integrator_str, Δt = $Δt =====" + plot(p1, p2, p3, p4, layout=(2, 2), title=suptitle) end +``` + +## Tests + +```julia +# Single pendulum +using Plots +using OrdinaryDiffEq -# Solve a single pendulum -# function singlependulum(k, integrator, Δt; t0 = 0.0, t1 = 100.0) - local H(p,q,params) = p[1]^2/2 - cos(q[1]) + 1 - local q0 = [0.0] - local p0 = [2k] + local H(p, q, params) = p[1]^2 / 2 - cos(q[1]) + 1 # Hamiltonian for single pendulum + local q0 = [0.0] # Initial position + local p0 = [2k] # Initial momentum local prob = HamiltonianProblem(H, p0, q0, (t0, t1)) local integrator_str = replace("$integrator", r"^[^.]*\." => "") @@ -157,28 +166,17 @@ function singlependulum(k, integrator, Δt; t0 = 0.0, t1 = 100.0) @time local sol = solve(prob, integrator, dt=Δt) sleep(0.1) - figure(figsize=(10,8)) - - subplot2grid((21,20), ( 1, 0), rowspan=10, colspan=10) - plotsol(sol) - - subplot2grid((21,20), ( 1,10), rowspan=10, colspan=10) - plotsol2(sol) - - subplot2grid((21,20), (11, 0), rowspan=10, colspan=10) - plotenergy(H, sol) - subplot2grid((21,20), (11,10), rowspan=10, colspan=10) - plotcomparison(k, sol) + # Create plots using Plots.jl + p1 = plot(sol.t, map(x -> x[1], sol.u), label="Position", title="Position vs Time") + p2 = plot(sol.t, map(x -> x[2], sol.u), label="Momentum", title="Momentum vs Time") + p3 = plot(sol.t, map(p -> H(p[1], p[2], nothing), sol.u), label="Energy", title="Energy vs Time") + p4 = plot(sol.t, map(x -> x[1] - k, sol.u), label="Comparison", title="Comparison Plot") - suptitle("===== $integrator_str, Δt = $Δt =====") + # Combine all plots in a layout + layout = @layout [a b; c d] + plot(p1, p2, p3, p4, layout=layout, size=(1000, 800), title="===== $integrator_str, Δt = $Δt =====") end -``` - -## Tests - -```julia -# Single pendulum k = rand() integrator = VelocityVerlet() @@ -189,8 +187,24 @@ singlependulum(k, integrator, Δt, t0=-20.0, t1=20.0) ```julia # Two single pendulums -H(q,p,param) = sum(p.^2/2 .- cos.(q) .+ 1) -q0 = pi*rand(2) +using Plots +using OrdinaryDiffEq + +function plotsolenergy(H, integrator, Δt, sol::ODESolution) + local integrator_str = replace("$integrator", r"^[^.]*\." => "") + + # Create plots using Plots.jl + p1 = plot(sol, label="Position", title="Position vs Time") + p2 = plot(sol, label="Momentum", title="Momentum vs Time") + p3 = plot(sol.t, map(p -> H(p[2], p[3], nothing), sol.u), label="Energy", title="Energy vs Time") + + # Combine all plots in a layout + layout = @layout [a b; c] + plot(p1, p2, p3, layout=layout, size=(1000, 800), title="===== $integrator_str, Δt = $Δt =====") +end + +H(q, p, param) = sum(p.^2 / 2 .- cos.(q) .+ 1) +q0 = pi * rand(2) p0 = zeros(2) t0, t1 = -20.0, 20.0 prob = HamiltonianProblem(H, q0, p0, (t0, t1)) @@ -257,4 +271,4 @@ singlependulum(k, SymplecticEuler(), Δt) ```julia, echo = false using SciMLBenchmarks SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) -``` +``` \ No newline at end of file diff --git a/benchmarks/IntervalNonlinearProblem/Project.toml b/benchmarks/IntervalNonlinearProblem/Project.toml index decf91efd..46bd106ba 100644 --- a/benchmarks/IntervalNonlinearProblem/Project.toml +++ b/benchmarks/IntervalNonlinearProblem/Project.toml @@ -7,7 +7,7 @@ SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" [compat] BenchmarkTools = "1" -NonlinearSolve = "1, 2, 3" +NonlinearSolve = "1, 2, 3, 4" Plots = "1.13" Roots = "2" SciMLBenchmarks = "0.1" diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 203363fec..365b901ea 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -1,56 +1,91 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.4" +julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "5ee291b24b9094a49a821013cd73c5a001368115" +project_hash = "3d2ea173539a83dd10895538ee44ea033ca2d5a7" [[deps.ADTypes]] -git-tree-sha1 = "332e5d7baeff8497b923b730b994fa480601efc7" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.5" +version = "1.9.0" +weakdeps = ["ChainRulesCore", "EnzymeCore"] -[[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "ce0cb2804273e9147a765501c719038247d7ccd9" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.33.0" + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.AbstractTrees]] -git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.4" +version = "0.4.5" + +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.38" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" + AccessorsUnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.1" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.2.0" +version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "247efbccf92448be332d154d6ca56b9fcdd93c31" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "d60a1922358aa203019b7857a2c8c37329b8736c" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.6.1" +version = "7.17.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -58,15 +93,20 @@ version = "7.6.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "af43df5704827c8618afd36eb56fcab20d3041ee" +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.4.3" +version = "1.10.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -77,9 +117,9 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "0b816941273b5b162be122a6c94d706e3b3125ca" +git-tree-sha1 = "a2c85f53ddcb15b4099da59867868bd40f005579" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.38" +version = "1.7.5" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -90,37 +130,77 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f" +git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.4.0" +version = "1.5.0" [[deps.Bijections]] -git-tree-sha1 = "c9b163bd832e023571e86d0b90d9de92a9879088" +git-tree-sha1 = "d8b0439d2be438a5f2cd68ec158fe08a7b2595b7" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" -version = "0.1.6" +version = "0.1.9" [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.5" +version = "0.1.6" + +[[deps.BlockArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] +git-tree-sha1 = "d434647f798823bcae510aee0bc0401927f64391" +uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" +version = "1.1.1" +weakdeps = ["BandedMatrices"] + + [deps.BlockArrays.extensions] + BlockArraysBandedMatricesExt = "BandedMatrices" [[deps.BoundaryValueDiffEq]] -deps = ["ArrayInterface", "BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces", "UnPack"] -git-tree-sha1 = "f7392ce20e6dafa8fee406142b1764de7d7cd911" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "98da8bd76b89a4ae1b8dde9fc6dcd75dcd6b5282" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "4.0.1" +version = "5.12.0" + + [deps.BoundaryValueDiffEq.extensions] + BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" + + [deps.BoundaryValueDiffEq.weakdeps] + ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" + +[[deps.BoundaryValueDiffEqCore]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "b4556571d1e80faa5f62ac8732a07bae0ee24dc6" +uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" +version = "1.0.2" + +[[deps.BoundaryValueDiffEqFIRK]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "35e1e7822d1c77d85ecf568606ca64d60fbd39de" +uuid = "85d9eb09-370e-4000-bb32-543851f73618" +version = "1.0.2" + +[[deps.BoundaryValueDiffEqMIRK]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "e1fa0dee3d8eca528ab96e765a52760fd7466ffa" +uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" +version = "1.0.1" + +[[deps.BoundaryValueDiffEqShooting]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "fac04445ab0fdfa29b62d84e1af6b21334753a94" +uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" +version = "1.0.2" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -129,45 +209,47 @@ version = "0.5.0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" +git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.4" +version = "0.2.6" [[deps.CSTParser]] deps = ["Tokenize"] -git-tree-sha1 = "3ddd48d200eb8ddf9cb3e0189fc059fd49b97c1f" +git-tree-sha1 = 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[[deps.Catalyst]] -deps = ["DataStructures", "DiffEqBase", "DocStringExtensions", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] -git-tree-sha1 = "8e7e57c2ed4ecfb798f5a8cb230a9dd84765e7b1" +deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"] +git-tree-sha1 = "dafd059c1d80ba02006978cd05ea7264ff1f362e" uuid = "479239e8-5488-4da2-87a7-35f2df7eef83" -version = "13.5.1" +version = "14.4.1" [deps.Catalyst.extensions] + CatalystBifurcationKitExtension = "BifurcationKit" + CatalystCairoMakieExtension = "CairoMakie" + CatalystGraphMakieExtension = "GraphMakie" CatalystHomotopyContinuationExtension = "HomotopyContinuation" + CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability" [deps.Catalyst.weakdeps] + BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" + CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" + GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2" HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "e0af648f0692ec1691b5d094b8724ba1346281cf" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.18.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -175,33 +257,39 @@ weakdeps = ["SparseArrays"] [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "cd67fc487743b2f0fd4380d4cbd3a24660d0eec8" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.3" +version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.24.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.12.0" + + [deps.ColorTypes.extensions] + StyledStringsExt = "StyledStrings" + + [deps.ColorTypes.weakdeps] + StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "a1f44953f2382ebb937d60dafbe2deea4bd23249" +git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.10.0" +version = "0.11.0" weakdeps = ["SpecialFunctions"] [deps.ColorVectorSpace.extensions] @@ -209,9 +297,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -219,10 +307,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] -git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" +deps = ["Crayons", "PrecompileTools"] +git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.12" +version = "0.8.15" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -230,16 +318,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] -deps = ["UUIDs"] -git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.10.1" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -248,12 +341,21 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.5+0" +version = "1.1.1+0" [[deps.CompositeTypes]] -git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" +git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.3" +version = "0.1.4" + +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" [[deps.ConcreteStructs]] git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" @@ -262,31 +364,31 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "8cfa272e8bdedfa88b6aefbbca7c19f1befac519" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.3.0" +version = "2.4.2" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "51cab8e982c5b598eea9c8ceaced4b58d9dd37c9" +git-tree-sha1 = "b19db3927f0db4151cb86d073689f2428e524576" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.10.0" +version = "1.10.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.4" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" [[deps.CpuId]] deps = ["Markdown"] @@ -300,21 +402,21 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.15.0" +version = "1.16.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.6.1" +version = "1.7.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.15" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -325,11 +427,17 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "df712c77bb43b37ea966feb72cb2e92d51a3face" +git-tree-sha1 = "066f60231c1b0ae2905ffd2651e207accd91f627" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.43.1" +version = "5.48.1" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -338,45 +446,50 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "0d9982e8dee851d519145857e79a17ee33ede154" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "f8eefbb7e910f59087c4bb09ce670f235758ee4a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.130.0" +version = "6.158.3" [deps.DiffEqBase.extensions] + DiffEqBaseCUDAExt = "CUDA" + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "4e4de57a0ac47b2f20aae62f132355b058e9f0cd" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.34.0" -weakdeps = ["OrdinaryDiffEq", "Sundials"] +version = "4.1.0" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "57ed4597a309c5b2a10cab5f9813adcb78f92117" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.19.0" +version = "5.23.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -398,15 +511,68 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "96a19f498504e4a3b39524196b73eb60ccef30e9" +git-tree-sha1 = "d55af9d6b51c54f81ae30d1a463206d32cc4c24a" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.10.0" +version = "7.15.0" + +[[deps.DifferentiationInterface]] +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" +uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +version = "0.6.22" + + [deps.DifferentiationInterface.extensions] + DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" + DifferentiationInterfaceDiffractorExt = "Diffractor" + DifferentiationInterfaceEnzymeExt = "Enzyme" + DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" + DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" + DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" + DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" + DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" + DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.DispatchDoctor]] +deps = ["MacroTools", "Preferences"] +git-tree-sha1 = "453df2ce2aef7de59c69a56d31dcd2ec3384dd77" +uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" +version = "0.4.17" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.DispatchDoctor.extensions] + DispatchDoctorChainRulesCoreExt = "ChainRulesCore" + DispatchDoctorEnzymeCoreExt = "EnzymeCore" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -418,10 +584,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "a6c00f894f24460379cb7136633cef54ac9f6f4a" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.103" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -440,27 +606,45 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "490392af2c7d63183bfa2c8aaa6ab981c5ba7561" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.6.7" +version = "0.7.14" + + [deps.DomainSets.extensions] + DomainSetsMakieExt = "Makie" + + [deps.DomainSets.weakdeps] + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.DynamicPolynomials]] -deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "fea68c84ba262b121754539e6ea0546146515d4f" +deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"] +git-tree-sha1 = "bbf1ace0781d9744cb697fb856bd2c3f6568dadb" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.5.3" +version = "0.6.0" + +[[deps.DynamicQuantities]] +deps = ["DispatchDoctor", "TestItems", "Tricks"] +git-tree-sha1 = "9f826f051e3d2c76f924d39c9aa4fcfd18cc9256" +uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" +version = "1.2.0" + + [deps.DynamicQuantities.extensions] + DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" + DynamicQuantitiesMeasurementsExt = "Measurements" + DynamicQuantitiesScientificTypesExt = "ScientificTypes" + DynamicQuantitiesUnitfulExt = "Unitful" + + [deps.DynamicQuantities.weakdeps] + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" @@ -468,10 +652,13 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -deps = ["Adapt"] -git-tree-sha1 = "2efe862de93cd87f620ad6ac9c9e3f83f1b2841b" +git-tree-sha1 = "04c777af6ef65530a96ab68f0a81a4608113aa1d" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.4" +version = "0.8.5" +weakdeps = ["Adapt"] + + [deps.EnzymeCore.extensions] + AdaptExt = "Adapt" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -481,32 +668,38 @@ version = "0.0.20230411+0" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96" +git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.9" +version = "0.1.10" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.5.0+0" +version = "2.6.2+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "602e4585bcbd5a25bc06f514724593d13ff9e862" +git-tree-sha1 = "8e18940a5ba7f4ddb41fe2b79b6acaac50880a86" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.25.0" +version = "1.26.1" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.Expronicon]] +deps = ["MLStyle", "Pkg", "TOML"] +git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" +uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" +version = "0.8.5" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -514,11 +707,17 @@ git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" version = "4.4.4+1" +[[deps.FastAlmostBandedMatrices]] +deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] +git-tree-sha1 = "3f03d94c71126b6cfe20d3cbcc41c5cd27e1c419" +uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" +version = "0.1.4" + [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.8" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -527,18 +726,39 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "b12f05108e405dadcc2aff0008db7f831374e051" +git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "2.0.0" +version = "2.0.4" + +[[deps.FastPower]] +git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" +uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" +version = "1.1.1" + + [deps.FastPower.extensions] + FastPowerEnzymeExt = "Enzyme" + FastPowerForwardDiffExt = "ForwardDiff" + FastPowerMeasurementsExt = "Measurements" + FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" + FastPowerReverseDiffExt = "ReverseDiff" + FastPowerTrackerExt = "Tracker" + + [deps.FastPower.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "01dba5dbad6b2766e2ddd7b9d64af0e6d68d95cd" +deps = ["LinearAlgebra"] +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.9.1" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -546,45 +766,51 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" +[[deps.FindFirstFunctions]] +git-tree-sha1 = "670e1d9ceaa4a3161d32fe2d2fb2177f8d78b330" +uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224" +version = "1.4.1" + [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = 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"Zlib_jll"] -git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.93+0" +version = "2.13.96+0" -[[deps.Formatting]] -deps = ["Printf"] -git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" -uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" -version = "0.4.2" +[[deps.Format]] +git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" +uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8" +version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -592,15 +818,15 @@ weakdeps = ["StaticArrays"] [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" +git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.1+0" +version = "2.13.2+0" [[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.10+0" +version = "1.0.14+0" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -615,43 +841,49 @@ version = "0.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "9a68d75d466ccc1218d0552a8e1631151c569545" +git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.5" +version = "0.4.12" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.8+0" +version = "3.4.0+1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = 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-git-tree-sha1 = "025d171a2847f616becc0f84c8dc62fe18f0f6dd" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.10+0" +version = "0.73.8+0" + +[[deps.GenericLinearAlgebra]] +deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] +git-tree-sha1 = "c4f9c87b74aedf20920034bd4db81d0bffc527d2" +uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" +version = "0.3.14" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.3" +version = "0.5.4" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -661,21 +893,21 @@ version = "0.21.0+0" [[deps.Git]] deps = ["Git_jll"] -git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d" +git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e" uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" -version = "1.3.0" +version = "1.3.1" [[deps.Git_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "bb8f7cc77ec1152414b2af6db533d9471cfbb2d1" +git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.42.0+0" +version = "2.46.2+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.76.5+0" +version = "2.80.5+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -690,62 +922,50 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.9.0" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.Groebner]] -deps = ["AbstractAlgebra", "Combinatorics", "ExprTools", "Logging", "MultivariatePolynomials", "PrecompileTools", "Primes", "Printf", "Random", "SIMD", "TimerOutputs"] -git-tree-sha1 = "909ce267252dde0d10cccad539021c245fcfa20f" -uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.5.0" - -[[deps.GroupsCore]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "9e1a5e9f3b81ad6a5c613d181664a0efc6fe6dd7" -uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" -version = "0.4.0" - [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "abbbb9ec3afd783a7cbd82ef01dcd088ea051398" +git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.1" +version = "1.10.10" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.3.1+0" [[deps.Highlights]] deps = ["DocStringExtensions", "InteractiveUtils", "REPL"] -git-tree-sha1 = "0341077e8a6b9fc1c2ea5edc1e93a956d2aec0c7" +git-tree-sha1 = "9e13b8d8b1367d9692a90ea4711b4278e4755c32" uuid = "eafb193a-b7ab-5a9e-9068-77385905fa72" -version = "0.5.2" +version = "0.5.3" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.24" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" +git-tree-sha1 = "1b1299f7d6617291f3d260e9f5b0250afdaac8c0" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.2" +version = "1.26.0" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -753,15 +973,22 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[deps.Inflate]] -git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.4" +version = "0.1.5" [[deps.InlineStrings]] -deps = ["Parsers"] -git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" +git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.0" +version = "1.4.2" + + [deps.InlineStrings.extensions] + ArrowTypesExt = "ArrowTypes" + ParsersExt = "Parsers" + + [deps.InlineStrings.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" + Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" @@ -769,25 +996,36 @@ uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" version = "0.1.2" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "31d6adb719886d4e32e38197aae466e98881320b" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.0.0+0" +version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.IntervalSets]] -deps = ["Dates", "Random"] -git-tree-sha1 = "3d8866c029dd6b16e69e0d4a939c4dfcb98fac47" +git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.8" -weakdeps = ["Statistics"] +version = "0.7.10" +weakdeps = ["Random", "RecipesBase", "Statistics"] [deps.IntervalSets.extensions] + IntervalSetsRandomExt = "Random" + IntervalSetsRecipesBaseExt = "RecipesBase" IntervalSetsStatisticsExt = "Statistics" +[[deps.InverseFunctions]] +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.17" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" @@ -805,15 +1043,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -823,61 +1061,58 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.91+0" +version = "3.0.4+0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "2d2f630931dcf9cc4f753777a9c9ffb48d504116" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"] +git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.43" +version = "1.0.62" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] -git-tree-sha1 = "ebb2557b4b6a0c2607cb4709393794ddc3b9f440" +git-tree-sha1 = "dfc7e84e51c5adbd76dedc73844fe373ffffddb9" uuid = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e" -version = "0.1.4" +version = "1.0.0" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] -git-tree-sha1 = "e047c47fca2ac1ac687e006a257f96632fb95a7b" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.9.0" +version = "9.14.0" weakdeps = ["FastBroadcast"] - [deps.JumpProcesses.extensions] - JumpProcessFastBroadcastExt = "FastBroadcast" - [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" +git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.1" +version = "0.6.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.4" +version = "0.9.8" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVMOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.4+0" +version = "18.1.7+0" [[deps.LSODA]] deps = ["Compat", "DiffEqBase", "LSODA_jll", "LinearAlgebra", "Parameters", "Printf", "SciMLBase"] @@ -892,52 +1127,55 @@ uuid = "aae0fff6-70f8-51e1-979a-8150c7cc74bd" version = "0.1.2+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LabelledArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "cd04158424635efd05ff38d5f55843397b7416a9" -uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.14.0" - -[[deps.LambertW]] -git-tree-sha1 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"Static", "StaticArrayInterface"] -git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.15" +version = "0.1.17" -[[deps.Lazy]] -deps = ["MacroTools"] -git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" -uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" -version = "0.15.1" +[[deps.LazyArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "360f6039babd6e4d6364eff0d4fc9120834a2d9a" +uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" +version = "2.2.1" + + [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" + LazyArraysStaticArraysExt = "StaticArrays" + + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -960,9 +1198,14 @@ uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" @@ -978,10 +1221,10 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -990,78 +1233,96 @@ uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" version = "1.6.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.35.0+0" +version = "2.40.1+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.36.0+0" +version = "2.40.1+0" + +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "9f27ba34f5821a0495efb09ea3a465c31326495a" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "591de175461afd8323aa24b7686062574527aa3a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.10.0" +version = "2.36.2" [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = "Enzyme" + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" +git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.26" +version = "0.3.28" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1078,15 +1339,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.166" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1094,10 +1355,10 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] SpecialFunctionsExt = "SpecialFunctions" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.0.0+0" +version = "2024.2.0+0" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1106,9 +1367,9 @@ version = "0.4.17" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.11" +version = "0.5.13" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1119,6 +1380,26 @@ version = "0.1.8" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MatrixFactorizations]] +deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] +git-tree-sha1 = "16a726dba99685d9e94c8d0a8f655383121fc608" +uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" +version = "3.0.1" +weakdeps = ["BandedMatrices"] + + [deps.MatrixFactorizations.extensions] + MatrixFactorizationsBandedMatricesExt = "BandedMatrices" + +[[deps.MaybeInplace]] +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" +uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" + [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf" @@ -1128,7 +1409,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1137,28 +1418,36 @@ version = "0.3.2" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "87a45c453295c1640a1fd011a85e42fda7a78d15" +deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "b96b0749d6d9c8d6480641dcfcc02a265cf6d9e7" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.70.0" +version = "9.50.0" [deps.ModelingToolkit.extensions] + MTKBifurcationKitExt = "BifurcationKit" + MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" + MTKHomotopyContinuationExt = "HomotopyContinuation" + MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] + BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" + HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1167,21 +1456,21 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "6ffb234d6d7c866a75c1879d2099049d3a35a83a" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.3" +version = "0.5.7" [[deps.Mustache]] deps = ["Printf", "Tables"] -git-tree-sha1 = "a7cefa21a2ff993bff0456bf7521f46fc077ddf1" +git-tree-sha1 = "3b2db451a872b20519ebb0cec759d3d81a1c6bcb" uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.19" +version = "1.0.20" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "806eea990fb41f9b36f1253e5697aa645bf6a9f8" +git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.0" +version = "1.5.2" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1206,16 +1495,41 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "e10debcea868cd6e51249e8eeaf191c25f68a640" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.10.1" +version = "3.15.1" + + [deps.NonlinearSolve.extensions] + NonlinearSolveBandedMatricesExt = "BandedMatrices" + NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" + NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + NonlinearSolveMINPACKExt = "MINPACK" + NonlinearSolveNLSolversExt = "NLSolvers" + NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" + NonlinearSolveSpeedMappingExt = "SpeedMapping" + + [deps.NonlinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" + LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + NLSolvers = 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["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" +git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.1" +version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.12+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1253,15 +1567,21 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "01f85d9269b13fedc61e63cc72ee2213565f7a72" +git-tree-sha1 = 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"TOML"] +[[deps.Pango_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +uuid = "36c8627f-9965-5494-a995-c6b170f724f3" +version = "1.54.1+0" + [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" @@ -1299,15 +1809,15 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf" +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.0" +version = "2.8.1" [[deps.PiecewiseDeterministicMarkovProcesses]] deps = ["DifferentialEquations", "Distributions", "ForwardDiff", "JumpProcesses", "LSODA", "LinearAlgebra", "Parameters", "PreallocationTools", "Random", "RecursiveArrayTools", "SciMLBase", "SparseArrays", "StatsBase", "Sundials", "Test"] -git-tree-sha1 = "d8d42ff533106135a50ab4e210c80225dae2207b" +git-tree-sha1 = "3cd4ecef2dbe4b2fb45c37273e9709548a4051d7" uuid = "86206cdf-4603-54e0-bd58-22a2dcbf57aa" -version = "0.0.7" +version = "0.0.8" [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" @@ -1316,32 +1826,32 @@ version = "1.3.0" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" +git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.42.2+0" +version = "0.43.4+0" [[deps.Pkg]] 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 = "1.9.2" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.1.0" +version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.5" +version = "1.4.3" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "45470145863035bb124ca51b320ed35d071cc6c2" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.39.0" +version = "1.40.8" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1364,16 +1874,34 @@ uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.4" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "fca25670784a1ae44546bcb17288218310af2778" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.9" +version = "0.7.16" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.2.1" +version = "0.2.2" + +[[deps.Polynomials]] +deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736" +uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" +version = "4.0.11" + + [deps.Polynomials.extensions] + PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsFFTWExt = "FFTW" + PolynomialsMakieCoreExt = "MakieCore" + PolynomialsMutableArithmeticsExt = "MutableArithmetics" + + [deps.Polynomials.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" + MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -1388,10 +1916,10 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] -git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" +deps = ["Adapt", "ArrayInterface", "ForwardDiff"] +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.12" +version = "0.4.24" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -1401,27 +1929,27 @@ version = "0.4.12" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.2.0" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.1" +version = "1.4.3" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.1" +version = "2.4.0" [[deps.Primes]] deps = ["IntegerMathUtils"] -git-tree-sha1 = "1d05623b5952aed1307bf8b43bec8b8d1ef94b6e" +git-tree-sha1 = "cb420f77dc474d23ee47ca8d14c90810cafe69e7" uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" -version = "0.5.5" +version = "0.5.6" [[deps.Printf]] deps = ["Unicode"] @@ -1431,49 +1959,78 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" deps = ["Printf"] uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" +[[deps.PtrArrays]] +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" +version = "1.2.1" + [[deps.PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] -git-tree-sha1 = "1cb97fa63a3629c6d892af4f76fcc4ad8191837c" +git-tree-sha1 = "9816a3826b0ebf49ab4926e2b18842ad8b5c8f04" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" -version = "1.96.2" +version = "1.96.4" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] -git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b" +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.5.3+1" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.1" +version = "2.11.1" + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" + + [deps.QuadGK.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" +git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.1" - -[[deps.RandomExtensions]] -deps = ["Random", "SparseArrays"] -git-tree-sha1 = "b8a399e95663485820000f26b6a43c794e166a49" -uuid = "fb686558-2515-59ef-acaa-46db3789a887" -version = "0.4.4" +version = "1.7.0" [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" + +[[deps.ReactionNetworkImporters]] +deps = ["Catalyst", "DataStructures", "ModelingToolkit", "SparseArrays", "Symbolics"] +git-tree-sha1 = "cbabb1145cf2e3400c0923314cdc1df595d22f73" +uuid = "b4db0fb7-de2a-5028-82bf-5021f5cfa881" +version = "0.15.1" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1488,28 +2045,36 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.10" +version = "3.27.3" [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] + FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "8bc86c78c7d8e2a5fe559e3721c0f9c9e303b2ed" +git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.21" +version = "0.2.23" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1536,32 +2101,36 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.5.1+0" + +[[deps.RootedTrees]] +deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] +git-tree-sha1 = "c0c464d3063e46e4128d21fd677ca575ace44fdc" +uuid = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c" +version = "2.23.1" +weakdeps = ["Plots"] + + [deps.RootedTrees.extensions] + PlotsExt = "Plots" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "d8911cc125da009051fb35322415641d02d9e37f" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.6" - [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1569,20 +2138,33 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.42" +version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "916b8a94c0d61fa5f7c5295649d3746afb866aff" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "ad0d4e32b7adf6871f60c3379d76fdc231b434c8" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.98.1" +version = "2.59.1" [deps.SciMLBase.extensions] - ZygoteExt = "Zygote" + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLBenchmarks]] @@ -1591,17 +2173,28 @@ git-tree-sha1 = "f4076dd5a103010d48bb6c4e50c5526f6622fa96" uuid = "31c91b34-3c75-11e9-0341-95557aab0344" version = "0.1.3" -[[deps.SciMLNLSolve]] -deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" -uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.9" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.7" +version = "0.3.12" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" + +[[deps.SciMLStructures]] +deps = ["ArrayInterface"] +git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.5.0" [[deps.Scratch]] deps = ["Dates"] @@ -1611,9 +2204,9 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "0e7508ff27ba32f26cd459474ca2ede1bc10991f" +git-tree-sha1 = "d0553ce4031a081cc42387a9b9c8441b7d99f32d" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.1" +version = "1.4.7" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1635,21 +2228,27 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "15ff97fa4881133caa324dacafe28b5ac47ad8a2" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.23" +version = "1.12.3" [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveNNlibExt = "NNlib" + SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" + SimpleNonlinearSolveTrackerExt = "Tracker" + SimpleNonlinearSolveZygoteExt = "Zygote" [deps.SimpleNonlinearSolve.weakdeps] - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1673,30 +2272,65 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "5165dfb9fd131cf0c6957a3a7605dede376e7b63" +git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.0" +version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" + +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "6914df6005bab9940e2a96879a97a43e1fb1ce78" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.8" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "07272c80c278947baca092df0a01da4a10622ad5" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = 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[deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1705,25 +2339,31 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "f295e0a1da4ca425659c57441bcb59abb035a4bc" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.8" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.1" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1732,23 +2372,24 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "5ef59aea6f18c25168842bded46b16662141ab87" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.7.0" -weakdeps = ["Statistics"] +version = "1.9.8" +weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1764,35 +2405,32 @@ version = "0.33.21" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" +git-tree-sha1 = 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"DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b341540a647b39728b6d64eaeda82178e848f76e" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "bf4bad73c80e058b1d53788ff520e10c8bad7c9d" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.62.0" +version = "6.70.0" [[deps.StrideArraysCore]] -deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.2" +version = "0.5.7" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1802,53 +2440,77 @@ version = "0.3.7" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.4.0" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] -deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "71dc65a2d7decdde5500299c9b04309e0138d1b4" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.20.1" +version = "4.26.1" [[deps.Sundials_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] -git-tree-sha1 = "04777432d74ec5bc91ca047c9e0e0fd7f81acdb6" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] +git-tree-sha1 = "ba4d38faeb62de7ef47155ed321dce40a549c305" uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" -version = "5.2.1+0" +version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] -deps = ["DocStringExtensions"] -git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "20cf607cafb31f922bce84d60379203e7a126911" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" +version = "0.3.34" + +[[deps.SymbolicLimits]] +deps = ["SymbolicUtils"] +git-tree-sha1 = "fabf4650afe966a2ba646cabd924c3fd43577fc3" +uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3" version = "0.2.2" [[deps.SymbolicUtils]] -deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "TimerOutputs", "Unityper"] -git-tree-sha1 = "2f3fa844bcd33e40d8c29de5ee8dded7a0a70422" +deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "1.4.0" +version = "3.7.2" + + [deps.SymbolicUtils.extensions] + SymbolicUtilsLabelledArraysExt = "LabelledArrays" + SymbolicUtilsReverseDiffExt = "ReverseDiff" + + [deps.SymbolicUtils.weakdeps] + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "RecursiveArrayTools", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils"] -git-tree-sha1 = "28f55dcd865e4a97f262fc476306cee14e8d4651" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "0caef7687abf7094132fa3112bf5514c36a99226" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.11.0" +version = "6.18.3" [deps.Symbolics.extensions] + SymbolicsForwardDiffExt = "ForwardDiff" + SymbolicsGroebnerExt = "Groebner" + SymbolicsLuxExt = "Lux" + SymbolicsNemoExt = "Nemo" + SymbolicsPreallocationToolsExt = ["PreallocationTools", "ForwardDiff"] SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" + Lux = "b2108857-7c20-44ae-9111-449ecde12c47" + Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a" + PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" [[deps.TOML]] @@ -1863,10 +2525,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1879,10 +2541,20 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" +[[deps.TermInterface]] +git-tree-sha1 = "d673e0aca9e46a2f63720201f55cc7b3e7169b16" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "2.0.0" + [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TestItems]] +git-tree-sha1 = "42fd9023fef18b9b78c8343a4e2f3813ffbcefcb" +uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe" +version = "1.0.0" + [[deps.ThreadingUtilities]] deps = ["ManualMemory"] git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" @@ -1891,34 +2563,30 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.25" [[deps.Tokenize]] -git-tree-sha1 = "0454d9a9bad2400c7ccad19ca832a2ef5a8bc3a1" +git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.26" +version = "0.5.29" [[deps.TranscodingStreams]] -git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.2" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.20" +version = "0.2.1" [[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +version = "0.1.9" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -1951,29 +2619,26 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.19.0" +version = "1.21.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.Unityper]] deps = ["ConstructionBase"] -git-tree-sha1 = "21c8fc7cd598ef49f11bc9e94871f5d7740e34b9" +git-tree-sha1 = "25008b734a03736c41e2a7dc314ecb95bd6bbdb0" uuid = "a7c27f48-0311-42f6-a7f8-2c11e75eb415" -version = "0.1.5" +version = "0.1.6" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1982,9 +2647,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.65" +version = "0.21.71" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -2011,9 +2676,9 @@ version = "1.21.0+1" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" +git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.25.0+0" +version = "1.31.0+0" [[deps.Weave]] deps = ["Base64", "Dates", "Highlights", "JSON", "Markdown", "Mustache", "Pkg", "Printf", "REPL", "RelocatableFolders", "Requires", "Serialization", "YAML"] @@ -2023,33 +2688,33 @@ version = "0.10.12" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "da69178aacc095066bad1f69d2f59a60a1dd8ad1" +git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.0+0" +version = "2.13.4+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "522b8414d40c4cbbab8dee346ac3a09f9768f25d" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.5+0" +version = "5.6.3+0" [[deps.Xorg_libICE_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "e5becd4411063bdcac16be8b66fc2f9f6f1e8fe5" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.0.10+1" +version = "1.1.1+0" [[deps.Xorg_libSM_jll]] -deps = ["Libdl", "Pkg", "Xorg_libICE_jll"] -git-tree-sha1 = "4a9d9e4c180e1e8119b5ffc224a7b59d3a7f7e18" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.3+0" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -2076,10 +2741,10 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -2106,10 +2771,10 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2119,9 +2784,9 @@ version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+0" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -2185,38 +2850,32 @@ version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" +git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.9" +version = "0.4.12" [[deps.ZMQ]] -deps = ["FileWatching", "Sockets", "ZeroMQ_jll"] -git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77" +deps = ["FileWatching", "PrecompileTools", "Sockets", "ZeroMQ_jll"] +git-tree-sha1 = "18cfd00df3cbbebf8ea4ec7ea6bbceb3af716bd0" uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1" -version = "1.2.2" +version = "1.3.0" [[deps.ZeroMQ_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "libsodium_jll"] -git-tree-sha1 = "fe5c65a526f066fb3000da137d5785d9649a8a47" +deps = ["Artifacts", "JLLWrappers", "Libdl", "libsodium_jll"] +git-tree-sha1 = "f02ce8f0fda1ed40f4d0d59a2ad05e35e8ac9b0e" uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568" -version = "4.3.4+0" +version = "4.3.5+1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "9d749cd449fb448aeca4feee9a2f4186dbb5d184" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.4" +version = "1.5.6+1" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] @@ -2226,9 +2885,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.53.0+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2237,21 +2896,27 @@ uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" version = "3.1.1+0" [[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" +version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" +version = "5.11.0+0" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2260,10 +2925,10 @@ uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" version = "1.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libinput_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] @@ -2272,22 +2937,22 @@ uuid = "36db933b-70db-51c0-b978-0f229ee0e533" version = "1.18.0+0" [[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" +version = "1.6.44+0" [[deps.libsodium_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e" +git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+0" +version = "1.0.20+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2300,10 +2965,16 @@ deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.52.0+1" +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/benchmarks/Jumps/Mendes_multistate_example.jmd b/benchmarks/Jumps/Mendes_multistate_example.jmd index 34aab6b66..7ee5ac7da 100644 --- a/benchmarks/Jumps/Mendes_multistate_example.jmd +++ b/benchmarks/Jumps/Mendes_multistate_example.jmd @@ -35,7 +35,7 @@ varsyms = [ ] varidxs = [] for vars in varsyms - push!(varidxs, [findfirst(isequal(sym),rn.states) for sym in vars]) + push!(varidxs, [findfirst(isequal(sym),unknowns(rn)) for sym in vars]) end ``` diff --git a/benchmarks/Jumps/Project.toml b/benchmarks/Jumps/Project.toml index 7d7b6b146..ba053d8d0 100644 --- a/benchmarks/Jumps/Project.toml +++ b/benchmarks/Jumps/Project.toml @@ -15,25 +15,27 @@ PiecewiseDeterministicMarkovProcesses = "86206cdf-4603-54e0-bd58-22a2dcbf57aa" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +ReactionNetworkImporters = "b4db0fb7-de2a-5028-82bf-5021f5cfa881" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [compat] BenchmarkTools = "1.4" -Catalyst = "13" +Catalyst = "14" Conda = "1.9.1" DataFrames = "1.3.4" DifferentialEquations = "7" Distributions = "0.25" Graphs = "1" -JumpProblemLibrary = "0.1.4" +JumpProblemLibrary = "1.0.0" JumpProcesses = "9.9" -ModelingToolkit = "8.7" +ModelingToolkit = "9" OrdinaryDiffEq = "6.5" -PiecewiseDeterministicMarkovProcesses = "0.0.7" +PiecewiseDeterministicMarkovProcesses = "0.0.8" Plots = "1.39" -PyCall = "1.96.1" +PyCall = "1.96.4" +ReactionNetworkImporters = "0.15" SciMLBenchmarks = "0.1" Statistics = "1" Sundials = "4" diff --git a/benchmarks/LinearSolve/LUFactorization.jmd b/benchmarks/LinearSolve/LUFactorization.jmd index 0ca556c60..4c29a2fd7 100644 --- a/benchmarks/LinearSolve/LUFactorization.jmd +++ b/benchmarks/LinearSolve/LUFactorization.jmd @@ -5,7 +5,7 @@ author: Chris Rackauckas ```julia using BenchmarkTools, Random, VectorizationBase -using LinearAlgebra, LinearSolve, MKL_jll +using LinearAlgebra, LinearSolve, RecursiveFactorization, MKL_jll nc = min(Int(VectorizationBase.num_cores()), Threads.nthreads()) BLAS.set_num_threads(nc) BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.5 diff --git a/benchmarks/LinearSolve/MatrixDepot.jmd b/benchmarks/LinearSolve/MatrixDepot.jmd index f979359cc..9f8de473f 100644 --- a/benchmarks/LinearSolve/MatrixDepot.jmd +++ b/benchmarks/LinearSolve/MatrixDepot.jmd @@ -30,9 +30,35 @@ cols = [:red, :blue, :green, :magenta, :turqoise] # one color per alg allmatrices_md = listnames("*/*") @info "Total number of matrices: $(allmatrices_md.content[1].rows)" + times = fill(NaN, length(allmatrices_md.content[1].rows), length(algs)) percentage_sparsity = fill(NaN, length(allmatrices_md.content[1].rows)) +spaced_out_sparsity = fill(NaN, length(allmatrices_md.content[1].rows)) matrix_size = fill(NaN, length(allmatrices_md.content[1].rows)) +bandedness_five = fill(NaN, length(allmatrices_md.content[1].rows)) +bandedness_ten = fill(NaN, length(allmatrices_md.content[1].rows)) +bandedness_twenty = fill(NaN, length(allmatrices_md.content[1].rows)) + +function compute_bandedness(A, bandwidth) + n = size(A, 1) + total_band_positions = 0 + non_zero_in_band = 0 + bandwidth = bandwidth + for r in 1:n + for c in 1:n + if abs(r - c) <= bandwidth + total_band_positions += 1 # This position belongs to the band + if A[r, c] != 0 + non_zero_in_band += 1 # This element is non-zero in the band + end + end + end + end + + percentage_filled = non_zero_in_band / total_band_positions * 100 + return percentage_filled +end + ``` ```julia @@ -47,12 +73,34 @@ for z in 1:length(allmatrices_md.content[1].rows) A = mdopen(currMTX).A A = convert(SparseMatrixCSC, A) n = size(A, 1) - matrix_size[z] = n - percentage_sparsity[z] = length(nonzeros(A)) / n^2 - @info "$n × $n" - - n > 500 && error("Skipping too large matrices") + + mtx_copy = copy(A) + @info "$n × $n" + n > 100 && error("Skipping too large matrices") + + ## COMPUTING SPACED OUT SPARSITY + rows, cols = size(mtx_copy) + new_rows = div(rows, 2) + new_cols = div(cols, 2) + condensed = zeros(Int, new_rows, new_cols) + while size(mtx_copy, 1) > 32 || size(mtx_copy, 2) > 32 + + rows, cols = size(mtx_copy) + new_rows = div(rows, 2) + new_cols = div(cols, 2) + condensed = sparse(zeros(Int, new_rows, new_cols)) + + for r in 1:2:rows-1 + for c in 1:2:cols-1 + block = mtx_copy[r:min(r+1, rows), c:min(c+1, cols)] + condensed[div(r-1, 2) + 1, div(c-1, 2) + 1] = (length(nonzeros(block)) >= 2) ? 1 : 0 + end + end + mtx_copy = condensed + end + + ## COMPUTING FACTORIZATION TIME b = rand(rng, n) u0 = rand(rng, n) @@ -65,6 +113,13 @@ for z in 1:length(allmatrices_md.content[1].rows) times[z,j] = bt end + bandedness_five[z] = compute_bandedness(A, 5) + bandedness_ten[z] = compute_bandedness(A, 10) + bandedness_twenty[z] = compute_bandedness(A, 20) + percentage_sparsity[z] = length(nonzeros(A)) / n^2 + spaced_out_sparsity[z] = length(nonzeros(mtx_copy)) * percentage_sparsity[z] + matrix_size[z] = n + #= p = bar(algnames, times[z, :]; ylabel = "Time/s", @@ -86,6 +141,19 @@ for z in 1:length(allmatrices_md.content[1].rows) println(e) end end + +percentage_sparsity = percentage_sparsity[.!isnan.(percentage_sparsity)] +spaced_out_sparsity = spaced_out_sparsity[.!isnan.(spaced_out_sparsity)] +spaced_out_sparsity = replace(spaced_out_sparsity, 0 => 1e-10) +bandedness_five = bandedness_five[.!isnan.(bandedness_five)] +bandedness_five = replace(bandedness_five, 0 => 1e-10) +bandedness_ten = bandedness_ten[.!isnan.(bandedness_ten)] +bandedness_ten = replace(bandedness_ten, 0 => 1e-10) +bandedness_twenty = bandedness_twenty[.!isnan.(bandedness_twenty)] +bandedness_twenty = replace(bandedness_twenty, 0 => 1e-10) +matrix_size = matrix_size[.!isnan.(matrix_size)] +nanrows = any(isnan, times; dims=2) +times = times[.!vec(nanrows), :] ``` ```julia @@ -122,6 +190,51 @@ p = scatter(matrix_size, times; legend = :outertopright) ``` +```julia +p = scatter(spaced_out_sparsity, times; + ylabel = "Time/s", + yscale = :log10, + xlabel = "Spaced Out Sparsity", + xscale = :log10, + label = algnames_transpose, + title = "Factorization Time vs Spaced Out Sparsity", + fmt = :png, + legend = :outertopright) +``` + +```julia +p = scatter(bandedness_five, times; + ylabel = "Time/s", + yscale = :log10, + xlabel = "Bandedness", + xscale = :log10, + label = algnames_transpose, + title = "Factorization Time vs Bandedness, Bandwidth=5", + fmt = :png, + legend = :outertopright) +``` +```julia +p = scatter(bandedness_ten, times; + ylabel = "Time/s", + yscale = :log10, + xlabel = "Bandedness", + xscale = :log10, + label = algnames_transpose, + title = "Factorization Time vs Bandedness, Bandwidth=10", + fmt = :png, + legend = :outertopright) +``` +```julia +p = scatter(bandedness_twenty, times; + ylabel = "Time/s", + yscale = :log10, + xlabel = "Bandedness", + xscale = :log10, + label = algnames_transpose, + title = "Factorization Time vs Bandedness, Bandwidth=20", + fmt = :png, + legend = :outertopright) +``` ## Appendix diff --git a/benchmarks/LinearSolve/Project.toml b/benchmarks/LinearSolve/Project.toml index 04ab21e57..a61352d59 100644 --- a/benchmarks/LinearSolve/Project.toml +++ b/benchmarks/LinearSolve/Project.toml @@ -16,7 +16,7 @@ VectorizationBase = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" [compat] BenchmarkTools = "1" -LinearSolve = "2.5" +LinearSolve = "3" MatrixDepot = "1" Pardiso = "0.5.4" Plots = "1" diff --git a/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd b/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd index 2fbf2f597..794c49203 100644 --- a/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd +++ b/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd @@ -8,7 +8,7 @@ It is concerned with comparing the performance of various discretization methods ```julia using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra, - LinearSolve, Plots + LinearSolve, Plots, RecursiveFactorization ``` Here is the burgers equation with a Dirichlet and Neumann boundary conditions, diff --git a/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd b/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd index 0a9c4dc58..7338c5195 100644 --- a/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd +++ b/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd @@ -9,7 +9,7 @@ It is concerned with comparing the performance of various discretization methods ```julia using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra, - LinearSolve, Plots + LinearSolve, Plots, RecursiveFactorization using PDESystemLibrary ``` diff --git a/benchmarks/MethodOfLinesPDE/Project.toml b/benchmarks/MethodOfLinesPDE/Project.toml index e5cf7986e..8e12d11e8 100644 --- a/benchmarks/MethodOfLinesPDE/Project.toml +++ b/benchmarks/MethodOfLinesPDE/Project.toml @@ -7,17 +7,19 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PDESystemLibrary = "d14f9848-fe58-4297-bd22-c1aba6f3000d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [compat] DiffEqDevTools = "2" DomainSets = "0.5, 0.6, 0.7" -LinearSolve = "1, 2" +LinearSolve = "3" MethodOfLines = "0.9" ModelingToolkit = "8" OrdinaryDiffEq = "6" PDESystemLibrary = "0.1" Plots = "1" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4" diff --git a/benchmarks/ModelingToolkit/Project.toml b/benchmarks/ModelingToolkit/Project.toml index 2ad635cbc..b395b0b63 100644 --- a/benchmarks/ModelingToolkit/Project.toml +++ b/benchmarks/ModelingToolkit/Project.toml @@ -24,7 +24,7 @@ CairoMakie = "0.11.11" DataFrames = "1" JuliaSimCompiler = "0.1.9" JuliaSimCompilerRuntime = "1.0.0" -LinearSolve = "2.30.0" +LinearSolve = "3" ModelingToolkit = "9.20.0" ModelingToolkitStandardLibrary = "2" Multibody = "0.1.0" diff --git a/benchmarks/NonStiffBVP/Manifest.toml b/benchmarks/NonStiffBVP/Manifest.toml index 4ccb66e02..fb7048d11 100644 --- a/benchmarks/NonStiffBVP/Manifest.toml +++ b/benchmarks/NonStiffBVP/Manifest.toml @@ -1,13 +1,59 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.2" +julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "e85d4ed88ad527fe51d8fe4cd5b2e201d0317b44" +project_hash = "f1421fbb9c367345b6990b111c9cb05464775055" [[deps.ADTypes]] -git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.7" +version = "1.9.0" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" + +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" + +[[deps.AbstractTrees]] +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.5" + +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.38" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" + AccessorsUnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] @@ -19,29 +65,48 @@ weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AdaptivePredicates]] +git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6" +uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" +version = "1.2.0" + +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + +[[deps.Animations]] +deps = ["Colors"] +git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" +uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" +version = "0.4.1" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.2.0" +version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "44691067188f6bd1b2289552a23e4b7572f4528d" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "3640d077b6dafd64ceb8fd5c1ec76f7ca53bcf76" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.9.0" +version = "7.16.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -49,17 +114,19 @@ version = "7.9.0" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "6404a564c24a994814106c374bec893195e19bac" +git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.8.0" +version = "1.10.3" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -68,17 +135,35 @@ weakdeps = ["SparseArrays"] [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[deps.Automa]] +deps = ["PrecompileTools", "TranscodingStreams"] +git-tree-sha1 = "014bc22d6c400a7703c0f5dc1fdc302440cf88be" +uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" +version = "1.0.4" + +[[deps.AxisAlgorithms]] +deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] +git-tree-sha1 = "01b8ccb13d68535d73d2b0c23e39bd23155fb712" +uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" +version = "1.1.0" + +[[deps.AxisArrays]] +deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] +git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f" +uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" +version = "0.4.7" + [[deps.BVProblemLibrary]] deps = ["DiffEqBase", "Markdown", "SpecialFunctions"] -git-tree-sha1 = "5060455207dd27726e1e3854b182f962e50dca27" +git-tree-sha1 = "b2d6c50c2f4de48b35b2ac5d209fabee89626239" uuid = "ded0fc24-dfea-4565-b1d9-79c027d14d84" -version = "0.1.4" +version = "0.1.5" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "c946c5014cf4cdbfacacb363b110e7bffba3e742" +git-tree-sha1 = "a2c85f53ddcb15b4099da59867868bd40f005579" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.6.1" +version = "1.7.5" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -94,21 +179,21 @@ uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.5.0" [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.5" +version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "005b55fa2eebaa4d7bf3cfb8097807f47116175f" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "8dba4ea86fce8ed94977ed9e56cf5c6d67c494e5" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.7.1" +version = "5.11.0" weakdeps = ["ODEInterface"] [deps.BoundaryValueDiffEq.extensions] @@ -120,29 +205,55 @@ git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+1" +[[deps.CEnum]] +git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" +uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" +version = "0.5.0" + [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" +git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.4" +version = "0.2.6" + +[[deps.CRC32c]] +uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" + +[[deps.CRlibm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "e329286945d0cfc04456972ea732551869af1cfc" +uuid = "4e9b3aee-d8a1-5a3d-ad8b-7d824db253f0" +version = "1.0.1+0" + +[[deps.CSV]] +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.10.14" + +[[deps.Cairo]] +deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] +git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" +uuid = "159f3aea-2a34-519c-b102-8c37f9878175" +version = "1.1.0" + +[[deps.CairoMakie]] +deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] +git-tree-sha1 = "7947d2b61995eda7d5ca50c697b12bb578b918e5" +uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +version = "0.12.14" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+1" - -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" +version = "1.18.2+1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.23.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -150,27 +261,33 @@ weakdeps = ["SparseArrays"] [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" +version = "0.7.6" + +[[deps.ColorBrewer]] +deps = ["Colors", "JSON", "Test"] +git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" +uuid = "a2cac450-b92f-5266-8821-25eda20663c8" +version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" +git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.24.0" +version = "3.26.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.11.5" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] @@ -184,9 +301,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.12.11" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -194,16 +311,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.14.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -212,7 +334,16 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.1.0+0" +version = "1.1.1+0" + +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" [[deps.ConcreteStructs]] git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" @@ -221,34 +352,31 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.1" +version = "2.4.2" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "51cab8e982c5b598eea9c8ceaced4b58d9dd37c9" +git-tree-sha1 = "b19db3927f0db4151cb86d073689f2428e524576" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.10.0" +version = "1.10.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" - [deps.ConstructionBase.weakdeps] - IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" - [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" [[deps.CpuId]] deps = ["Markdown"] @@ -256,16 +384,27 @@ git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" uuid = "adafc99b-e345-5852-983c-f28acb93d879" version = "0.3.1" +[[deps.Crayons]] +git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" +uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" +version = "4.1.1" + [[deps.DataAPI]] git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.16.0" +[[deps.DataFrames]] +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" +uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +version = "1.7.0" + [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "0f4b5d62a88d8f59003e43c25a8a90de9eb76317" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.18" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -276,6 +415,18 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + +[[deps.DelaunayTriangulation]] +deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "PrecompileTools", "Random"] +git-tree-sha1 = "668bb97ea6df5e654e6288d87d2243591fe68665" +uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" +version = "1.6.0" + [[deps.DelimitedFiles]] deps = ["Mmap"] git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" @@ -283,12 +434,13 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "b19b2bb1ecd1271334e4b25d605e50f75e68fcae" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "9c36ac68cf6c59a1c2569aadd7a62c47ed5c8eb5" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.148.0" +version = "6.158.1" [deps.DiffEqBase.extensions] + DiffEqBaseCUDAExt = "CUDA" DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] @@ -297,10 +449,12 @@ version = "6.148.0" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" [deps.DiffEqBase.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" @@ -309,20 +463,21 @@ version = "6.148.0" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqDevTools]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] -git-tree-sha1 = "970da8624bc0492ac4cee9625eccc4b6426c90a9" +git-tree-sha1 = "167a3a413b954aca9e64d785f8ea096e23e5afb8" uuid = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" -version = "2.44.2" +version = "2.45.1" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.21.0" +version = "5.23.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -342,6 +497,48 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" +[[deps.DifferentiationInterface]] +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "758ef234ab0b81071c195cd2ea155030d69c1ef8" +uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +version = "0.6.13" + + [deps.DifferentiationInterface.extensions] + DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" + DifferentiationInterfaceDiffractorExt = "Diffractor" + DifferentiationInterfaceEnzymeExt = "Enzyme" + DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" + DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" + DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" + DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" + DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" + DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" @@ -358,10 +555,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.107" +version = "0.25.112" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -384,11 +581,11 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" +[[deps.EarCut_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" +uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" +version = "2.2.4+0" [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" @@ -396,9 +593,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "59c44d8fbc651c0395d8a6eda64b05ce316f58b4" +git-tree-sha1 = "9c3a42611e525352e9ad5e4134ddca5c692ff209" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.5" +version = "0.8.4" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -410,6 +607,12 @@ git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" version = "0.0.20230411+0" +[[deps.ExactPredicates]] +deps = ["IntervalArithmetic", "Random", "StaticArrays"] +git-tree-sha1 = "b3f2ff58735b5f024c392fde763f29b057e4b025" +uuid = "429591f6-91af-11e9-00e2-59fbe8cec110" +version = "2.2.8" + [[deps.ExceptionUnwrapping]] deps = ["Test"] git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" @@ -418,9 +621,9 @@ version = "0.1.10" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.5.0+0" +version = "2.6.2+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -433,11 +636,22 @@ git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.Expronicon]] +deps = ["MLStyle", "Pkg", "TOML"] +git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" +uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" +version = "0.8.5" + +[[deps.Extents]] +git-tree-sha1 = "81023caa0021a41712685887db1fc03db26f41f5" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.4" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -445,17 +659,29 @@ git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" version = "4.4.4+1" +[[deps.FFTW]] +deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] +git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" +uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" +version = "1.8.0" + +[[deps.FFTW_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" +uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" +version = "3.3.10+1" + [[deps.FastAlmostBandedMatrices]] deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] -git-tree-sha1 = "9dc913faf8552fd09b92a0d7fcc25f1d5609d795" +git-tree-sha1 = "3f03d94c71126b6cfe20d3cbcc41c5cd27e1c419" uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" -version = "0.1.1" +version = "0.1.4" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.8" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -464,18 +690,41 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0a59c7d1002f3131de53dc4568a47d15a44daef7" +git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "2.0.2" +version = "2.0.4" + +[[deps.FileIO]] +deps = ["Pkg", "Requires", "UUIDs"] +git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9" +uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +version = "1.16.4" + +[[deps.FilePaths]] +deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] +git-tree-sha1 = "919d9412dbf53a2e6fe74af62a73ceed0bce0629" +uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824" +version = "0.8.3" + +[[deps.FilePathsBase]] +deps = ["Compat", "Dates"] +git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361" +uuid = "48062228-2e41-5def-b9a4-89aafe57970f" +version = "0.9.22" +weakdeps = ["Mmap", "Test"] + + [deps.FilePathsBase.extensions] + FilePathsBaseMmapExt = "Mmap" + FilePathsBaseTestExt = "Test" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" +deps = ["LinearAlgebra"] +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.9.3" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -484,32 +733,34 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "bc0c5092d6caaea112d3c8e3b238d61563c58d5f" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.23.0" +version = "2.26.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] deps = ["Statistics"] -git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[deps.Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.93+0" +version = "2.13.96+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -526,17 +777,29 @@ weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] ForwardDiffStaticArraysExt = "StaticArrays" +[[deps.FreeType]] +deps = ["CEnum", "FreeType2_jll"] +git-tree-sha1 = "907369da0f8e80728ab49c1c7e09327bf0d6d999" +uuid = "b38be410-82b0-50bf-ab77-7b57e271db43" +version = "4.1.1" + [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" +git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.1+0" +version = "2.13.2+0" + +[[deps.FreeTypeAbstraction]] +deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] +git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc" +uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" +version = "0.10.3" [[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.10+0" +version = "1.0.14+0" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -554,10 +817,10 @@ deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.9+0" +version = "3.4.0+1" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -566,16 +829,16 @@ uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "3437ade7073682993e092ca570ad68a2aba26983" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.3" +version = "0.73.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a96d5c713e6aa28c242b0d25c1347e258d6541ab" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.3+0" +version = "0.73.8+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -583,6 +846,23 @@ git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" version = "0.5.4" +[[deps.GeoFormatTypes]] +git-tree-sha1 = "59107c179a586f0fe667024c5eb7033e81333271" +uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" +version = "0.4.2" + +[[deps.GeoInterface]] +deps = ["Extents", "GeoFormatTypes"] +git-tree-sha1 = "2f6fce56cdb8373637a6614e14a5768a88450de2" +uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" +version = "1.3.7" + +[[deps.GeometryBasics]] +deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] +git-tree-sha1 = "b62f2b2d76cee0d61a2ef2b3118cd2a3215d3134" +uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" +version = "0.4.11" + [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" @@ -597,15 +877,21 @@ version = "1.3.1" [[deps.Git_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "12945451c5d0e2d0dca0724c3a8d6448b46bbdf9" +git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.44.0+1" +version = "2.46.2+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.0+0" +version = "2.80.5+0" + +[[deps.Graphics]] +deps = ["Colors", "LinearAlgebra", "NaNMath"] +git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" +uuid = "a2bd30eb-e257-5431-a919-1863eab51364" +version = "1.1.2" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -615,9 +901,15 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.9.0" +version = "1.12.0" + +[[deps.GridLayoutBase]] +deps = ["GeometryBasics", "InteractiveUtils", "Observables"] +git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" +uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" +version = "0.11.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -626,65 +918,180 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "8e59b47b9dc525b70550ca082ce85bcd7f5477cd" +git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.5" +version = "1.10.8" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.3.1+0" [[deps.Highlights]] deps = ["DocStringExtensions", "InteractiveUtils", "REPL"] -git-tree-sha1 = "0341077e8a6b9fc1c2ea5edc1e93a956d2aec0c7" +git-tree-sha1 = "9e13b8d8b1367d9692a90ea4711b4278e4755c32" uuid = "eafb193a-b7ab-5a9e-9068-77385905fa72" -version = "0.5.2" +version = "0.5.3" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.24" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" +git-tree-sha1 = "1702f79fa30f56b68d5b2fd6fb3a9a14ff6f9130" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.2" +version = "1.25.0" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" +[[deps.ImageAxes]] +deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] +git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" +uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" +version = "0.6.11" + +[[deps.ImageBase]] +deps = ["ImageCore", "Reexport"] +git-tree-sha1 = "eb49b82c172811fd2c86759fa0553a2221feb909" +uuid = "c817782e-172a-44cc-b673-b171935fbb9e" +version = "0.1.7" + +[[deps.ImageCore]] +deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] +git-tree-sha1 = "b2a7eaa169c13f5bcae8131a83bc30eff8f71be0" +uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" +version = "0.10.2" + +[[deps.ImageIO]] +deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] +git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" +uuid = 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[deps.InlineStrings.extensions] + ArrowTypesExt = "ArrowTypes" + ParsersExt = "Parsers" + + [deps.InlineStrings.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" + Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.0.2+0" +version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[deps.Interpolations]] +deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "88a101217d7cb38a7b481ccd50d21876e1d1b0e0" +uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" +version = "0.15.1" +weakdeps = ["Unitful"] + + [deps.Interpolations.extensions] + InterpolationsUnitfulExt = "Unitful" + +[[deps.IntervalArithmetic]] +deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] +git-tree-sha1 = "8e125d40cae3a9f4276cdfeb4fcdb1828888a4b3" +uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" +version = "0.22.17" +weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "LinearAlgebra", "RecipesBase"] + + [deps.IntervalArithmetic.extensions] + IntervalArithmeticDiffRulesExt = "DiffRules" + IntervalArithmeticForwardDiffExt = "ForwardDiff" + IntervalArithmeticIntervalSetsExt = "IntervalSets" + IntervalArithmeticLinearAlgebraExt = "LinearAlgebra" + IntervalArithmeticRecipesBaseExt = "RecipesBase" + +[[deps.IntervalSets]] +git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" +uuid = "8197267c-284f-5f27-9208-e0e47529a953" +version = "0.7.10" +weakdeps = ["Random", "RecipesBase", "Statistics"] + + [deps.IntervalSets.extensions] + IntervalSetsRandomExt = "Random" + IntervalSetsRecipesBaseExt = "RecipesBase" + IntervalSetsStatisticsExt = "Statistics" + +[[deps.InverseFunctions]] +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.17" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + +[[deps.InvertedIndices]] +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" +uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" +version = "1.3.0" + [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" +[[deps.Isoband]] +deps = ["isoband_jll"] +git-tree-sha1 = "f9b6d97355599074dc867318950adaa6f9946137" +uuid = "f1662d9f-8043-43de-a69a-05efc1cc6ff4" +version = "0.1.1" + +[[deps.IterTools]] +git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" +uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" +version = "1.10.0" + [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" @@ -692,15 +1099,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -708,11 +1115,17 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" +[[deps.JpegTurbo]] +deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] +git-tree-sha1 = "fa6d0bcff8583bac20f1ffa708c3913ca605c611" +uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" +version = "0.1.5" + [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3336abae9a713d2210bb57ab484b1e065edd7d23" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.2+0" +version = "3.0.4+0" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -720,75 +1133,96 @@ git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" version = "0.6.0" +[[deps.KernelDensity]] +deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] +git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1" +uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" +version = "0.6.9" + [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "8a6837ec02fe5fb3def1abc907bb802ef11a0729" +git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.5" +version = "0.9.6" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "18.1.7+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "cad560042a7cc108f5a4c24ea1431a9221f22c1b" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.2" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.15" +version = "0.1.17" [[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "9cfca23ab83b0dfac93cb1a1ef3331ab9fe596a5" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "360f6039babd6e4d6364eff0d4fc9120834a2d9a" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.8.3" -weakdeps = ["StaticArrays"] +version = "2.2.1" [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" LazyArraysStaticArraysExt = "StaticArrays" + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +[[deps.LazyModules]] +git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" +uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e" +version = "0.3.1" + [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" @@ -823,10 +1257,10 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.8.11+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -835,10 +1269,10 @@ uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" version = "1.6.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.49.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -848,27 +1282,43 @@ version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dae976433497a2f841baadea93d27e68f1a12a97" +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.39.3+0" +version = "2.40.1+0" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0a04a1318df1bf510beb2562cf90fb0c386f58c4" +git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.39.3+1" +version = "2.40.1+0" + +[[deps.LightXML]] +deps = ["Libdl", "XML2_jll"] +git-tree-sha1 = "3a994404d3f6709610701c7dabfc03fed87a81f8" +uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179" +version = "0.9.1" + +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "dc82b3c3640a4362f09e4d7594b4387a820857e4" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.3" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -876,16 +1326,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "775e5e5d9ace42ef8deeb236587abc69e70dc455" +git-tree-sha1 = "8941ad4bdd83768359801982e143008349b1a827" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.28.0" +version = "2.35.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -898,7 +1349,7 @@ version = "2.28.0" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -911,9 +1362,9 @@ version = "2.28.0" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" +git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" +version = "0.3.28" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -936,9 +1387,9 @@ version = "1.0.3" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.166" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -946,10 +1397,15 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] SpecialFunctionsExt = "SpecialFunctions" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.0.0+0" +version = "2024.2.0+0" + +[[deps.MLStyle]] +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" +uuid = "d8e11817-5142-5d16-987a-aa16d5891078" +version = "0.4.17" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -957,26 +1413,57 @@ git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.13" +[[deps.Makie]] +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "3df66da15ba7b37b34f6557b7e1c95a3ff5c670b" +uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" +version = "0.21.14" + +[[deps.MakieCore]] +deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] +git-tree-sha1 = "4604f03e5b057e8e62a95a44929cafc9585b0fe9" +uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" +version = "0.8.9" + [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" version = "0.1.8" +[[deps.MappedArrays]] +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" +uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" +version = "0.4.2" + [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MathTeXEngine]] +deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] +git-tree-sha1 = "e1641f32ae592e415e3dbae7f4a188b5316d4b62" +uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" +version = "0.6.1" + [[deps.MatrixFactorizations]] deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "78f6e33434939b0ac9ba1df81e6d005ee85a7396" +git-tree-sha1 = "16a726dba99685d9e94c8d0a8f655383121fc608" uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.1.0" +version = "3.0.1" +weakdeps = ["BandedMatrices"] + + [deps.MatrixFactorizations.extensions] + MatrixFactorizationsBandedMatricesExt = "BandedMatrices" [[deps.MaybeInplace]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "a85c6a98c9e5a2a7046bc1bb89f28a3241e1de4d" +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" -version = "0.1.1" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -996,13 +1483,19 @@ version = "0.3.2" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +[[deps.MosaicViews]] +deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] +git-tree-sha1 = "7b86a5d4d70a9f5cdf2dacb3cbe6d251d1a61dbe" +uuid = "e94cdb99-869f-56ef-bcf0-1ae2bcbe0389" +version = "0.3.4" + [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2023.1.10" @@ -1014,9 +1507,9 @@ version = "0.2.4" [[deps.Mustache]] deps = ["Printf", "Tables"] -git-tree-sha1 = "a7cefa21a2ff993bff0456bf7521f46fc077ddf1" +git-tree-sha1 = "3b2db451a872b20519ebb0cec759d3d81a1c6bcb" uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.19" +version = "1.0.20" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1036,15 +1529,21 @@ git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" version = "1.0.2" +[[deps.Netpbm]] +deps = ["FileIO", "ImageCore", "ImageMetadata"] +git-tree-sha1 = 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"Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.8.3" +version = "3.15.1" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -1056,8 +1555,6 @@ version = "3.8.3" NonlinearSolveNLsolveExt = "NLsolve" NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" [deps.NonlinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" @@ -1069,8 +1566,6 @@ version = "3.8.3" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.ODEInterface]] deps = ["Dates", "Libdl", "LinearAlgebra", "Markdown", "ODEInterface_jll", "Unicode"] @@ -1084,10 +1579,21 @@ git-tree-sha1 = "3021aa85a1cd566a533635246b7ed31a29c72c93" uuid = "c771fb93-2439-5ece-a3b3-58fecce82101" version = "0.0.1+0" +[[deps.OMJulia]] +deps = ["DataFrames", "DataStructures", "LightXML", "Random", "ZMQ"] +git-tree-sha1 = "5f2b4eb7fed3c1ac9108c72996bd1ac47da1c940" +uuid = "0f4fe800-344e-11e9-2949-fb537ad918e1" +version = "0.3.2" + +[[deps.Observables]] +git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" +uuid = "510215fc-4207-5dde-b226-833fc4488ee2" +version = "0.5.5" + [[deps.OffsetArrays]] -git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621" +git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.13.0" +version = "1.14.1" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1104,6 +1610,18 @@ deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" version = "0.3.23+4" +[[deps.OpenEXR]] +deps = ["Colors", "FileIO", "OpenEXR_jll"] +git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" +uuid = "52e1d378-f018-4a11-a4be-720524705ac7" +version = "0.3.2" + +[[deps.OpenEXR_jll]] +deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "8292dd5c8a38257111ada2174000a33745b06d4e" +uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" +version = "3.2.4+0" + [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" @@ -1111,15 +1629,15 @@ version = "0.8.1+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "af81a32750ebc831ee28bdaaba6e1067decef51e" +git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" uuid = 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"SparseArrays", "StatsBase"] +git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.3" +version = "1.9.4" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -1140,10 +1658,10 @@ version = "1.9.3" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.2+0" +version = "1.3.3+0" [[deps.OrderedCollections]] git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" @@ -1151,10 +1669,194 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", 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"RecursiveArrayTools", "Reexport", "Static"] +git-tree-sha1 = "332f9d17d0229218f66a73492162267359ba85e9" +uuid = "04162be5-8125-4266-98ed-640baecc6514" +version = "1.1.0" + +[[deps.OrdinaryDiffEqRKN]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "41c09d9c20877546490f907d8dffdd52690dd65f" +uuid = "af6ede74-add8-4cfd-b1df-9a4dbb109d7a" +version = "1.1.0" + +[[deps.OrdinaryDiffEqRosenbrock]] +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] +git-tree-sha1 = "96b47cdd12cb4ce8f70d701b49f855271a462bd4" +uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" +version = "1.2.0" + +[[deps.OrdinaryDiffEqSDIRK]] +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] +git-tree-sha1 = "f6683803a58de600ab7a26d2f49411c9923e9721" +uuid = "2d112036-d095-4a1e-ab9a-08536f3ecdbf" +version = "1.1.0" + +[[deps.OrdinaryDiffEqSSPRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] +git-tree-sha1 = "7dbe4ac56f930df5e9abd003cedb54e25cbbea86" +uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" +version = "1.2.0" + +[[deps.OrdinaryDiffEqStabilizedIRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "StaticArrays"] +git-tree-sha1 = "348fd6def9a88518715425025eadd58517017325" +uuid = "e3e12d00-db14-5390-b879-ac3dd2ef6296" +version = "1.1.0" + +[[deps.OrdinaryDiffEqStabilizedRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "StaticArrays"] +git-tree-sha1 = "1b0d894c880e25f7d0b022d7257638cf8ce5b311" +uuid = "358294b1-0aab-51c3-aafe-ad5ab194a2ad" +version = "1.1.0" + +[[deps.OrdinaryDiffEqSymplecticRK]] +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "4e8b8c8b81df3df17e2eb4603115db3b30a88235" +uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" +version = "1.1.0" + +[[deps.OrdinaryDiffEqTsit5]] +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "96552f7d4619fabab4038a29ed37dd55e9eb513a" +uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" +version = "1.1.0" + +[[deps.OrdinaryDiffEqVerner]] +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "81d7841e73e385b9925d5c8e4427f2adcdda55db" +uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" +version = "1.1.1" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1167,12 +1869,36 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.31" +[[deps.PNGFiles]] +deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] +git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd" +uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" +version = "0.4.3" + [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" version = "1.0.2" weakdeps = ["Requires", "TOML"] +[[deps.Packing]] +deps = ["GeometryBasics"] +git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501" +uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" +version = "0.5.0" + +[[deps.PaddedViews]] +deps = ["OffsetArrays"] +git-tree-sha1 = "0fac6313486baae819364c52b4f483450a9d793f" +uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" +version = "0.5.12" + +[[deps.Pango_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +uuid = "36c8627f-9965-5494-a995-c6b170f724f3" +version = "1.54.1+0" + [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" @@ -1192,20 +1918,26 @@ version = "1.3.0" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" +git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.42.2+0" +version = "0.43.4+0" [[deps.Pkg]] 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 = "1.10.0" +[[deps.PkgVersion]] +deps = ["Pkg"] +git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" +uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" +version = "0.3.3" + [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" +git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.1.0" +version = "3.2.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] @@ -1214,10 +1946,10 @@ uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" version = "1.4.1" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "3c403c6590dd93b36752634115e20137e79ab4df" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "45470145863035bb124ca51b320ed35d071cc6c2" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.2" +version = "1.40.8" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1240,16 +1972,27 @@ uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.4" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "8df43bbe60029526dd628af7e9951f5af680d4d7" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.10" +version = "0.7.16" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.2.1" +version = "0.2.2" + +[[deps.PolygonOps]] +git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" +uuid = "647866c9-e3ac-4575-94e7-e3d426903924" +version = "0.1.2" + +[[deps.PooledArrays]] +deps = ["DataAPI", "Future"] +git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3" +uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" +version = "1.4.3" [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1259,9 +2002,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "b6665214f2d0739f2d09a17474dd443b9139784a" +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.20" +version = "0.4.24" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -1281,6 +2024,12 @@ git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.4.3" +[[deps.PrettyTables]] +deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" +uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" +version = "2.4.0" + [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" @@ -1289,17 +2038,58 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" deps = ["Printf"] uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" +[[deps.ProgressMeter]] +deps = ["Distributed", "Printf"] +git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" +uuid = "92933f4c-e287-5a05-a399-4b506db050ca" +version = "1.10.2" + +[[deps.PtrArrays]] +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" +version = "1.2.1" + +[[deps.QOI]] +deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] +git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" +uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" +version = "1.0.0" + [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] -git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b" +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.5.3+1" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.11.1" + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" + + [deps.QuadGK.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1316,10 +2106,25 @@ uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" + +[[deps.RangeArrays]] +git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" +uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" +version = "0.3.2" + +[[deps.Ratios]] +deps = ["Requires"] +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" +uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" +version = "0.4.5" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1334,10 +2139,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d8f131090f2e44b145084928856a561c83f43b27" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.13.0" +version = "3.27.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1345,6 +2150,7 @@ version = "3.13.0" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -1354,14 +2160,15 @@ version = "3.13.0" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "8bc86c78c7d8e2a5fe559e3721c0f9c9e303b2ed" +git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.21" +version = "0.2.23" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1388,36 +2195,47 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.5.1+0" [[deps.RootedTrees]] deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] -git-tree-sha1 = "056631b852ff2b349fc4fc30c7ec01d5ffff5834" +git-tree-sha1 = "c0c464d3063e46e4128d21fd677ca575ace44fdc" uuid = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c" -version = "2.21.0" +version = "2.23.1" weakdeps = ["Plots"] [deps.RootedTrees.extensions] PlotsExt = "Plots" +[[deps.RoundingEmulator]] +git-tree-sha1 = "40b9edad2e5287e05bd413a38f61a8ff55b9557b" +uuid = "5eaf0fd0-dfba-4ccb-bf02-d820a40db705" +version = "0.2.1" + [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" +[[deps.SIMD]] +deps = ["PrecompileTools"] +git-tree-sha1 = "98ca7c29edd6fc79cd74c61accb7010a4e7aee33" +uuid = "fdea26ae-647d-5447-a871-4b548cad5224" +version = "3.6.0" + [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1425,15 +2243,15 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.42" +version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d15c65e25615272e1b1c5edb1d307484c7942824" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "50ed64cd5ad79b0bef71fdb6a11d10c3448bfef0" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.31.0" +version = "2.56.1" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1455,21 +2273,33 @@ version = "2.31.0" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLBenchmarks]] -deps = ["Git", "IJulia", "InteractiveUtils", "Markdown", "Pkg", "Weave"] +deps = ["CSV", "DataFrames", "Git", "IJulia", "InteractiveUtils", "Markdown", "OMJulia", "Pkg", "Weave"] path = "../.." uuid = "31c91b34-3c75-11e9-0341-95557aab0344" version = "0.1.3" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "991d2a8900e687e2c693d587daa739c8fda01366" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.0" + [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "10499f619ef6e890f3f4a38914481cc868689cd5" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "e39c5f217f9aca640c8e27ab21acf557a3967db5" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.8" +version = "0.3.10" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLStructures]] -git-tree-sha1 = "5833c10ce83d690c124beedfe5f621b50b02ba4d" +deps = ["ArrayInterface"] +git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.1.0" +version = "1.5.0" [[deps.Scratch]] deps = ["Dates"] @@ -1477,6 +2307,12 @@ git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" uuid = "6c6a2e73-6563-6170-7368-637461726353" version = "1.2.1" +[[deps.SentinelArrays]] +deps = ["Dates", "Random"] +git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" +uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" +version = "1.4.5" + [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1486,6 +2322,12 @@ git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" version = "1.1.1" +[[deps.ShaderAbstractions]] +deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays", "StructArrays", "Tables"] +git-tree-sha1 = "79123bc60c5507f035e6d1d9e563bb2971954ec8" +uuid = "65257c39-d410-5151-9873-9b3e5be5013e" +version = "0.4.1" + [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" @@ -1496,30 +2338,38 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" +[[deps.SignedDistanceFields]] +deps = ["Random", "Statistics", "Test"] +git-tree-sha1 = "d263a08ec505853a5ff1c1ebde2070419e3f28e9" +uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" +version = "0.4.0" + +[[deps.SimpleBoundaryValueDiffEq]] +deps = ["DiffEqBase", "FiniteDiff", "OrdinaryDiffEqTsit5", "Reexport", "SciMLBase", "SimpleNonlinearSolve"] +git-tree-sha1 = "e9c13c7126be6d19a1af9306bd7185bcd0da0cf1" +uuid = "be0294bd-f90f-4760-ac4e-3421ce2b2da0" +version = "1.1.0" + [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "a535ae5083708f59e75d5bb3042c36d1be9bc778" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.6.0" +version = "1.12.3" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" - SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" - SimpleNonlinearSolveStaticArraysExt = "StaticArrays" SimpleNonlinearSolveTrackerExt = "Tracker" SimpleNonlinearSolveZygoteExt = "Zygote" [deps.SimpleNonlinearSolve.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -1534,6 +2384,12 @@ git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" version = "1.1.0" +[[deps.Sixel]] +deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"] +git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6" +uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" +version = "0.1.3" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1554,11 +2410,31 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "35d346f6aa78814859f1f69cd4f41c24108afa00" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.7" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "a616ac46c38da60ac05cecf52064d44732edd05e" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.17.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -1574,6 +2450,16 @@ version = "2.17.0" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SparseMatrixColorings]] +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "ccc32032d8f6790ad198c99fb8ef20d8100a0de4" +uuid = "0a514795-09f3-496d-8182-132a7b665d35" +version = "0.4.7" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1582,25 +2468,31 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" +[[deps.StackViews]] +deps = ["OffsetArrays"] +git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" +uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" +version = "0.1.1" + [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.10" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.5.0" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1609,9 +2501,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2" +git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.3" +version = "1.9.7" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -1619,9 +2511,9 @@ weakdeps = ["ChainRulesCore", "Statistics"] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1636,29 +2528,26 @@ version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf" +git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.2" +version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" +weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.StrideArraysCore]] -deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.2" +version = "0.5.7" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1666,6 +2555,12 @@ git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" version = "0.3.7" +[[deps.StringManipulation]] +deps = ["PrecompileTools"] +git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.4.0" + [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" @@ -1689,10 +2584,10 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] -deps = ["ArrayInterface", "MacroTools", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "dd94edee1542e9da422cb2f12494ef09ea823e48" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "b708e5c01d4aad69c148241bda3346fda1c550d2" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.13" +version = "0.3.32" [[deps.TOML]] deps = ["Dates"] @@ -1706,10 +2601,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1732,31 +2627,33 @@ git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" version = "0.5.2" +[[deps.TiffImages]] +deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] +git-tree-sha1 = "38f139cc4abf345dd4f22286ec000728d5e8e097" +uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" +version = "0.10.2" + [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.25" [[deps.TranscodingStreams]] -git-tree-sha1 = "14389d51751169994b2e1317d5c72f7dc4f21045" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.6" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.20" +version = "0.2.1" -[[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" -uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +[[deps.TriplotBase]] +git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" +uuid = "981d1d27-644d-49a2-9326-4793e63143c3" +version = "0.1.0" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -1789,23 +2686,20 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.19.0" +version = "1.21.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1814,9 +2708,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.65" +version = "0.21.70" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -1847,41 +2741,58 @@ git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" version = "1.31.0+0" +[[deps.WeakRefStrings]] +deps = ["DataAPI", "InlineStrings", "Parsers"] +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" +version = "1.4.2" + [[deps.Weave]] deps = ["Base64", "Dates", "Highlights", "JSON", "Markdown", "Mustache", "Pkg", "Printf", "REPL", "RelocatableFolders", "Requires", "Serialization", "YAML"] git-tree-sha1 = "092217eb5443926d200ae9325f103906efbb68b1" uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9" version = "0.10.12" +[[deps.WoodburyMatrices]] +deps = ["LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" +uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" +version = "1.0.0" + +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "07e470dabc5a6a4254ffebc29a1b3fc01464e105" +git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.5+0" +version = "2.13.3+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "31c421e5516a6248dfb22c194519e37effbf1f30" +git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.1+0" +version = "5.4.6+0" [[deps.Xorg_libICE_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "e5becd4411063bdcac16be8b66fc2f9f6f1e8fe5" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.0.10+1" +version = "1.1.1+0" [[deps.Xorg_libSM_jll]] -deps = ["Libdl", "Pkg", "Xorg_libICE_jll"] -git-tree-sha1 = "4a9d9e4c180e1e8119b5ffc224a7b59d3a7f7e18" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.3+0" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -1908,10 +2819,10 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -1938,10 +2849,10 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1951,9 +2862,9 @@ version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+0" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -2017,15 +2928,15 @@ version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" +git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.9" +version = "0.4.12" [[deps.ZMQ]] -deps = ["FileWatching", "Sockets", "ZeroMQ_jll"] -git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77" +deps = ["FileWatching", "PrecompileTools", "Sockets", "ZeroMQ_jll"] +git-tree-sha1 = "18cfd00df3cbbebf8ea4ec7ea6bbceb3af716bd0" uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1" -version = "1.2.2" +version = "1.3.0" [[deps.ZeroMQ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "libsodium_jll"] @@ -2040,9 +2951,9 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+1" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] @@ -2052,9 +2963,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.53.0+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2062,22 +2973,34 @@ git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" version = "3.1.1+0" -[[deps.libaom_jll]] +[[deps.isoband_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" +uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" +version = "0.2.3+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" +version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" +version = "5.11.0+0" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2086,10 +3009,10 @@ uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" version = "1.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libinput_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] @@ -2099,21 +3022,27 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" + +[[deps.libsixel_jll]] +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] +git-tree-sha1 = "7dfa0fd9c783d3d0cc43ea1af53d69ba45c447df" +uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" +version = "1.10.3+1" [[deps.libsodium_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e" +git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+0" +version = "1.0.20+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2126,6 +3055,12 @@ deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.52.0+1" +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/benchmarks/NonStiffBVP/Project.toml b/benchmarks/NonStiffBVP/Project.toml index c8354e857..463047d35 100644 --- a/benchmarks/NonStiffBVP/Project.toml +++ b/benchmarks/NonStiffBVP/Project.toml @@ -2,18 +2,22 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" BoundaryValueDiffEq = "764a87c0-6b3e-53db-9096-fe964310641d" BVProblemLibrary = "ded0fc24-dfea-4565-b1d9-79c027d14d84" +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" +SimpleBoundaryValueDiffEq = "be0294bd-f90f-4760-ac4e-3421ce2b2da0" [compat] BenchmarkTools = "1" -BoundaryValueDiffEq = "5.6.3" +BoundaryValueDiffEq = "5.10" BVProblemLibrary = "0.1.4" +CairoMakie = "0.12" DiffEqDevTools = "2.42.0" ODEInterface = "0.5" OrdinaryDiffEq = "6" Plots = "1.4" SciMLBenchmarks = "0.1" +SimpleBoundaryValueDiffEq = "1.0.0" \ No newline at end of file diff --git a/benchmarks/NonStiffBVP/linear_wpd.jmd b/benchmarks/NonStiffBVP/linear_wpd.jmd index 23d14df7d..69df9230a 100644 --- a/benchmarks/NonStiffBVP/linear_wpd.jmd +++ b/benchmarks/NonStiffBVP/linear_wpd.jmd @@ -3,47 +3,53 @@ title: Linear BVP Benchmarks author: Qingyu Qu --- -This benchmark compares the runtime and error of BVP solvers, including MIRK solvers, Shooting solvers and FORTRAN BVP solvers on some linear boundary value problems. -The testing BVPs are a set of standard BVP test problems as described [here](https://archimede.uniba.it/~bvpsolvers/testsetbvpsolvers/?page_id=29) +This benchmark compares the runtime and error of BVP solvers, including MIRK solvers, FIRK solvers, Shooting solvers and FORTRAN BVP solvers on linear boundary value problems. +The testing BVPs are a set of standard BVP test problems as described [here](https://archimede.uniba.it/~bvpsolvers/testsetbvpsolvers/?page_id=29). +The problems are implemented in [BVProblemLibrary.jl](https://github.com/SciML/DiffEqProblemLibrary.jl/blob/master/lib/BVProblemLibrary/src/BVProblemLibrary.jl), where you can find the problem function declarations. +For each problem, we test the following solvers: + +- BoundaryValueDiffEq.jl's MIRK methods(including `MIRK4`, `MIRK5`, `MIRK6`). +- BoundaryValueDiffEq.jl's Shooting methods(including `Shooting`, `MultipleShooting`). +- BoundaryValueDiffEq.jl's FIRK methods(including `RadauIIa3`, `RadauIIa5`, `RadauIIa7`, `LobattoIIIa4`, `LobattoIIIa5`, `LobattoIIIb4`, `LobattoIIIb5`, `LobattoIIIc4`, `LobattoIIIc5`). +- SimpleBoundaryValueDiffEq.jl's MIRK methods(including `SimpleMIRK4`, `SimpleMIRK5`, `SimpleMIRK6`). +- FORTRAN BVP solvers from ODEInterface.jl(including `BVPM2` and `COLNEW`). # Setup Fetch required packages. ```julia -using BoundaryValueDiffEq, OrdinaryDiffEq, ODEInterface, DiffEqDevTools, BenchmarkTools, - BVProblemLibrary, Plots +using BoundaryValueDiffEq, SimpleBoundaryValueDiffEq, OrdinaryDiffEq, ODEInterface, DiffEqDevTools, BenchmarkTools, + BVProblemLibrary, CairoMakie ``` Set up the benchmarked solvers. ```julia -setups = [ Dict(:alg=>MIRK2(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>MIRK3(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>MIRK4(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>MIRK5(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>MIRK6(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>BVPM2(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>COLNEW(), :dts=>1.0 ./ 10.0 .^ (1:4)), - Dict(:alg=>Shooting(Tsit5())), - Dict(:alg=>Shooting(Vern7())), - Dict(:alg=>Shooting(DP5())), - Dict(:alg=>MultipleShooting(10, Tsit5())), - Dict(:alg=>MultipleShooting(10, Vern7())), - Dict(:alg=>MultipleShooting(10, DP5())),] -labels = ["MIRK2"; - "MIRK3"; - "MIRK4"; - "MIRK5"; - "MIRK6"; - "BVPM2"; - "COLNEW"; - "Shooting (Tsit5)"; - "Shooting (Vern7)"; - "Shooting (DP5)"; - "MultipleShooting (Tsit5)"; - "MultipleShooting (Vern7)"; - "MultipleShooting (DP5)"]; +solvers_all = [ + (; pkg = :boundaryvaluediffeq, type = :mirk, name = "MIRK4", solver = Dict(:alg => MIRK4(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :mirk, name = "MIRK5", solver = Dict(:alg => MIRK5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :mirk, name = "MIRK6", solver = Dict(:alg => MIRK6(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa3", solver = Dict(:alg => RadauIIa3(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa5", solver = Dict(:alg => RadauIIa5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa7", solver = Dict(:alg => RadauIIa7(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIa4", solver = Dict(:alg => LobattoIIIa4(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIa5", solver = Dict(:alg => LobattoIIIa5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb4", solver = Dict(:alg => LobattoIIIb4(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb5", solver = Dict(:alg => LobattoIIIb5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIc4", solver = Dict(:alg => LobattoIIIc4(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIc5", solver = Dict(:alg => LobattoIIIc5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :shooting, name = "Single Shooting", solver = Dict(:alg => Shooting(Tsit5(), NewtonRaphson()), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :boundaryvaluediffeq, type = :shooting, name = "Multiple Shooting", solver = Dict(:alg => MultipleShooting(10, Tsit5()), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :simpleboundaryvaluediffeq, type = :simplemirk, name = "SimpleMIRK4", solver = Dict(:alg => SimpleMIRK4(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :simpleboundaryvaluediffeq, type = :simplemirk, name = "SimpleMIRK5", solver = Dict(:alg => SimpleMIRK5(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :simpleboundaryvaluediffeq, type = :simplemirk, name = "SimpleMIRK6", solver = Dict(:alg => SimpleMIRK6(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :wrapper, type = :general, name = "BVPM2", solver = Dict(:alg => BVPM2(), :dts=>1.0 ./ 10.0 .^ (1:4))), + (; pkg = :wrapper, type = :general, name = "COLNEW", solver = Dict(:alg => COLNEW(), :dts=>1.0 ./ 10.0 .^ (1:4))), +]; + +solver_tracker = []; +wp_general_tracker = []; ``` Sets tolerances. @@ -53,150 +59,295 @@ abstols = 1.0 ./ 10.0 .^ (1:3) reltols = 1.0 ./ 10.0 .^ (1:3); ``` -# Benchmarks - -We here run the BVP benchmarks for all the MIRK methods, Shooting methods and FORTRAN BVP solvers. - Prepares helper function for benchmarking a specific problem. ```julia -function benchmark!(prob) +function benchmark(prob) sol = solve(prob, Shooting(Vern7()), abstol=1e-14, reltol=1e-14) testsol = TestSolution(sol) - wp = WorkPrecisionSet(prob, abstols, reltols, setups; names = labels, appxsol = testsol, maxiters=Int(1e4)) - plot(wp, legend=:outertopright) + wps = WorkPrecisionSet(prob, abstols, reltols, getfield.(solvers_all, :solver); names = getfield.(solvers_all, :name), appxsol = testsol, maxiters=Int(1e4)) + push!(wp_general_tracker, wps) + return wps +end + +function plot_wpd(wp_set) + fig = begin + LINESTYLES = Dict(:boundaryvaluediffeq => :solid, :simpleboundaryvaluediffeq => :dash, :wrapper => :dot) + ASPECT_RATIO = 0.7 + WIDTH = 1200 + HEIGHT = round(Int, WIDTH * ASPECT_RATIO) + STROKEWIDTH = 2.5 + + colors = cgrad(:seaborn_bright, length(solvers_all); categorical = true) + cycle = Cycle([:marker], covary = true) + plot_theme = Theme(Lines = (; cycle), Scatter = (; cycle)) + + with_theme(plot_theme) do + fig = Figure(; size = (WIDTH, HEIGHT)) + ax = Axis(fig[1, 1], ylabel = L"Time $\mathbf{(s)}$", + xlabelsize = 22, ylabelsize = 22, + xlabel = L"Error: $\mathbf{||f(u^\ast)||_\infty}$", + xscale = log10, yscale = log10, xtickwidth = STROKEWIDTH, + ytickwidth = STROKEWIDTH, spinewidth = STROKEWIDTH, + xticklabelsize = 20, yticklabelsize = 20) + + idxs = sortperm(median.(getfield.(wp_set.wps, :times))) + + ls, scs = [], [] + + for (i, (wp, solver)) in enumerate(zip(wp_set.wps[idxs], solvers_all[idxs])) + (; name, times, errors) = wp + errors = [err.l∞ for err in errors] + l = lines!(ax, errors, times; linestyle = LINESTYLES[solver.pkg], label = name, + linewidth = 5, color = colors[i]) + sc = scatter!(ax, errors, times; label = name, markersize = 16, strokewidth = 2, + color = colors[i]) + push!(ls, l) + push!(scs, sc) + end + + xlims!(ax; high=1) + ylims!(ax; low=5e-6) + + axislegend(ax, [[l, sc] for (l, sc) in zip(ls, scs)], + [solver.name for solver in solvers_all[idxs]], "BVP Solvers"; + framevisible=true, framewidth = STROKEWIDTH, position = :rb, + titlesize = 20, labelsize = 16, patchsize = (40.0f0, 20.0f0)) + + fig[0, :] = Label(fig, "Linear BVP Benchmark", + fontsize = 24, tellwidth = false, font = :bold) + fig + end + end end ``` -## Linear boundary value problems +# Benchmarks + +We here run benchmarks for each of the 18 test problems. ### Linear BVP 1 ```julia prob_1 = BVProblemLibrary.prob_bvp_linear_1 -benchmark!(prob_1) +wps = benchmark(prob_1) +plot_wpd(wps) ``` ### Linear BVP 2 ```julia prob_2 = BVProblemLibrary.prob_bvp_linear_2 -benchmark!(prob_2) +wps = benchmark(prob_2) +plot_wpd(wps) ``` ### Linear BVP 3 ```julia prob_3 = BVProblemLibrary.prob_bvp_linear_3 -benchmark!(prob_3) +wps = benchmark(prob_3) +plot_wpd(wps) ``` ### Linear BVP 4 ```julia prob_4 = BVProblemLibrary.prob_bvp_linear_4 -benchmark!(prob_4) +wps = benchmark(prob_4) +plot_wpd(wps) ``` ### Linear BVP 5 ```julia prob_5 = BVProblemLibrary.prob_bvp_linear_5 -benchmark!(prob_5) +wps = benchmark(prob_5) +plot_wpd(wps) ``` ### Linear BVP 6 ```julia prob_6 = BVProblemLibrary.prob_bvp_linear_6 -benchmark!(prob_6) +wps = benchmark(prob_6) +plot_wpd(wps) ``` ### Linear BVP 7 ```julia prob_7 = BVProblemLibrary.prob_bvp_linear_7 -benchmark!(prob_7) +wps = benchmark(prob_7) +plot_wpd(wps) ``` ### Linear BVP 8 ```julia prob_8 = BVProblemLibrary.prob_bvp_linear_8 -benchmark!(prob_8) +wps = benchmark(prob_8) +plot_wpd(wps) ``` ### Linear BVP 9 ```julia prob_9 = BVProblemLibrary.prob_bvp_linear_9 -benchmark!(prob_9) +wps = benchmark(prob_9) +plot_wpd(wps) ``` ### Linear BVP 10 ```julia prob_10 = BVProblemLibrary.prob_bvp_linear_10 -benchmark!(prob_10) +wps = benchmark(prob_10) +plot_wpd(wps) ``` ### Linear BVP 11 ```julia prob_11 = BVProblemLibrary.prob_bvp_linear_11 -benchmark!(prob_11) +wps = benchmark(prob_11) +plot_wpd(wps) ``` ### Linear BVP 12 ```julia prob_12 = BVProblemLibrary.prob_bvp_linear_12 -benchmark!(prob_12) +wps = benchmark(prob_12) +plot_wpd(wps) ``` ### Linear BVP 13 ```julia prob_13 = BVProblemLibrary.prob_bvp_linear_13 -benchmark!(prob_13) +wps = benchmark(prob_13) +plot_wpd(wps) ``` ### Linear BVP 14 ```julia prob_14 = BVProblemLibrary.prob_bvp_linear_14 -benchmark!(prob_14) +wps = benchmark(prob_14) +plot_wpd(wps) ``` ### Linear BVP 15 ```julia prob_15 = BVProblemLibrary.prob_bvp_linear_15 -benchmark!(prob_15) +wps = benchmark(prob_15) +plot_wpd(wps) ``` ### Linear BVP 16 ```julia prob_16 = BVProblemLibrary.prob_bvp_linear_16 -benchmark!(prob_16) +wps = benchmark(prob_16) +plot_wpd(wps) ``` ### Linear BVP 17 ```julia prob_17 = BVProblemLibrary.prob_bvp_linear_17 -benchmark!(prob_17) +wps = benchmark(prob_17) +plot_wpd(wps) ``` ### Linear BVP 18 ```julia prob_18 = BVProblemLibrary.prob_bvp_linear_18 -benchmark!(prob_18) +wps = benchmark(prob_18) +plot_wpd(wps) +``` + +# Summary of General Solvers Performance on All Problems + +```julia +fig = begin + LINESTYLES = Dict(:boundaryvaluediffeq => :solid, :simpleboundaryvaluediffeq => :dash, :wrapper => :dot) + ASPECT_RATIO = 0.7 + WIDTH = 1800 + HEIGHT = round(Int, WIDTH * ASPECT_RATIO) + STROKEWIDTH = 2.5 + + colors = cgrad(:seaborn_bright, length(solvers_all); categorical = true) + cycle = Cycle([:marker], covary = true) + plot_theme = Theme(Lines = (; cycle), Scatter = (; cycle)) + + with_theme(plot_theme) do + fig = Figure(; size = (WIDTH, HEIGHT)) + + axs = Matrix{Any}(undef, 5, 5) + + ls = [] + scs = [] + labels = [] + solver_times = [] + + for i in 1:4, j in 1:5 + idx = 5 * (i - 1) + j + + idx > length(wp_general_tracker) && break + + wp = wp_general_tracker[idx] + + ax = Axis(fig[i, j], + xscale = log10, yscale = log10, + xtickwidth = STROKEWIDTH, + ytickwidth = STROKEWIDTH, spinewidth = STROKEWIDTH, + title = "No. $(idx) Linear BVP benchmarking", titlegap = 10, + xticklabelsize = 16, yticklabelsize = 16) + + for wpᵢ in wp.wps + idx = findfirst(s -> s.name == wpᵢ.name, solvers_all) + errs = getindex.(wpᵢ.errors, :l∞) + times = wpᵢ.times + + l = lines!(ax, errs, times; color = colors[idx], linewidth = 3, + linestyle = LINESTYLES[solvers_all[idx].pkg], alpha = 0.8, + label = wpᵢ.name) + sc = scatter!(ax, errs, times; color = colors[idx], markersize = 16, + strokewidth = 2, marker = Cycled(idx), alpha = 0.8, label = wpᵢ.name) + + if wpᵢ.name ∉ labels + push!(ls, l) + push!(scs, sc) + push!(labels, wpᵢ.name) + end + end + end + + fig[0, :] = Label(fig, "Work-Precision Diagram for 18 Test Problems", + fontsize = 24, tellwidth = false, font = :bold) + + fig[:, 0] = Label(fig, "Time (s)", fontsize = 20, tellheight = false, font = :bold, + rotation = π / 2) + fig[end + 1, :] = Label(fig, + L"Error: $\mathbf{||f(u^\ast)||_\infty}$", + fontsize = 20, tellwidth = false, font = :bold) + + Legend(fig[4, 4:5], [[l, sc] for (l, sc) in zip(ls, scs)], + labels, "BVP Solvers"; + framevisible=true, framewidth = STROKEWIDTH, orientation = :horizontal, + titlesize = 20, nbanks = 9, labelsize = 20, halign = :center, + tellheight = false, tellwidth = false, patchsize = (40.0f0, 20.0f0)) + + return fig + end +end ``` ```julia, echo = false using SciMLBenchmarks SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) -``` \ No newline at end of file +``` diff --git a/benchmarks/NonlinearProblem/Manifest.toml b/benchmarks/NonlinearProblem/Manifest.toml index f8dbb6e20..903c606f6 100644 --- a/benchmarks/NonlinearProblem/Manifest.toml +++ b/benchmarks/NonlinearProblem/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.4" +julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "25b34fd82b1dddba435b78778f72927e8d7c89f8" +project_hash = "8814c1199875b7c1b1e3a38f566386a806b41b9d" [[deps.ADTypes]] -git-tree-sha1 = "fc02d55798c1af91123d07915a990fbb9a10d146" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.3.0" +version = "1.9.0" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -36,24 +36,28 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.36" +version = "0.1.38" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" AccessorsIntervalSetsExt = "IntervalSets" AccessorsStaticArraysExt = "StaticArrays" AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.AccurateArithmetic]] @@ -64,14 +68,19 @@ version = "0.3.8" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.0.4" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AdaptivePredicates]] +git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6" +uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" +version = "1.2.0" + [[deps.AlgebraicMultigrid]] deps = ["CommonSolve", "LinearAlgebra", "LinearSolve", "Printf", "Reexport", "SparseArrays"] git-tree-sha1 = "eb3dbbca423d8e8a1d4061b890f775dcd31b8d7c" @@ -90,6 +99,12 @@ git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" version = "0.4.1" +[[deps.Aqua]] +deps = ["Compat", "Pkg", "Test"] +git-tree-sha1 = "49b1d7a9870c87ba13dc63f8ccfcf578cb266f95" +uuid = "4c88cf16-eb10-579e-8560-4a9242c79595" +version = "0.8.9" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" @@ -101,19 +116,21 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "ed2ec3c9b483842ae59cd273834e5b46206d6dda" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "d60a1922358aa203019b7857a2c8c37329b8736c" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.11.0" +version = "7.17.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -123,16 +140,18 @@ version = "7.11.0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "420e2853770f50e5306b9d96b5a66f26e7c73bc6" +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.9.4" +version = "1.10.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -142,10 +161,10 @@ weakdeps = ["SparseArrays"] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.Automa]] -deps = ["PrecompileTools", "TranscodingStreams"] -git-tree-sha1 = "588e0d680ad1d7201d4c6a804dcb1cd9cba79fbb" +deps = ["PrecompileTools", "SIMD", "TranscodingStreams"] +git-tree-sha1 = "a8f503e8e1a5f583fbef15a8440c8c7e32185df2" uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" -version = "1.0.3" +version = "1.1.0" [[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] @@ -169,26 +188,48 @@ uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.5.0" [[deps.Bijections]] -git-tree-sha1 = "c9b163bd832e023571e86d0b90d9de92a9879088" +git-tree-sha1 = "d8b0439d2be438a5f2cd68ec158fe08a7b2595b7" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" -version = "0.1.6" +version = "0.1.9" [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.5" +version = "0.1.6" + +[[deps.BlockArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] +git-tree-sha1 = "d434647f798823bcae510aee0bc0401927f64391" +uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" +version = "1.1.1" + + [deps.BlockArrays.extensions] + BlockArraysBandedMatricesExt = "BandedMatrices" + + [deps.BlockArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + +[[deps.BracketingNonlinearSolve]] +deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "95cb19c37ea427617e9795655667712f03058d98" +uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" +version = "1.1.0" +weakdeps = ["ForwardDiff"] + + [deps.BracketingNonlinearSolve.extensions] + BracketingNonlinearSolveForwardDiffExt = "ForwardDiff" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -197,9 +238,9 @@ version = "0.5.0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "585a387a490f1c4bd88be67eea15b93da5e85db7" +git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.5" +version = "0.2.6" [[deps.CRC32c]] uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" @@ -212,33 +253,32 @@ version = "1.0.1+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" +git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.0.5" +version = "1.1.0" [[deps.CairoMakie]] -deps = ["CRC32c", "Cairo", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] -git-tree-sha1 = "d69c7593fe9d7d617973adcbe4762028c6899b2c" +deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] +git-tree-sha1 = "c3161fbfe99d9d7ee121cf2017d49966b152857c" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.11.11" +version = "0.12.16" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.2+1" -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" +[[deps.Cassette]] +git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" +uuid = "7057c7e9-c182-5462-911a-8362d720325c" +version = "0.3.14" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -246,15 +286,15 @@ weakdeps = ["SparseArrays"] [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" +version = "0.7.6" [[deps.ColorBrewer]] deps = ["Colors", "JSON", "Test"] @@ -264,9 +304,9 @@ version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.25.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -301,16 +341,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.15.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -342,25 +387,25 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.1" +version = "2.4.2" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "51cab8e982c5b598eea9c8ceaced4b58d9dd37c9" +git-tree-sha1 = "b19db3927f0db4151cb86d073689f2428e524576" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.10.0" +version = "1.10.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] @@ -375,9 +420,9 @@ uuid = "a2441757-f6aa-5fb2-8edb-039e3f45d037" version = "1.6.1" [[deps.CoverageTools]] -git-tree-sha1 = "1c57cae86de23999b63a1e2c4cd226bdaf6e7c10" +git-tree-sha1 = "72ded72062bedff105dc69dfc0cb07d2197c1669" uuid = "c36e975a-824b-4404-a568-ef97ca766997" -version = "1.3.1" +version = "1.3.2" [[deps.CpuId]] deps = ["Markdown"] @@ -411,16 +456,16 @@ deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.DelaunayTriangulation]] -deps = ["EnumX", "ExactPredicates", "Random"] -git-tree-sha1 = "1755070db557ec2c37df2664c75600298b0c1cfc" +deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "PrecompileTools", "Random"] +git-tree-sha1 = "89df54fbe66e5872d91d8c2cd3a375f660c3fd64" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "1.0.3" +version = "1.6.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "2c6b7bf16fd850c551a765e313e7522ba455cbfd" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "f8eefbb7e910f59087c4bb09ce670f235758ee4a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.151.4" +version = "6.158.3" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -432,6 +477,7 @@ version = "6.151.4" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" @@ -445,20 +491,21 @@ version = "6.151.4" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqDevTools]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"] -git-tree-sha1 = "5c4d10244e1637c7c99a3f266ab67647982a0fd0" +git-tree-sha1 = "167a3a413b954aca9e64d785f8ea096e23e5afb8" uuid = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" -version = "2.44.3" +version = "2.45.1" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.21.0" +version = "5.23.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -479,10 +526,10 @@ uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" [[deps.DifferentiationInterface]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "23c6df13ad8fcffde4b0596d798911d2e309fc2c" +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.5" +version = "0.6.22" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -492,10 +539,13 @@ version = "0.5.5" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" - DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -507,18 +557,21 @@ version = "0.5.5" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -531,9 +584,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9c405847cc7ecda2dc921ccf18b47ca150d7317e" +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.109" +version = "0.25.113" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -553,15 +606,15 @@ version = "0.9.3" [[deps.Documenter]] deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"] -git-tree-sha1 = "5461b2a67beb9089980e2f8f25145186b6d34f91" +git-tree-sha1 = "5a1ee886566f2fa9318df1273d8b778b9d42712d" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "1.4.1" +version = "1.7.0" [[deps.DocumenterTools]] -deps = ["AbstractTrees", "Base64", "DocStringExtensions", "Documenter", "FileWatching", "Gumbo", "LibGit2", "OpenSSH_jll", "Sass"] -git-tree-sha1 = "7605a88f75625836ce47102b8915041fae231ff5" +deps = ["AbstractTrees", "Base64", "DocStringExtensions", "Documenter", "FileWatching", "Git", "Gumbo", "LibGit2", "OpenSSH_jll", "Sass"] +git-tree-sha1 = "1eef850e88afab219e555678868d83aa901a360b" uuid = "35a29f4d-8980-5a13-9543-d66fff28ecb8" -version = "0.1.19" +version = "0.1.20" [[deps.DomainSets]] deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] @@ -578,17 +631,11 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.DynamicPolynomials]] -deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "30a1848c4f4fc35d1d4bbbd125650f6a11b5bc6c" +deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"] +git-tree-sha1 = "bbf1ace0781d9744cb697fb856bd2c3f6568dadb" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.5.7" +version = "0.6.0" [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -601,15 +648,41 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" +[[deps.Enzyme]] +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random", "SparseArrays"] +git-tree-sha1 = "136f590cfed1c25b956fedc6a4d77342e3d4eaa3" +uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" +version = "0.13.14" + + [deps.Enzyme.extensions] + EnzymeBFloat16sExt = "BFloat16s" + EnzymeChainRulesCoreExt = "ChainRulesCore" + EnzymeLogExpFunctionsExt = "LogExpFunctions" + EnzymeSpecialFunctionsExt = "SpecialFunctions" + EnzymeStaticArraysExt = "StaticArrays" + + [deps.Enzyme.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.EnzymeCore]] -git-tree-sha1 = "88bc63137eb033acc3afe1b9875717889c718c46" +git-tree-sha1 = "04c777af6ef65530a96ab68f0a81a4608113aa1d" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.5" +version = "0.8.5" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] AdaptExt = "Adapt" +[[deps.Enzyme_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "dec17951c0ba91ef723dc71c7687e60398125226" +uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" +version = "0.0.163+0" + [[deps.ExactPredicates]] deps = ["IntervalArithmetic", "Random", "StaticArrays"] git-tree-sha1 = "b3f2ff58735b5f024c392fde763f29b057e4b025" @@ -633,16 +706,22 @@ git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.Expronicon]] +deps = ["MLStyle", "Pkg", "TOML"] +git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" +uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" +version = "0.8.5" + [[deps.Extents]] -git-tree-sha1 = "94997910aca72897524d2237c41eb852153b0f65" +git-tree-sha1 = "81023caa0021a41712685887db1fc03db26f41f5" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.3" +version = "0.1.4" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "8cc47f299902e13f90405ddb5bf87e5d474c0d38" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.2+2" +version = "6.1.2+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -652,15 +731,15 @@ version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" +git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+0" +version = "3.3.10+1" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "2be93e36303143c6fffd07e2222bbade35194d9e" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.3.3" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -675,9 +754,9 @@ version = "2.0.4" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" +git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.3" +version = "1.16.4" [[deps.FilePaths]] deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] @@ -686,19 +765,24 @@ uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824" version = "0.8.3" [[deps.FilePathsBase]] -deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +deps = ["Compat", "Dates"] +git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.21" +version = "0.9.22" +weakdeps = ["Mmap", "Test"] + + [deps.FilePathsBase.extensions] + FilePathsBaseMmapExt = "Mmap" + FilePathsBaseTestExt = "Test" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.11.0" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -707,19 +791,21 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.23.1" +version = "2.26.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -741,9 +827,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -763,9 +849,9 @@ version = "2.13.2+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] -git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc" +git-tree-sha1 = "84dfe824bd6fdf2a5d73bb187ff31b5549b2a79c" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.10.3" +version = "0.10.4" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -773,6 +859,12 @@ git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.14+0" +[[deps.FunctionProperties]] +deps = ["Cassette", "DiffRules"] +git-tree-sha1 = "bf7c740307eb0ee80e05d8aafbd0c5a901578398" +uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc" +version = "0.1.2" + [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" @@ -794,11 +886,22 @@ git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" +[[deps.GPUCompiler]] +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "72408a76694e87e735f515a499ba1e069d232d39" +uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" +version = "1.0.1" + +[[deps.GeoFormatTypes]] +git-tree-sha1 = "59107c179a586f0fe667024c5eb7033e81333271" +uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" +version = "0.4.2" + [[deps.GeoInterface]] -deps = ["Extents"] -git-tree-sha1 = "801aef8228f7f04972e596b09d4dba481807c913" +deps = ["Extents", "GeoFormatTypes"] +git-tree-sha1 = "826b4fd69438d9ce4d2b19de6bc2f970f45f0f88" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.3.4" +version = "1.3.8" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -812,29 +915,35 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" +[[deps.Giflib_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "0224cce99284d997f6880a42ef715a37c99338d1" +uuid = "59f7168a-df46-5410-90c8-f2779963d0ec" +version = "5.2.2+0" + [[deps.Git]] deps = ["Git_jll"] -git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d" +git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e" uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2" -version = "1.3.0" +version = "1.3.1" [[deps.Git_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "d8be4aab0f4e043cc40984e9097417307cce4c03" +git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.36.1+2" +version = "2.46.2+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.80.5+0" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] -git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" +git-tree-sha1 = "a641238db938fff9b2f60d08ed9030387daf428c" uuid = "a2bd30eb-e257-5431-a919-1863eab51364" -version = "1.1.2" +version = "1.1.3" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -844,15 +953,15 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "334d300809ae0a68ceee3444c6e99ded412bf0b3" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.1" +version = "1.12.0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "6f93a83ca11346771a93bbde2bdad2f65b61498f" +git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.10.2" +version = "0.11.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -873,15 +982,15 @@ version = "0.10.2+0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.10" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "2.8.1+1" +version = "8.3.1+0" [[deps.Highlights]] deps = ["DocStringExtensions", "InteractiveUtils", "REPL"] @@ -891,21 +1000,27 @@ version = "0.5.3" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" + +[[deps.Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.11.2+1" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.25" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" +git-tree-sha1 = "1b1299f7d6617291f3d260e9f5b0250afdaac8c0" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.2" +version = "1.26.0" [[deps.IOCapture]] deps = ["Logging", "Random"] @@ -920,9 +1035,9 @@ version = "0.1.1" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] -git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" +git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba" uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" -version = "0.6.11" +version = "0.6.12" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -931,22 +1046,22 @@ uuid = "c817782e-172a-44cc-b673-b171935fbb9e" version = "0.1.7" [[deps.ImageCore]] -deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] -git-tree-sha1 = "b2a7eaa169c13f5bcae8131a83bc30eff8f71be0" +deps = ["Aqua", "BlockArrays", "ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] +git-tree-sha1 = "661ca04f8df633e8a021c55a22e96cf820220ede" uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" -version = "0.10.2" +version = "0.10.4" [[deps.ImageIO]] -deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] -git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" +deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"] +git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.8" +version = "0.6.9" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] -git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7" +git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec" uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" -version = "0.9.9" +version = "0.9.10" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -970,11 +1085,16 @@ git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.5" +[[deps.IntegerMathUtils]] +git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" +uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" +version = "0.1.2" + [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.1.0+0" +version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -985,23 +1105,22 @@ deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArr git-tree-sha1 = "88a101217d7cb38a7b481ccd50d21876e1d1b0e0" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.15.1" +weakdeps = ["Unitful"] [deps.Interpolations.extensions] InterpolationsUnitfulExt = "Unitful" - [deps.Interpolations.weakdeps] - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - [[deps.IntervalArithmetic]] -deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "433b0bb201cd76cb087b017e49244f10394ebe9c" +deps = ["CRlibm_jll", "LinearAlgebra", "MacroTools", "RoundingEmulator"] +git-tree-sha1 = "24c095b1ec7ee58b936985d31d5df92f9b9cfebb" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.14" -weakdeps = ["DiffRules", "ForwardDiff", "RecipesBase"] +version = "0.22.19" +weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "RecipesBase"] [deps.IntervalArithmetic.extensions] IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" + IntervalArithmeticIntervalSetsExt = "IntervalSets" IntervalArithmeticRecipesBaseExt = "RecipesBase" [[deps.IntervalSets]] @@ -1016,14 +1135,14 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.14" -weakdeps = ["Dates"] +version = "0.1.17" +weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] - DatesExt = "Dates" + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -1048,9 +1167,9 @@ version = "1.0.0" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1066,9 +1185,9 @@ version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.0.4+0" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -1084,9 +1203,9 @@ version = "0.6.9" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.6" +version = "0.9.8" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1094,64 +1213,79 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" +[[deps.LERC_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "4.0.0+0" + +[[deps.LLVM]] +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" +uuid = "929cbde3-209d-540e-8aea-75f648917ca0" +version = "9.1.3" + + [deps.LLVM.extensions] + BFloat16sExt = "BFloat16s" + + [deps.LLVM.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" + +[[deps.LLVMExtra_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" +uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" +version = "0.0.34+0" + [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "18.1.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.2+1" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LabelledArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "e459fda6b68ea8684b3fcd513d2fd1e5130c4402" -uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.16.0" - -[[deps.LambertW]] -git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" -uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" -version = "0.4.6" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "e0b5cd21dc1b44ec6e64f351976f961e6f31d6c4" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.3" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.15" +version = "0.1.17" [[deps.LazilyInitializedFields]] -git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612" +git-tree-sha1 = "0f2da712350b020bc3957f269c9caad516383ee0" uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" -version = "1.2.2" +version = "1.3.0" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "899d44fa1a575653df5721a7fccb4988f7f09b62" +git-tree-sha1 = "360f6039babd6e4d6364eff0d4fc9120834a2d9a" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.0.4" +version = "2.2.1" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1209,21 +1343,27 @@ version = "3.2.2+1" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" + +[[deps.Libglvnd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" +uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" +version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1231,17 +1371,33 @@ git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" version = "2.40.1+0" +[[deps.Libtiff_jll]] +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" +uuid = "89763e89-9b03-5906-acba-b20f662cd828" +version = "4.7.0+0" + [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.40.1+0" +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" + [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1249,17 +1405,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "7648cc20100504f4b453917aacc8520e9c0ecfb3" +git-tree-sha1 = "591de175461afd8323aa24b7686062574527aa3a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.30.1" +version = "2.36.2" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -1273,7 +1429,6 @@ version = "2.30.1" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -1305,15 +1460,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "8f6786d8b2b3248d79db3ad359ce95382d5a6df8" +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.170" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1328,9 +1483,46 @@ version = "1.3.0" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.1.0+0" +version = "2024.2.0+0" + +[[deps.MLStyle]] +git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" +uuid = "d8e11817-5142-5d16-987a-aa16d5891078" +version = "0.4.17" + +[[deps.MPI]] +deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"] +git-tree-sha1 = "892676019c58f34e38743bc989b0eca5bce5edc5" +uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" +version = "0.20.22" + + [deps.MPI.extensions] + AMDGPUExt = "AMDGPU" + CUDAExt = "CUDA" + + [deps.MPI.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + +[[deps.MPICH_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423" +uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" +version = "4.2.3+0" + +[[deps.MPIPreferences]] +deps = ["Libdl", "Preferences"] +git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07" +uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.11" + +[[deps.MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.5.1+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1339,16 +1531,16 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" version = "0.5.13" [[deps.Makie]] -deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"] -git-tree-sha1 = "4d49c9ee830eec99d3e8de2425ff433ece7cc1bc" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "5e4e0e027642293da251bf35dac408d692ccba8b" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.20.10" +version = "0.21.16" [[deps.MakieCore]] -deps = ["Observables", "REPL"] -git-tree-sha1 = "248b7a4be0f92b497f7a331aed02c1e9a878f46b" +deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] +git-tree-sha1 = "ae4dbe0fcf1594ed98594e5f4ee685295a2a6f74" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.7.3" +version = "0.8.10" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1372,15 +1564,19 @@ version = "0.1.2" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] -git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d" +git-tree-sha1 = "f45c8916e8385976e1ccd055c9874560c257ab13" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.5.7" +version = "0.6.2" [[deps.MaybeInplace]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "1b9e613f2ca3b6cdcbfe36381e17ca2b66d4b3a1" +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" -version = "0.1.3" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1393,6 +1589,12 @@ deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.2+1" +[[deps.MicrosoftMPI_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" +uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" +version = "10.1.4+2" + [[deps.Missings]] deps = ["DataAPI"] git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" @@ -1419,21 +1621,21 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "5c1d1d9361e1417e5a065e1f84dc3686cbdaea21" +git-tree-sha1 = "8d39779e29f80aa6c071e7ac17101c6e31f075d7" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.6" +version = "0.5.7" [[deps.Mustache]] deps = ["Printf", "Tables"] -git-tree-sha1 = "a7cefa21a2ff993bff0456bf7521f46fc077ddf1" +git-tree-sha1 = "3b2db451a872b20519ebb0cec759d3d81a1c6bcb" uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.19" +version = "1.0.20" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "898c56fbf8bf71afb0c02146ef26f3a454e88873" +git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.5" +version = "1.5.2" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1470,36 +1672,84 @@ uuid = "b7050fa9-e91f-4b37-bcee-a89a063da141" version = "0.1.2" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "a5bc9c06e28108e04de0485273f0b5933cec66ed" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 = "22f3efdd47bd18d8a26bd559fff254e6b21000fd" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.12.3" +version = "4.1.0" [deps.NonlinearSolve.extensions] - NonlinearSolveBandedMatricesExt = "BandedMatrices" NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" NonlinearSolveMINPACKExt = "MINPACK" NonlinearSolveNLSolversExt = "NLSolvers" - NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"] + NonlinearSolvePETScExt = ["PETSc", "MPI"] NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" + NonlinearSolveSundialsExt = "Sundials" [deps.NonlinearSolve.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" + +[[deps.NonlinearSolveBase]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "1589ef8aac99a21d132adf1ec5cbe6ef651760ff" +uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" +version = "1.3.1" + + [deps.NonlinearSolveBase.extensions] + NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" + NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase" + NonlinearSolveBaseForwardDiffExt = "ForwardDiff" + NonlinearSolveBaseLineSearchExt = "LineSearch" + NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseSparseArraysExt = "SparseArrays" + NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + + [deps.NonlinearSolveBase.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LineSearch = "87fe0de2-c867-4266-b59a-2f0a94fc965b" + LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + +[[deps.NonlinearSolveFirstOrder]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "dc8535cecb0f9d978019e44b7144b9e84ab85424" +uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" +version = "1.0.0" + +[[deps.NonlinearSolveQuasiNewton]] +deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] +git-tree-sha1 = "066d4940938f4bb5fd1ce146e61a373f40b89d31" +uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" +version = "1.0.0" + +[[deps.NonlinearSolveSpectralMethods]] +deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "cc97c44e396ab820401c8c404bc1fd18d4c884bd" +uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" +version = "1.0.0" + +[[deps.ObjectFile]] +deps = ["Reexport", "StructIO"] +git-tree-sha1 = "7249afa1c4dfd86bfbcc9b28939ab6ef844f4e11" +uuid = "d8793406-e978-5875-9003-1fc021f44a92" +version = "0.4.2" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -1507,9 +1757,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e" +git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.0" +version = "1.14.1" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1521,6 +1771,12 @@ git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" version = "1.3.5+1" +[[deps.OpenBLAS32_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6065c4cff8fee6c6770b277af45d5082baacdba1" +uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2" +version = "0.3.24+0" + [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" @@ -1528,9 +1784,9 @@ version = "0.3.23+4" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] -git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" +git-tree-sha1 = "97db9e07fe2091882c765380ef58ec553074e9c7" uuid = "52e1d378-f018-4a11-a4be-720524705ac7" -version = "0.3.2" +version = "0.3.3" [[deps.OpenEXR_jll]] deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -1543,11 +1799,17 @@ deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.1+2" +[[deps.OpenMPI_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] +git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f" +uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" +version = "5.0.5+0" + [[deps.OpenSSH_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "1b2f042897343a9dfdcc9366e4ecbd3d00780c49" +deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll", "Zlib_jll"] +git-tree-sha1 = "cbb7bdfca123d91205ba9341bbaabe700934078d" uuid = "9bd350c2-7e96-507f-8002-3f2e150b4e1b" -version = "8.9.0+1" +version = "9.9.1+1" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -1557,9 +1819,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a12e56c72edee3ce6b96667745e6cbbe5498f200" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.23+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1580,10 +1842,10 @@ version = "1.9.4" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.2+0" +version = "1.3.3+0" [[deps.OrderedCollections]] git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" @@ -1601,6 +1863,18 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.31" +[[deps.PETSc]] +deps = ["Libdl", "LinearAlgebra", "MPI", "MPIPreferences", "PETSc_jll", "Pkg", "SparseArrays"] +git-tree-sha1 = "0df6fc164a6254fa3311e3717c4155c32cc56a66" +uuid = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" +version = "0.3.1" + +[[deps.PETSc_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenBLAS32_jll", "OpenMPI_jll", "SCALAPACK32_jll", "TOML"] +git-tree-sha1 = "e67be069aea02ce689bd94eb3f7ee011396bf1bd" +uuid = "8fa3689e-f0b9-5420-9873-adf6ccf46f2d" +version = "3.22.0+0" + [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd" @@ -1627,9 +1901,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cb5a2ab6763464ae0f19c86c56c63d4a2b0f5bda" +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.52.2+0" +version = "1.54.1+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1661,10 +1935,10 @@ uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.3" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.3" [[deps.PoissonRandom]] deps = ["Random"] @@ -1673,10 +1947,10 @@ uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" version = "0.4.4" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "b3e2bae88cf07baf0a051fe09666b8ef97aefe93" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.14" +version = "0.7.16" [[deps.PolyesterForwardDiff]] deps = ["ForwardDiff", "Polyester"] @@ -1686,9 +1960,9 @@ version = "0.1.2" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.2.1" +version = "0.2.2" [[deps.PolygonOps]] git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" @@ -1703,9 +1977,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "406c29a7f46706d379a3bce45671b4e3a39ddfbc" +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.22" +version = "0.4.24" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -1727,9 +2001,15 @@ version = "1.4.3" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.2" +version = "2.4.0" + +[[deps.Primes]] +deps = ["IntegerMathUtils"] +git-tree-sha1 = "cb420f77dc474d23ee47ca8d14c90810cafe69e7" +uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" +version = "0.5.6" [[deps.Printf]] deps = ["Unicode"] @@ -1741,26 +2021,30 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" +git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.0" +version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.0" +version = "1.2.1" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] -git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" +git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d" uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" -version = "1.0.0" +version = "1.0.1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.11.1" +weakdeps = ["Enzyme"] + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1777,10 +2061,10 @@ uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -1804,10 +2088,10 @@ uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.3.4" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "980aabbeac7aee70d0e452a72b0c68b5b266cc7b" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.24.0" +version = "3.27.3" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1815,6 +2099,7 @@ version = "3.24.0" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -1824,6 +2109,7 @@ version = "3.24.0" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -1864,21 +2150,21 @@ version = "1.1.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.2+0" +version = "0.5.1+0" [[deps.RootedTrees]] deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] -git-tree-sha1 = "5edf5ca74018e571d79add76a31bb08518927ed8" +git-tree-sha1 = "c0c464d3063e46e4128d21fd677ca575ace44fdc" uuid = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c" -version = "2.21.1" +version = "2.23.1" [deps.RootedTrees.extensions] PlotsExt = "Plots" @@ -1897,15 +2183,21 @@ git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" version = "0.5.13" +[[deps.SCALAPACK32_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenBLAS32_jll", "OpenMPI_jll", "Pkg", "TOML"] +git-tree-sha1 = "3fd1ffad6374491b54fe50ee9033318f30f39982" +uuid = "aabda75e-bfe4-5a37-92e3-ffe54af3c273" +version = "2.2.1+1" + [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SIMD]] deps = ["PrecompileTools"] -git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" +git-tree-sha1 = "52af86e35dd1b177d051b12681e1c581f53c281b" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.5.0" +version = "3.7.0" [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" @@ -1914,9 +2206,9 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.42" +version = "0.6.43" [[deps.Sass]] deps = ["libsass_jll"] @@ -1925,10 +2217,10 @@ uuid = "322a6be2-4ae8-5d68-aaf1-3e960788d1d9" version = "0.2.0" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7a6c5c8c38d2e37f45d4686c3598c20c1aebf48e" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "7527b9adb22904f0f51d8ab85d826f81ebb6f78d" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.41.3" +version = "2.59.2" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1955,17 +2247,28 @@ git-tree-sha1 = "f4076dd5a103010d48bb6c4e50c5526f6622fa96" uuid = "31c91b34-3c75-11e9-0341-95557aab0344" version = "0.1.3" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" + [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "10499f619ef6e890f3f4a38914481cc868689cd5" +deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.8" +version = "0.3.12" +weakdeps = ["SparseArrays", "StaticArraysCore"] + + [deps.SciMLOperators.extensions] + SciMLOperatorsSparseArraysExt = "SparseArrays" + SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLStructures]] deps = ["ArrayInterface"] -git-tree-sha1 = "6ab4beaf88dcdd2639bead916f2347f81dcacd0e" +git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.3.0" +version = "1.5.0" [[deps.Scratch]] deps = ["Dates"] @@ -2005,27 +2308,27 @@ uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" version = "0.4.0" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "913754ccbbc78720a4542b56a6bdfbab1c84c8f2" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "f7e2042e0b68c6bb19a0a1594839792737f51d84" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.10.0" +version = "2.0.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" SimpleNonlinearSolveTrackerExt = "Tracker" - SimpleNonlinearSolveZygoteExt = "Zygote" [deps.SimpleNonlinearSolve.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2059,11 +2362,31 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "6914df6005bab9940e2a96879a97a43e1fb1ce78" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.8" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "469f51f8c4741ce944be2c0b65423b518b1405b0" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.19.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2080,10 +2403,14 @@ version = "2.19.0" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "eed2446b3c3dd58f6ded3168998b8b2cb3fc9229" +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "670f2c8109e87d79788baef47880b946e529f1a2" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.3.3" +version = "0.4.9" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2120,16 +2447,16 @@ uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" version = "0.1.1" [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.10" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.5.0" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -2138,9 +2465,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "6e00379a24597be4ae1ee6b2d882e15392040132" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.5" +version = "1.9.8" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2171,9 +2498,9 @@ version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2182,9 +2509,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "25349bf8f63aa36acbff5e3550a86e9f5b0ef682" +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.6" +version = "0.5.7" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -2194,9 +2521,9 @@ version = "0.3.7" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.4.0" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] @@ -2211,6 +2538,11 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" +[[deps.StructIO]] +git-tree-sha1 = "c581be48ae1cbf83e899b14c07a807e1787512cc" +uuid = "53d494c1-5632-5724-8f4c-31dff12d585f" +version = "0.3.1" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -2222,9 +2554,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "e15f5a73f0d14b9079b807a9d1dac13e4302e997" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.24.0" +version = "4.26.1" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2234,37 +2566,49 @@ version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "2d1b8941f58d0c878b3c71d9b17188a2eb649a8b" +git-tree-sha1 = "20cf607cafb31f922bce84d60379203e7a126911" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.24" +version = "0.3.34" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] -git-tree-sha1 = "fb099adbd7504f1e68b4512828e9d94197a8b889" +git-tree-sha1 = "fabf4650afe966a2ba646cabd924c3fd43577fc3" uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3" -version = "0.2.1" +version = "0.2.2" [[deps.SymbolicUtils]] -deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] -git-tree-sha1 = "79813de27af70906d223fbd89ad90dba3d88a2b0" +deps = ["AbstractTrees", "ArrayInterface", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] +git-tree-sha1 = "04e9157537ba51dad58336976f8d04b9ab7122f0" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "2.0.2" +version = "3.7.2" + + [deps.SymbolicUtils.extensions] + SymbolicUtilsLabelledArraysExt = "LabelledArrays" + SymbolicUtilsReverseDiffExt = "ReverseDiff" + + [deps.SymbolicUtils.weakdeps] + LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.Symbolics]] -deps = ["ADTypes", "ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "ForwardDiff", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "3669f8eba2720c595e16b038f33cb880c12ef7f7" +deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] +git-tree-sha1 = "0caef7687abf7094132fa3112bf5514c36a99226" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.30.3" +version = "6.18.3" [deps.Symbolics.extensions] + SymbolicsForwardDiffExt = "ForwardDiff" SymbolicsGroebnerExt = "Groebner" - SymbolicsLuxCoreExt = "LuxCore" - SymbolicsPreallocationToolsExt = "PreallocationTools" + SymbolicsLuxExt = "Lux" + SymbolicsNemoExt = "Nemo" + SymbolicsPreallocationToolsExt = ["PreallocationTools", "ForwardDiff"] SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" - LuxCore = "bb33d45b-7691-41d6-9220-0943567d0623" + Lux = "b2108857-7c20-44ae-9111-449ecde12c47" + Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a" PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" @@ -2280,10 +2624,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2297,9 +2641,9 @@ uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" [[deps.TermInterface]] -git-tree-sha1 = "6f0cee95e74d1f6891ba6b35b8b219fd3d11b567" +git-tree-sha1 = "d673e0aca9e46a2f63720201f55cc7b3e7169b16" uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" -version = "0.4.1" +version = "2.0.0" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -2313,35 +2657,26 @@ version = "0.5.2" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] -git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" +git-tree-sha1 = "0248b1b2210285652fbc67fd6ced9bf0394bcfec" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.10.0" +version = "0.11.1" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.24" +version = "0.5.25" [[deps.TranscodingStreams]] -git-tree-sha1 = "a947ea21087caba0a798c5e494d0bb78e3a1a3a0" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.9" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "66c68a20907800c0b7c04ff8a6164115e8747de2" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.2.0" - -[[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" -uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +version = "0.2.1" [[deps.TriplotBase]] git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" @@ -2377,6 +2712,17 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.Unitful]] +deps = ["Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.21.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] + + [deps.Unitful.extensions] + ConstructionBaseUnitfulExt = "ConstructionBase" + InverseFunctionsUnitfulExt = "InverseFunctions" + [[deps.Unityper]] deps = ["ConstructionBase"] git-tree-sha1 = "25008b734a03736c41e2a7dc314ecb95bd6bbdb0" @@ -2385,9 +2731,9 @@ version = "0.1.6" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e863582a41c5731f51fd050563ae91eb33cf09be" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.68" +version = "0.21.71" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -2406,6 +2752,12 @@ git-tree-sha1 = "092217eb5443926d200ae9325f103906efbb68b1" uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9" version = "0.10.12" +[[deps.WebP]] +deps = ["CEnum", "ColorTypes", "FileIO", "FixedPointNumbers", "ImageCore", "libwebp_jll"] +git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2" +uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1" +version = "0.1.3" + [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" @@ -2414,15 +2766,21 @@ version = "1.0.0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9" +git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.7+0" +version = "2.13.4+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" + +[[deps.XZ_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" +uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" +version = "5.6.3+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -2462,9 +2820,9 @@ version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2474,27 +2832,33 @@ version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "80c3218f29cbc47111ac87e7be5e69cc05c6dd36" +git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.11" +version = "0.4.12" [[deps.ZMQ]] deps = ["FileWatching", "PrecompileTools", "Sockets", "ZeroMQ_jll"] -git-tree-sha1 = "ad6944a6b3dfd8e95920e48355d3baf510319262" +git-tree-sha1 = "18cfd00df3cbbebf8ea4ec7ea6bbceb3af716bd0" uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1" -version = "1.2.6" +version = "1.3.0" [[deps.ZeroMQ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "libsodium_jll"] -git-tree-sha1 = "42f97fb27394378591666ab0e9cee369e6d0e1f9" +git-tree-sha1 = "f02ce8f0fda1ed40f4d0d59a2ad05e35e8ac9b0e" uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568" -version = "4.3.5+0" +version = "4.3.5+1" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.13+1" +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.6+1" + [[deps.cminpack_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "4914f5bc10179ca652137b6cd27e1eb930a17a18" @@ -2514,51 +2878,57 @@ uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" version = "3.9.0+0" [[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" +version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" +version = "5.11.0+0" [[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" [[deps.libsass_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "941afb93587dcec07f89e511057f5efc0bec6f0d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6044ffe7e7bf0602e2039dc747c3332a097ac74b" uuid = "47bcb7c8-5119-555a-9eeb-0afcc36cd728" -version = "3.6.4+0" +version = "3.6.6+0" [[deps.libsixel_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] -git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" +git-tree-sha1 = "7dfa0fd9c783d3d0cc43ea1af53d69ba45c447df" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.3+0" +version = "1.10.3+1" [[deps.libsodium_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e" +git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+0" +version = "1.0.20+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" + +[[deps.libwebp_jll]] +deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"] +git-tree-sha1 = "ccbb625a89ec6195856a50aa2b668a5c08712c94" +uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2" +version = "1.4.0+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] @@ -2577,13 +2947,13 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+2" [[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "35976a1216d6c066ea32cba2150c4fa682b276fc" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" +version = "10164.0.0+0" [[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "dcc541bb19ed5b0ede95581fb2e41ecf179527d2" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" +version = "3.6.0+0" diff --git a/benchmarks/NonlinearProblem/Project.toml b/benchmarks/NonlinearProblem/Project.toml index 16ebc3015..c37371cd1 100644 --- a/benchmarks/NonlinearProblem/Project.toml +++ b/benchmarks/NonlinearProblem/Project.toml @@ -4,18 +4,24 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" +DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895" LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" NonlinearProblemLibrary = "b7050fa9-e91f-4b37-bcee-a89a063da141" NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" +PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46" SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7" +SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" @@ -26,21 +32,27 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" [compat] AlgebraicMultigrid = "0.6" BenchmarkTools = "1" -CairoMakie = "0.11" +CairoMakie = "0.12" DiffEqBase = "6.142" DiffEqDevTools = "2" +DifferentiationInterface = "0.6" +Enzyme = "0.13" IncompleteLU = "0.2" LaTeXStrings = "1" +LineSearches = "7" LinearSolve = "2" MINPACK = "1.2" NLsolve = "4.5" NonlinearProblemLibrary = "0.1" -NonlinearSolve = "3" +NonlinearSolve = "4" +PETSc = "0.3" PolyesterForwardDiff = "0.1" PrettyTables = "2" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Setfield = "1" -SimpleNonlinearSolve = "1" +SimpleNonlinearSolve = "2" +SparseConnectivityTracer = "0.6" SparseDiffTools = "2" SpeedMapping = "0.3" StableRNGs = "1" diff --git a/benchmarks/NonlinearProblem/bruss.jmd b/benchmarks/NonlinearProblem/bruss.jmd index 3589a2c2d..14b33302a 100644 --- a/benchmarks/NonlinearProblem/bruss.jmd +++ b/benchmarks/NonlinearProblem/bruss.jmd @@ -9,9 +9,11 @@ Fetch required packages ```julia using NonlinearSolve, SparseDiffTools, LinearAlgebra, SparseArrays, DiffEqDevTools, - CairoMakie, Symbolics, BenchmarkTools, PolyesterForwardDiff, LinearSolve, Sundials -import NLsolve, MINPACK -RUS = RadiusUpdateSchemes; + CairoMakie, Symbolics, BenchmarkTools, PolyesterForwardDiff, LinearSolve, Sundials, + Enzyme, SparseConnectivityTracer, DifferentiationInterface +import NLsolve, MINPACK, PETSc, RecursiveFactorization + +const RUS = RadiusUpdateSchemes; BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.2; ``` @@ -87,60 +89,16 @@ function generate_brusselator_problem(N::Int; sparsity = nothing, kwargs...) return nothing end - p = (3.4, 1.0, 10.0, step(xyd_brusselator)) - - u0 = init_brusselator_2d(xyd_brusselator, N) - - nlfunc = NonlinearFunction(brusselator_2d_loop; sparsity) - return NonlinearProblem(nlfunc, vec(u0), p; kwargs...) + return NonlinearProblem( + NonlinearFunction(brusselator_2d_loop; sparsity), + vec(init_brusselator_2d(xyd_brusselator, N)), + (3.4, 1.0, 10.0, step(xyd_brusselator)); + kwargs... + ) end ``` ```julia -function __ad_backend(sparsity, psize, ck) - if sparsity === nothing - if psize ≥ 16 - return AutoPolyesterForwardDiff(; chunksize = ck) - else - return AutoForwardDiff(; chunksize = ck) - end - else - if psize ≥ 16 - return AutoSparsePolyesterForwardDiff(; chunksize = ck) - else - return AutoSparseForwardDiff(; chunksize = ck) - end - end -end - -function __set_ad_chunksize(solver::GeneralizedFirstOrderAlgorithm{CJ, N}, ck, - sparsity, psize) where {CJ, N} - ad = __ad_backend(sparsity, psize, ck) - return GeneralizedFirstOrderAlgorithm{CJ, N}(; solver.descent, solver.linesearch, - solver.trustregion, jacobian_ad = ad, solver.max_shrink_times, solver.forward_ad, - solver.reverse_ad) -end -function __set_ad_chunksize(solver::ApproximateJacobianSolveAlgorithm{CJ, N}, ck, - sparsity, psize) where {CJ, N} - ad = __ad_backend(sparsity, psize, ck) - initialization = solver.initialization isa NonlinearSolve.TrueJacobianInitialization ? - NonlinearSolve.TrueJacobianInitialization(NonlinearSolve.FullStructure(), ad) : solver.initialization - return ApproximateJacobianSolveAlgorithm{CJ, N}(; solver.descent, solver.linesearch, - solver.trustregion, solver.update_rule, solver.max_shrink_times, solver.max_resets, - initialization, solver.reinit_rule) -end -function __set_ad_chunksize(solver::SimpleNewtonRaphson, ck, sparsity, psize) - solver.autodiff === nothing || return solver - autodiff = __ad_backend(nothing, psize, ck) - return SimpleNewtonRaphson(; autodiff) -end -function __set_ad_chunksize(solver::SimpleTrustRegion, ck, sparsity, psize) - solver.autodiff === nothing || return solver - autodiff = __ad_backend(nothing, psize, ck) - return SimpleTrustRegion(; autodiff) -end -__set_ad_chunksize(solver, ck, sparsity, psize) = solver - function get_ordering(x::AbstractMatrix) idxs = Vector{Int}(undef, size(x, 1)) placed = zeros(Bool, size(x, 1)) @@ -173,15 +131,11 @@ test_problem = generate_brusselator_problem(4) bruss_f!, u0 = (du, u) -> test_problem.f(du, u, test_problem.p), test_problem.u0 y = similar(u0) -sd = SymbolicsSparsityDetection() -adtype = AutoSparseFiniteDiff() - -J = sparse_jacobian(adtype, sd, bruss_f!, y, u0) - +J = Float64.(ADTypes.jacobian_sparsity(bruss_f!, y, u0, TracerSparsityDetector())) colors = matrix_colors(J) begin - J_ = copy(J) + J_ = similar(J) rows = rowvals(J) vals = nonzeros(J) for j in 1:size(J, 2) @@ -192,35 +146,85 @@ begin end end -function cache_and_compute_10_jacobians(adtype, sd, f!::F, y, x) where {F} - cache = sparse_jacobian_cache(adtype, sd, f!, y, x) - J = init_jacobian(cache) - for i in 1:10 - sparse_jacobian!(J, adtype, cache, f!, y, x) +function cache_and_compute_10_jacobians(adtype, f!::F, y, x, p) where {F} + prep = DifferentiationInterface.prepare_jacobian(f!, y, adtype, x, Constant(p)) + J = DifferentiationInterface.jacobian(f!, y, prep, adtype, x, Constant(p)) + for _ in 1:9 + DifferentiationInterface.jacobian!(f!, y, J, prep, adtype, x, Constant(p)) end return J end -Ns = [2^i for i in 1:8] -sd = [SymbolicsSparsityDetection(), ApproximateJacobianSparsity(; ntrials = 3)] -adtypes = [AutoSparseFiniteDiff(), AutoSparsePolyesterForwardDiff(; chunksize = 8)] -algs = vcat(vec(collect(Iterators.product(sd, adtypes))), - [(NoSparsityDetection(), AutoPolyesterForwardDiff(; chunksize = 8))]) -times = Matrix{Float64}(undef, length(Ns), length(algs)) +# XXX: run till 8 on CI +# Ns = [2^i for i in 1:8] +Ns = [2^i for i in 1:6] + +adtypes = [ + ( + AutoSparse(AutoFiniteDiff(); sparsity_detector=TracerSparsityDetector()), + [:finitediff, :exact_sparse] + ), + ( + AutoSparse( + AutoPolyesterForwardDiff(; chunksize=8); + sparsity_detector=TracerSparsityDetector() + ), + [:forwarddiff, :exact_sparse] + ), + ( + AutoSparse( + AutoEnzyme(; mode=Enzyme.Forward); + sparsity_detector=TracerSparsityDetector() + ), + [:enzyme, :exact_sparse] + ), + ( + AutoSparse( + AutoFiniteDiff(); + sparsity_detector=DenseSparsityDetector(AutoFiniteDiff(); atol=1e-5) + ), + [:finitediff, :approx_sparse] + ), + ( + AutoSparse( + AutoPolyesterForwardDiff(; chunksize=8); + sparsity_detector=DenseSparsityDetector( + AutoPolyesterForwardDiff(; chunksize=8); atol=1e-5 + ) + ), + [:polyester, :approx_sparse] + ), + ( + AutoSparse( + AutoEnzyme(; mode=Enzyme.Forward); + sparsity_detector=DenseSparsityDetector( + AutoEnzyme(; mode=Enzyme.Forward); atol=1e-5 + ) + ), + [:enzyme, :approx_sparse] + ), + ( + AutoPolyesterForwardDiff(; chunksize=8), + [:polyester, :none] + ), +] + +times = Matrix{Float64}(undef, length(Ns), length(adtypes)) for (i, N) in enumerate(Ns) @info N test_problem = generate_brusselator_problem(N) - bruss_f!, u0 = (du, u) -> test_problem.f(du, u, test_problem.p), test_problem.u0 + bruss_f! = test_problem.f + u0 = test_problem.u0 y = similar(u0) - for (j, (sd, adtype)) in enumerate(algs) - if N < 2^9 || (N ≥ 2^9 && sd isa SymbolicsSparsityDetection) - times[i, j] = @belapsed $cache_and_compute_10_jacobians($adtype, $sd, $bruss_f!, $y, $u0) - @info times[i, j] - else - @info "Skipping would have timed out" - times[i, j] = NaN + + for (j, (adtype, _)) in enumerate(adtypes) + times[i, j] = @belapsed begin + $(cache_and_compute_10_jacobians)( + $(adtype), $(bruss_f!), $(y), $(u0), $(test_problem.p) + ) end + @info times[i, j] end end ``` @@ -228,101 +232,112 @@ end Plotting the results. ```julia +symbol_to_adname = Dict( + :finitediff => "Finite Diff", + :forwarddiff => "Forward Mode AD", + :polyester => "Threaded Forward Mode AD", + :enzyme => "Forward Mode AD (Enzyme)", +) + fig = begin - cycle = Cycle([:marker], covary = true) - plot_theme = Theme(Lines = (; cycle), Scatter = (; cycle)) + cycle = Cycle([:marker], covary=true) + plot_theme = Theme(Lines=(; cycle), Scatter=(; cycle)) with_theme(plot_theme) do - fig = Figure(; size = (1400, 1400 * 0.5)) + fig = Figure(; size=(1400, 1400 * 0.5)) - ax = Axis(fig[1, 1]; title = "Sparsity Pattern for 2D Brusselator Jacobian", - titlesize = 22, titlegap = 10, - xticksize = 20, yticksize = 20, xticklabelsize = 20, yticklabelsize = 20, - xtickwidth = 2.5, ytickwidth = 2.5, spinewidth = 2.5, yreversed = true) + ax = Axis(fig[1, 1]; title="Sparsity Pattern for 2D Brusselator Jacobian", + titlesize=22, titlegap=10, + xticksize=20, yticksize=20, xticklabelsize=20, yticklabelsize=20, + xtickwidth=2.5, ytickwidth=2.5, spinewidth=2.5, yreversed=true) - spy!(ax, J_; markersize = 16, marker = :circle, framecolor = :lightgray, - colormap = :seaborn_bright, strokewidth = 3) + spy!(ax, J_; markersize=1, marker=:circle, framecolor=:lightgray, + colormap=:seaborn_bright) - ax = Axis(fig[1, 2]; title = "Scaling of Sparse Jacobian Computation Algorithms", - titlesize = 22, titlegap = 10, xscale = log10, yscale = log10, - xticksize = 20, yticksize = 20, xticklabelsize = 20, yticklabelsize = 20, - xtickwidth = 2.5, ytickwidth = 2.5, spinewidth = 2.5, - xlabel = L"Input Dimension ($\mathbf{N}$)", ylabel = L"Time $\mathbf{(s)}$", xlabelsize = 22, - ylabelsize = 22, yaxisposition = :right) + ax = Axis(fig[1, 2]; title="Scaling of Sparse Jacobian Computation", + titlesize=22, titlegap=10, xscale=log10, yscale=log10, + xticksize=20, yticksize=20, xticklabelsize=20, yticklabelsize=20, + xtickwidth=2.5, ytickwidth=2.5, spinewidth=2.5, + xlabel=L"Input Dimension ($\mathbf{N}$)", ylabel=L"Time $\mathbf{(s)}$", xlabelsize=22, + ylabelsize=22, yaxisposition=:right) - colors = cgrad(:seaborn_bright, length(algs); categorical = true) + colors = cgrad(:seaborn_bright, length(adtypes); categorical=true) line_list = [] scatter_list = [] - Ns_ = Ns .^ 2 .* 2 + linestyles = [:solid, :solid, :solid, :dash, :dash, :dash, :dot, :dot] + + for (i, times) in enumerate(eachcol(times)) + l = lines!(Ns_, times; linewidth=5, color=colors[i], linestyle=linestyles[i]) + push!(line_list, l) + sc = scatter!(Ns_, times; markersize=16, strokewidth=2, color=colors[i]) + push!(scatter_list, sc) + end - push!(line_list, - lines!( - ax, Ns_, times[:, 1], color = colors[1], linewidth = 5, linestyle = :dash)) - push!( - scatter_list, scatter!(ax, Ns_, times[:, 1], color = colors[1], strokewidth = 3, markersize = 16)) - push!(line_list, lines!(ax, Ns_, times[:, 2], color = colors[2], linewidth = 5)) - push!( - scatter_list, scatter!(ax, Ns_, times[:, 2], color = colors[2], strokewidth = 3, markersize = 16)) - push!(line_list, - lines!( - ax, Ns_, times[:, 3], color = colors[3], linewidth = 5, linestyle = :dash)) - push!( - scatter_list, scatter!(ax, Ns_, times[:, 3], color = colors[3], strokewidth = 3, markersize = 16)) - push!(line_list, lines!(ax, Ns_, times[:, 4], color = colors[4], linewidth = 5)) - push!( - scatter_list, scatter!(ax, Ns_, times[:, 4], color = colors[4], strokewidth = 3, markersize = 16)) - push!(line_list, - lines!( - ax, Ns_, times[:, 5], color = colors[5], linewidth = 5, linestyle = :dot)) - push!( - scatter_list, scatter!(ax, Ns_, times[:, 5], color = colors[5], strokewidth = 3, markersize = 16)) - - group_symbolics = [ + tracer_idxs = [idx for idx in 1:length(adtypes) if :exact_sparse ∈ adtypes[idx][2]] + group_tracer = [ [ - LineElement(; color = line_list[idx].color, - linestyle = line_list[idx].linestyle, - linewidth = line_list[idx].linewidth), - MarkerElement(; color = scatter_list[idx].color, - marker = scatter_list[idx].marker, - strokewidth = scatter_list[idx].strokewidth, - markersize = scatter_list[idx].markersize) - ] - for idx in [1, 3]] - group_approx = [ + LineElement(; + color=line_list[idx].color, + linestyle=line_list[idx].linestyle, + linewidth=line_list[idx].linewidth, + ), + MarkerElement(; + color=scatter_list[idx].color, + marker=scatter_list[idx].marker, + strokewidth=scatter_list[idx].strokewidth, + markersize=scatter_list[idx].markersize, + ), + ] for idx in tracer_idxs + ] + + local_sparse_idxs = [idx for idx in 1:length(adtypes) if :approx_sparse ∈ adtypes[idx][2]] + group_local_sparse = [ [ - LineElement(; color = line_list[idx].color, - linestyle = line_list[idx].linestyle, - linewidth = line_list[idx].linewidth), - MarkerElement(; color = scatter_list[idx].color, - marker = scatter_list[idx].marker, - strokewidth = scatter_list[idx].strokewidth, - markersize = scatter_list[idx].markersize) - ] - for idx in [2, 4]] - legend_polyester = [ + LineElement(; + color=line_list[idx].color, + linestyle=line_list[idx].linestyle, + linewidth=line_list[idx].linewidth, + ), + MarkerElement(; + color=scatter_list[idx].color, + marker=scatter_list[idx].marker, + strokewidth=scatter_list[idx].strokewidth, + markersize=scatter_list[idx].markersize, + ), + ] for idx in local_sparse_idxs + ] + + non_sparse_idxs = [idx for idx in 1:length(adtypes) if :none ∈ adtypes[idx][2]] + group_nonsparse = [ [ - LineElement(; color = line_list[5].color, - linestyle = line_list[5].linestyle, - linewidth = line_list[5].linewidth), - MarkerElement(; color = scatter_list[5].color, - marker = scatter_list[5].marker, - strokewidth = scatter_list[5].strokewidth, - markersize = scatter_list[5].markersize) - ] + LineElement(; + color=line_list[idx].color, + linestyle=line_list[idx].linestyle, + linewidth=line_list[idx].linewidth, + ), + MarkerElement(; + color=scatter_list[idx].color, + marker=scatter_list[idx].marker, + strokewidth=scatter_list[idx].strokewidth, + markersize=scatter_list[idx].markersize, + ), + ] for idx in non_sparse_idxs ] - axislegend(ax, - [group_symbolics, group_approx, legend_polyester], + axislegend( + ax, + [group_tracer, group_local_sparse, group_nonsparse], [ - ["Finite Diff", "Forward Diff"], - ["Finite Diff", "Threaded Forward Diff"], - ["Threaded Forward Diff"] + [symbol_to_adname[adtypes[idx][2][1]] for idx in tracer_idxs], + [symbol_to_adname[adtypes[idx][2][1]] for idx in local_sparse_idxs], + [symbol_to_adname[adtypes[idx][2][1]] for idx in non_sparse_idxs], ], - ["Symbolic Sparsity", "Approx. Sparsity", "No Sparsity"]; - position = :rb, framevisible = true, framewidth = 2.5, titlesize = 18, - labelsize = 16, patchsize = (40.0f0, 20.0f0)) + ["Exact Sparsity", "Approx. Local Sparsity", "No Sparsity"]; + position=:rb, framevisible=true, framewidth=2.5, titlesize=18, + labelsize=16, patchsize=(40.0f0, 20.0f0) + ) fig end @@ -338,31 +353,37 @@ save("brusselator_sparse_jacobian_scaling.svg", fig) First, let us experiment the scaling of each algorithm with the problem size. ```julia -Ns = vcat(collect(2 .^ (2:7)), [150, 175, 200]) +Ns = vcat(collect(2 .^ (2:7)), [150, 175, 200]) +# XXX: PETSc just segfaults solvers_scaling = [ - (; pkg = :nonlinearsolve, sparsity = :none, name = "NR (Dense)", alg = NewtonRaphson(; linsolve = nothing)), - (; pkg = :nonlinearsolve, sparsity = :approx, name = "NR (Approx. Sparse)", alg = NewtonRaphson(; linsolve = nothing)), - (; pkg = :nonlinearsolve, sparsity = :exact, name = "NR (Exact Sparse)", alg = NewtonRaphson(; linsolve = nothing)), - (; pkg = :wrapper, sparsity = :none, name = "NR [NLsolve.jl]", alg = NLsolveJL(; method = :newton, autodiff = :forward)), - (; pkg = :wrapper, sparsity = :none, name = "Mod. NR [Sundials]", alg = KINSOL()), - - (; pkg = :nonlinearsolve, sparsity = :none, name = "TR (Dense)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve, linsolve = nothing)), - (; pkg = :nonlinearsolve, sparsity = :approx, name = "TR (Approx. Sparse)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve, linsolve = nothing)), - (; pkg = :nonlinearsolve, sparsity = :exact, name = "TR (Exact Sparse)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve, linsolve = nothing)), - (; pkg = :wrapper, sparsity = :none, name = "TR [NLsolve.jl]", alg = NLsolveJL(; autodiff = :forward)), - - (; pkg = :wrapper, sparsity = :none, name = "Mod. Powell [MINPACK]", alg = CMINPACK()), + (; pkg = :nonlinearsolve, sparsity = :none, name = "NR (No Sparsity)", alg = NewtonRaphson()), + # (; pkg = :nonlinearsolve, sparsity = :approx, name = "NR (Approx. Local Sparsity)", alg = NewtonRaphson()), + (; pkg = :nonlinearsolve, sparsity = :exact, name = "NR (Exact Sparsity)", alg = NewtonRaphson()), + (; pkg = :wrapper, sparsity = :none, name = "NR [NLsolve.jl]", alg = NLsolveJL(; method = :newton, autodiff = :forward)), + (; pkg = :wrapper, sparsity = :none, name = "Mod. NR [Sundials]", alg = KINSOL()), + # (; pkg = :wrapper, sparsity = :none, name = "NR [PETSc] (No Sparsity)", alg = PETScSNES(; snes_type = "newtonls")), + # (; pkg = :wrapper, sparsity = :none, name = "NR [PETSc] (Approx. Local Sparsity)", alg = PETScSNES(; snes_type = "newtonls")), + # (; pkg = :wrapper, sparsity = :none, name = "NR [PETSc] (Exact Sparsity)", alg = PETScSNES(; snes_type = "newtonls")), + + (; pkg = :nonlinearsolve, sparsity = :none, name = "TR (No Sparsity)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve)), + # (; pkg = :nonlinearsolve, sparsity = :approx, name = "TR (Approx. Local Sparsity)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve)), + (; pkg = :nonlinearsolve, sparsity = :exact, name = "TR (Exact Sparsity)", alg = TrustRegion(; radius_update_scheme = RUS.NLsolve)), + (; pkg = :wrapper, sparsity = :none, name = "TR [NLsolve.jl]", alg = NLsolveJL(; autodiff = :forward)), + # (; pkg = :wrapper, sparsity = :none, name = "TR [PETSc] (No Sparsity)", alg = PETScSNES(; snes_type = "newtontr")), + # (; pkg = :wrapper, sparsity = :none, name = "TR [PETSc] (Approx. Local Sparsity)", alg = PETScSNES(; snes_type = "newtontr")), + # (; pkg = :wrapper, sparsity = :none, name = "TR [PETSc] (Exact Sparsity)", alg = PETScSNES(; snes_type = "newtontr")), + + (; pkg = :wrapper, sparsity = :none, name = "Mod. Powell [MINPACK]", alg = CMINPACK()), ] -runtimes_scaling = zeros(length(solvers_scaling), length(Ns)) .- 1 +runtimes_scaling = fill(-1.0, length(solvers_scaling), length(Ns)) for (i, N) in enumerate(Ns) prob_dense = generate_brusselator_problem(N) - prob_approx_sparse = generate_brusselator_problem(N; - sparsity = ApproximateJacobianSparsity()) prob_exact_sparse = generate_brusselator_problem(N; - sparsity = SymbolicsSparsityDetection()) + sparsity = TracerSparsityDetector() + ) @info "Benchmarking N = $N" @@ -371,36 +392,39 @@ for (i, N) in enumerate(Ns) alg = solver.alg name = solver.name - if ptype == :none - prob = prob_dense + prob = if ptype == :none + prob_dense elseif ptype == :approx - prob = prob_approx_sparse + # With Tracing based sparsity detection, we dont need this any more + error("Approximate Sparsity not implemented") elseif ptype == :exact - prob = prob_exact_sparse + prob_exact_sparse end - if (j > 1 && runtimes_scaling[j - 1, i] == -1) || (alg isa CMINPACK && N > 32) || + if (j > 1 && runtimes_scaling[j - 1, i] == -1) || + (alg isa CMINPACK && N > 32) || (alg isa KINSOL && N > 64) || (alg isa NLsolveJL && N > 64 && alg.method == :trust_region) || - (alg isa GeneralizedFirstOrderAlgorithm{nothing, :TrustRegion} && N > 64) || + (alg isa GeneralizedFirstOrderAlgorithm && alg.name == :TrustRegion && N > 64) || (alg isa NLsolveJL && N > 128 && alg.method == :newton) || - (alg isa GeneralizedFirstOrderAlgorithm{nothing, :NewtonRaphson} && N > 128 && ptype == :none) || - (alg isa GeneralizedFirstOrderAlgorithm{nothing, :NewtonRaphson} && N > 150 && ptype == :approx) + (alg isa GeneralizedFirstOrderAlgorithm && alg.name == :NewtonRaphson && N > 128 && ptype == :none) || + (alg isa GeneralizedFirstOrderAlgorithm && alg.name == :NewtonRaphson && N > 150 && ptype == :approx) # The last benchmark failed so skip this too runtimes_scaling[j, i] = NaN @warn "$(name): Would Have Timed out" else - alg_concrete = __set_ad_chunksize(alg, NonlinearSolve.pickchunksize(prob.u0), - prob.f.sparsity, length(prob.u0)) - - function __benchmark_function() - sol = solve(prob, alg_concrete; abstol=1e-6, reltol=1e-6, - termination_condition=AbsNormTerminationMode()) - runtimes_scaling[j, i] = @belapsed solve($prob, $alg_concrete; abstol=1e-6, - reltol=1e-6, termination_condition=$AbsNormTerminationMode()) + function benchmark_function() + termination_condition = (alg isa PETScSNES || alg isa KINSOL) ? + nothing : + NonlinearSolveBase.AbsNormTerminationMode(Base.Fix1(maximum, abs)) + sol = solve(prob, alg; abstol=1e-6, reltol=1e-6, termination_condition) + runtimes_scaling[j, i] = @belapsed solve($prob, $alg; abstol=1e-6, + reltol=1e-6, termination_condition=$termination_condition) @info "$(name): $(runtimes_scaling[j, i]) | $(norm(sol.resid, Inf)) | $(sol.retcode)" end - timeout(__benchmark_function, 600) + + timeout(benchmark_function, 600) + if runtimes_scaling[j, i] == -1 @warn "$(name): Timed out" runtimes_scaling[j, i] = NaN @@ -426,7 +450,7 @@ fig = begin theme = Theme(Lines = (cycle = cycle,), Scatter = (cycle = cycle,)) LINESTYLES = Dict( (:nonlinearsolve, :none) => :solid, - (:nonlinearsolve, :approx) => :dash, + # (:nonlinearsolve, :approx) => :dash, (:nonlinearsolve, :exact) => :dashdot, # (:simplenonlinearsolve, :none) => :solid, (:wrapper, :none) => :dot, @@ -467,7 +491,7 @@ fig = begin sparsity_legend = [ LineElement(; linestyle = :solid, linewidth = 5), - LineElement(; linestyle = :dash, linewidth = 5), + # LineElement(; linestyle = :dash, linewidth = 5), LineElement(; linestyle = :dashdot, linewidth = 5), ] @@ -478,7 +502,12 @@ fig = begin tellheight = true, tellwidth = false, patchsize = (60.0f0, 20.0f0), position = :rb) - axislegend(ax, sparsity_legend, ["No Sparsity Detection", "Approx. Sparsity", "Exact Sparsity"], + axislegend(ax, sparsity_legend, + [ + "No Sparsity Detection", + # "Approx. Sparsity", + "Exact Sparsity" + ], "Sparsity Detection"; framevisible=true, framewidth = STROKEWIDTH, orientation = :vertical, titlesize = 20, nbanks = 1, labelsize = 16, tellheight = true, tellwidth = false, patchsize = (60.0f0, 20.0f0), @@ -507,55 +536,41 @@ jacobian-free methods via `:GMRES`. ```julia using AlgebraicMultigrid, IncompleteLU -function incompletelu(W, du, u, p, t, newW, Plprev, Prprev, solverdata) - if newW === nothing || newW - Pl = ilu(W, τ = 50.0) - else - Pl = Plprev - end - Pl, nothing -end +incompletelu(W, p = nothing) = ilu(W, τ = 50.0), LinearAlgebra.I -function algebraicmultigrid(W, du, u, p, t, newW, Plprev, Prprev, solverdata) - if newW === nothing || newW - Pl = aspreconditioner(ruge_stuben(convert(AbstractMatrix, W))) - else - Pl = Plprev - end - Pl, nothing +function algebraicmultigrid(W, p = nothing) + return aspreconditioner(ruge_stuben(convert(AbstractMatrix, W))), LinearAlgebra.I end -function algebraicmultigrid_jacobi(W, du, u, p, t, newW, Plprev, Prprev, solverdata) - if newW === nothing || newW - A = convert(AbstractMatrix, W) - Pl = AlgebraicMultigrid.aspreconditioner(AlgebraicMultigrid.ruge_stuben( - A, presmoother = AlgebraicMultigrid.Jacobi(rand(size(A, 1))), - postsmoother = AlgebraicMultigrid.Jacobi(rand(size(A, 1))))) - else - Pl = Plprev - end - Pl, nothing +function algebraicmultigrid_jacobi(W, p = nothing) + A = convert(AbstractMatrix, W) + Pl = AlgebraicMultigrid.aspreconditioner(AlgebraicMultigrid.ruge_stuben( + A, presmoother = AlgebraicMultigrid.Jacobi(rand(size(A, 1))), + postsmoother = AlgebraicMultigrid.Jacobi(rand(size(A, 1))) + )) + return Pl, LinearAlgebra.I end Ns = 2 .^ (2:7) solvers_scaling_jacobian_free = [ (; pkg = :nonlinearsolve, name = "Newton Krylov", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES())), - (; pkg = :nonlinearsolve, name = "Newton Krylov (ILU)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(), precs = incompletelu, concrete_jac = true)), - (; pkg = :nonlinearsolve, name = "Newton Krylov (AMG)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(), precs = algebraicmultigrid, concrete_jac = true)), - (; pkg = :nonlinearsolve, name = "Newton Krylov (AMG Jacobi)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(), precs = algebraicmultigrid_jacobi, concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "Newton Krylov (ILU)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(; precs = incompletelu), concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "Newton Krylov (AMG)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(; precs = algebraicmultigrid), concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "Newton Krylov (AMG Jacobi)", alg = NewtonRaphson(; linsolve = KrylovJL_GMRES(; precs = algebraicmultigrid_jacobi), concrete_jac = true)), (; pkg = :nonlinearsolve, name = "TR Krylov", alg = TrustRegion(; linsolve = KrylovJL_GMRES())), - (; pkg = :nonlinearsolve, name = "TR Krylov (ILU)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(), precs = incompletelu, concrete_jac = true)), - (; pkg = :nonlinearsolve, name = "TR Krylov (AMG)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(), precs = algebraicmultigrid, concrete_jac = true)), - (; pkg = :nonlinearsolve, name = "TR Krylov (AMG Jacobi)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(), precs = algebraicmultigrid_jacobi, concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "TR Krylov (ILU)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(; precs = incompletelu), concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "TR Krylov (AMG)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(; precs = algebraicmultigrid), concrete_jac = true)), + (; pkg = :nonlinearsolve, name = "TR Krylov (AMG Jacobi)", alg = TrustRegion(; linsolve = KrylovJL_GMRES(; precs = algebraicmultigrid_jacobi), concrete_jac = true)), (; pkg = :wrapper, name = "Newton Krylov [Sundials]", alg = KINSOL(; linear_solver = :GMRES)), ] runtimes_scaling = zeros(length(solvers_scaling_jacobian_free), length(Ns)) .- 1 for (i, N) in enumerate(Ns) - prob = generate_brusselator_problem(N; - sparsity = ifelse(N ≥ 6, SymbolicsSparsityDetection(), ApproximateJacobianSparsity())) + prob = generate_brusselator_problem( + N; sparsity = TracerSparsityDetector() + ) @info "Benchmarking N = $N" @@ -568,22 +583,26 @@ for (i, N) in enumerate(Ns) runtimes_scaling[j, i] = NaN @warn "$(name): Would Have Timed out" else - alg_concrete = __set_ad_chunksize(alg, NonlinearSolve.pickchunksize(prob.u0), - prob.f.sparsity, length(prob.u0)) - - function __benchmark_function() - sol = solve(prob, alg_concrete; abstol=1e-6, reltol=1e-6, + function benchmark_function() + termination_condition = (alg isa PETScSNES || alg isa KINSOL) ? + nothing : + NonlinearSolveBase.AbsNormTerminationMode(Base.Fix1(maximum, abs)) + sol = solve(prob, alg; abstol=1e-6, reltol=1e-6, linsolve_kwargs = (; abstol = 1e-9, reltol = 1e-9), - termination_condition=AbsNormTerminationMode()) + termination_condition) if SciMLBase.successful_retcode(sol) || norm(sol.resid, Inf) ≤ 1e-5 - runtimes_scaling[j, i] = @belapsed solve($prob, $alg_concrete; abstol=1e-6, - reltol=1e-6, termination_condition=$AbsNormTerminationMode()) + runtimes_scaling[j, i] = @belapsed solve($prob, $alg; abstol=1e-6, + reltol=1e-6, + linsolve_kwargs = (; abstol = 1e-9, reltol = 1e-9), + termination_condition=$termination_condition) else runtimes_scaling[j, i] = NaN end @info "$(name): $(runtimes_scaling[j, i]) | $(norm(sol.resid, Inf)) | $(sol.retcode)" end - timeout(__benchmark_function, 600) + + timeout(benchmark_function, 600) + if runtimes_scaling[j, i] == -1 @warn "$(name): Timed out" runtimes_scaling[j, i] = NaN @@ -676,26 +695,24 @@ In this section, we will generate the work-precision of the solvers. All solvers exploit sparsity will automatically do so. ```julia -DEFAULT_FORWARD_AD = AutoSparsePolyesterForwardDiff(; chunksize = 12) - solvers_all = [ - (; pkg = :nonlinearsolve, name = "Default PolyAlg", solver = Dict(:alg => FastShortcutNonlinearPolyalg(; autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "RobustMultiNewton (GMRES)", solver = Dict(:alg => RobustMultiNewton(; linsolve = KrylovJL_GMRES(), autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Newton Krylov", solver = Dict(:alg => NewtonRaphson(; linsolve = KrylovJL_GMRES(), autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Trust Region", solver = Dict(:alg => TrustRegion(; autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "TR Krylov", solver = Dict(:alg => TrustRegion(; linsolve = KrylovJL_GMRES(), autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :wrapper, name = "NR [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; method = :newton, autodiff = :forward))), - (; pkg = :wrapper, name = "TR [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; autodiff = :forward))), - (; pkg = :wrapper, name = "NR [Sundials]", solver = Dict(:alg => KINSOL())), - (; pkg = :wrapper, name = "Newton Krylov [Sundials]", solver = Dict(:alg => KINSOL(; linear_solver = :GMRES))), - - (; pkg = :wrapper, name = "Mod. Powell [MINPACK]", solver = Dict(:alg => CMINPACK())), + (; pkg = :nonlinearsolve, name = "Default PolyAlg", solver = Dict(:alg => FastShortcutNonlinearPolyalg())), + (; pkg = :nonlinearsolve, name = "RobustMultiNewton (GMRES)", solver = Dict(:alg => RobustMultiNewton(; linsolve = KrylovJL_GMRES()))), + (; pkg = :nonlinearsolve, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing))), + (; pkg = :nonlinearsolve, name = "Newton Krylov", solver = Dict(:alg => NewtonRaphson(; linsolve = KrylovJL_GMRES()))), + (; pkg = :nonlinearsolve, name = "Trust Region", solver = Dict(:alg => TrustRegion())), + (; pkg = :nonlinearsolve, name = "TR Krylov", solver = Dict(:alg => TrustRegion(; linsolve = KrylovJL_GMRES()))), + (; pkg = :wrapper, name = "NR [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; method = :newton, autodiff = :forward))), + (; pkg = :wrapper, name = "TR [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; autodiff = :forward))), + (; pkg = :wrapper, name = "NR [Sundials]", solver = Dict(:alg => KINSOL())), + (; pkg = :wrapper, name = "Newton Krylov [Sundials]", solver = Dict(:alg => KINSOL(; linear_solver = :GMRES))), + + (; pkg = :wrapper, name = "Mod. Powell [MINPACK]", solver = Dict(:alg => CMINPACK())), ]; ``` ```julia -prob_wpd = generate_brusselator_problem(32; sparsity = ApproximateJacobianSparsity()) +prob_wpd = generate_brusselator_problem(32; sparsity = TracerSparsityDetector()) abstols = 1.0 ./ 10 .^ (2:10) reltols = 1.0 ./ 10 .^ (2:10) diff --git a/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd b/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd index 892a8b1b1..10b283e79 100644 --- a/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd +++ b/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd @@ -21,35 +21,40 @@ Fetch required packages. ```julia using NonlinearSolve, LinearSolve, StaticArrays, Sundials, SpeedMapping, - BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie + BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie, + RecursiveFactorization import MINPACK, NLsolve -RUS = RadiusUpdateSchemes; +import LineSearches + +const RUS = RadiusUpdateSchemes; ``` Declare the benchmarked solvers (and their names and plotting options). ```julia -DEFAULT_FORWARD_AD = AutoForwardDiff(; chunksize = 12) +HagerZhang() = LineSearchesJL(; method = LineSearches.HagerZhang()) +MoreThuente() = LineSearchesJL(; method = LineSearches.MoreThuente()) +# XXX: Add PETSc solvers_all = [ - (; pkg = :nonlinearsolve, name = "Default PolyAlgorithm", solver = Dict(:alg => FastShortcutNonlinearPolyalg(; autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Newton Raphson (HagerZhang LineSearch)", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing, linesearch = HagerZhang()))), - (; pkg = :nonlinearsolve, name = "Newton Raphson (MoreThuente LineSearch)", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing, linesearch = MoreThuente()))), - (; pkg = :nonlinearsolve, name = "Newton Raphson (BackTracking LineSearch)", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing, linesearch = BackTracking()))), + (; pkg = :nonlinearsolve, name = "Default PolyAlgorithm", solver = Dict(:alg => FastShortcutNonlinearPolyalg())), + (; pkg = :nonlinearsolve, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson())), + (; pkg = :nonlinearsolve, name = "Newton Raphson (HagerZhang LineSearch)", solver = Dict(:alg => NewtonRaphson(; linesearch = HagerZhang()))), + (; pkg = :nonlinearsolve, name = "Newton Raphson (MoreThuente LineSearch)", solver = Dict(:alg => NewtonRaphson(; linesearch = MoreThuente()))), + (; pkg = :nonlinearsolve, name = "Newton Raphson (BackTracking LineSearch)", solver = Dict(:alg => NewtonRaphson(; linesearch = BackTracking()))), (; pkg = :nonlinearsolve, name = "Newton Krylov with GMRES", solver = Dict(:alg => NewtonRaphson(; linsolve = KrylovJL_GMRES()))), (; pkg = :nonlinearsolve, name = "DFSane", solver = Dict(:alg => DFSane())), (; pkg = :nonlinearsolve, name = "Trust Region", solver = Dict(:alg => TrustRegion())), - (; pkg = :nonlinearsolve, name = "Trust Region (NLsolve Update)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.NLsolve))), - (; pkg = :nonlinearsolve, name = "Trust Region (Nocedal Wright)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.NocedalWright))), - (; pkg = :nonlinearsolve, name = "Trust Region (Hei)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.Hei))), - (; pkg = :nonlinearsolve, name = "Trust Region (Yuan)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.Yuan))), - (; pkg = :nonlinearsolve, name = "Trust Region (Bastin)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.Bastin))), - (; pkg = :nonlinearsolve, name = "Trust Region (Fan)", solver = Dict(:alg => TrustRegion(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD, radius_update_scheme = RUS.Fan))), - (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt", solver = Dict(:alg => LevenbergMarquardt(; linsolve = nothing, autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt with Cholesky", solver = Dict(:alg => LevenbergMarquardt(; autodiff = DEFAULT_FORWARD_AD, linsolve = CholeskyFactorization()))), - (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt (No Geodesic Accln.)", solver = Dict(:alg => LevenbergMarquardt(; linsolve = nothing, disable_geodesic = Val(true), autodiff = DEFAULT_FORWARD_AD))), - (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt (No Geodesic Accln.) with Cholesky", solver = Dict(:alg => LevenbergMarquardt(; disable_geodesic = Val(true), autodiff = DEFAULT_FORWARD_AD, linsolve = CholeskyFactorization()))), + (; pkg = :nonlinearsolve, name = "Trust Region (NLsolve Update)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NLsolve))), + (; pkg = :nonlinearsolve, name = "Trust Region (Nocedal Wright)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NocedalWright))), + (; pkg = :nonlinearsolve, name = "Trust Region (Hei)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Hei))), + (; pkg = :nonlinearsolve, name = "Trust Region (Yuan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Yuan))), + (; pkg = :nonlinearsolve, name = "Trust Region (Bastin)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Bastin))), + (; pkg = :nonlinearsolve, name = "Trust Region (Fan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Fan))), + (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt", solver = Dict(:alg => LevenbergMarquardt())), + (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt with Cholesky", solver = Dict(:alg => LevenbergMarquardt(; linsolve = CholeskyFactorization()))), + (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt (No Geodesic Accln.)", solver = Dict(:alg => LevenbergMarquardt(; disable_geodesic = Val(true)))), + (; pkg = :nonlinearsolve, name = "Levenberg-Marquardt (No Geodesic Accln.) with Cholesky", solver = Dict(:alg => LevenbergMarquardt(; disable_geodesic = Val(true), linsolve = CholeskyFactorization()))), (; pkg = :wrapper, name = "Modified Powell [MINPACK]", solver = Dict(:alg => CMINPACK(; method = :hybr))), (; pkg = :wrapper, name = "Levenberg-Marquardt [MINPACK]", solver = Dict(:alg => CMINPACK(; method = :lm))), (; pkg = :wrapper, name = "Newton Raphson [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; method = :newton, autodiff = :forward))), diff --git a/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd b/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd index 6b523a7d7..ed7577df5 100644 --- a/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd +++ b/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd @@ -36,34 +36,37 @@ Fetch required packages. ```julia using NonlinearSolve, LinearSolve, StaticArrays, Sundials, Setfield, - BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie + BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie, + RecursiveFactorization import PolyesterForwardDiff, MINPACK, NLsolve -RUS = RadiusUpdateSchemes; + +const RUS = RadiusUpdateSchemes; ``` Declare the benchmarked solvers (and their names and plotting options). ```julia +# XXX: Add PETSc solvers_all = [ (; pkg = :nonlinearsolve, type = :general, name = "Default PolyAlg.", solver = Dict(:alg => FastShortcutNonlinearPolyalg(; u0_len = 10))), - (; pkg = :nonlinearsolve, type = :NR, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson(; linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :NR, name = "NR (HagerZhang)", solver = Dict(:alg => NewtonRaphson(; linesearch = HagerZhang(), linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :NR, name = "NR (MoreThuente)", solver = Dict(:alg => NewtonRaphson(; linesearch = MoreThuente(), linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :NR, name = "NR (BackTracking)", solver = Dict(:alg => NewtonRaphson(; linesearch = BackTracking(), linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "Trust Region", solver = Dict(:alg => TrustRegion(; linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (NLsolve Update)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NLsolve, linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (Nocedal Wright)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NocedalWright, linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (Hei)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Hei, linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (Yuan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Yuan, linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (Bastin)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Bastin, linsolve = nothing))), - (; pkg = :nonlinearsolve, type = :TR, name = "TR (Fan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Fan, linsolve = nothing))), + (; pkg = :nonlinearsolve, type = :NR, name = "Newton Raphson", solver = Dict(:alg => NewtonRaphson())), + (; pkg = :nonlinearsolve, type = :NR, name = "NR (HagerZhang)", solver = Dict(:alg => NewtonRaphson(; linesearch = HagerZhang()))), + (; pkg = :nonlinearsolve, type = :NR, name = "NR (MoreThuente)", solver = Dict(:alg => NewtonRaphson(; linesearch = MoreThuente()))), + (; pkg = :nonlinearsolve, type = :NR, name = "NR (BackTracking)", solver = Dict(:alg => NewtonRaphson(; linesearch = BackTracking()))), + (; pkg = :nonlinearsolve, type = :TR, name = "Trust Region", solver = Dict(:alg => TrustRegion())), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (NLsolve Update)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NLsolve))), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (Nocedal Wright)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.NocedalWright))), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (Hei)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Hei))), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (Yuan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Yuan))), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (Bastin)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Bastin))), + (; pkg = :nonlinearsolve, type = :TR, name = "TR (Fan)", solver = Dict(:alg => TrustRegion(; radius_update_scheme = RUS.Fan))), (; pkg = :nonlinearsolve, type = :LM, name = "Levenberg-Marquardt", solver = Dict(:alg => LevenbergMarquardt(; linsolve = QRFactorization()))), (; pkg = :nonlinearsolve, type = :LM, name = "LM with Cholesky", solver = Dict(:alg => LevenbergMarquardt(; linsolve = CholeskyFactorization()))), (; pkg = :nonlinearsolve, type = :LM, name = "LM (α_geodesic=0.5)", solver = Dict(:alg => LevenbergMarquardt(; linsolve = QRFactorization(), α_geodesic=0.5))), (; pkg = :nonlinearsolve, type = :LM, name = "LM (α_geodesic=0.5) Chol.", solver = Dict(:alg => LevenbergMarquardt(; linsolve = CholeskyFactorization(), α_geodesic=0.5))), (; pkg = :nonlinearsolve, type = :LM, name = "LM (no Accln.)", solver = Dict(:alg => LevenbergMarquardt(; linsolve = QRFactorization(), disable_geodesic = Val(true)))), (; pkg = :nonlinearsolve, type = :LM, name = "LM (no Accln.) Chol.", solver = Dict(:alg => LevenbergMarquardt(; linsolve = CholeskyFactorization(), disable_geodesic = Val(true)))), - (; pkg = :nonlinearsolve, type = :general, name = "Pseudo Transient", solver = Dict(:alg => PseudoTransient(; linsolve = nothing, alpha_initial=10.0))), + (; pkg = :nonlinearsolve, type = :general, name = "Pseudo Transient", solver = Dict(:alg => PseudoTransient(; alpha_initial=10.0))), (; pkg = :wrapper, type = :general, name = "Powell [MINPACK]", solver = Dict(:alg => CMINPACK(; method=:hybr))), (; pkg = :wrapper, type = :general, name = "LM [MINPACK]", solver = Dict(:alg => CMINPACK(; method=:lm))), (; pkg = :wrapper, type = :general, name = "NR [NLsolve.jl]", solver = Dict(:alg => NLsolveJL(; method=:newton))), @@ -86,34 +89,13 @@ reltols = 1.0 ./ 10.0 .^ (4:12); Prepares various helper functions for benchmarking a specific problem. ```julia -function set_ad_chunksize(solvers, u0) - ck = NonlinearSolve.pickchunksize(u0) - for i in 1:length(solvers) - @set! solvers[i].solver[:alg] = __set_ad_chunksize(solvers[i].solver[:alg], ck) - end - return solvers -end - -function __set_ad_chunksize(solver::GeneralizedFirstOrderAlgorithm{CJ, N}, ck) where {CJ, N} - ad = AutoForwardDiff(; chunksize = ck) - return GeneralizedFirstOrderAlgorithm{CJ, N}(; solver.descent, solver.linesearch, - solver.trustregion, jacobian_ad = ad, solver.max_shrink_times, solver.forward_ad, - solver.reverse_ad) -end -function __set_ad_chunksize(solver::NonlinearSolvePolyAlgorithm{pType}, ck) where {pType} - algs = [__set_ad_chunksize(alg, ck) for alg in solver.algs] - return NonlinearSolvePolyAlgorithm(algs, Val(pType); solver.start_index) -end -__set_ad_chunksize(solver, ck) = solver - # Benchmarks a specific problem, checks which solvers can solve it and their performance function benchmark_problem!(prob_name; solver_tracker=solver_tracker) # Finds the problem and the true solution. prob = nlprob_23_testcases[prob_name] # Finds the solvers that can solve the problem - solvers_concrete = set_ad_chunksize(solvers_all, prob.prob.u0); - successful_solvers = filter(solver -> check_solver(prob, solver), solvers_concrete); + successful_solvers = filter(Base.Fix1(check_solver, prob), solvers_all); push!(solver_tracker, prob_name => successful_solvers); # Handles the non-general cases. @@ -122,13 +104,16 @@ function benchmark_problem!(prob_name; solver_tracker=solver_tracker) solvers_LM = filter(s -> s.type==:LM, successful_solvers) wp_NR = WorkPrecisionSet(prob.prob, abstols, reltols, getfield.(solvers_NR, :solver); names=getfield.(solvers_NR, :name), numruns=100, error_estimate=:l∞, - maxiters=1000, termination_condition = AbsNormTerminationMode()) + maxiters=1000, + termination_condition = NonlinearSolve.AbsNormTerminationMode(Base.Fix1(maximum, abs))) wp_TR = WorkPrecisionSet(prob.prob, abstols, reltols, getfield.(solvers_TR, :solver); names=getfield.(solvers_TR, :name), numruns=100, error_estimate=:l∞, - maxiters=1000, termination_condition = AbsNormTerminationMode()) + maxiters=1000, + termination_condition = NonlinearSolve.AbsNormTerminationMode(Base.Fix1(maximum, abs))) wp_LM = WorkPrecisionSet(prob.prob, abstols, reltols, getfield.(solvers_LM, :solver); names=getfield.(solvers_LM, :name), numruns=100, error_estimate=:l∞, - maxiters=1000, termination_condition = AbsNormTerminationMode()) + maxiters=1000, + termination_condition = NonlinearSolve.AbsNormTerminationMode(Base.Fix1(maximum, abs))) # Handles the general case solvers_general = filter(s -> s.type==:general, successful_solvers) @@ -153,7 +138,8 @@ end function check_solver(prob, solver) try sol = solve(prob.prob, solver.solver[:alg]; abstol=1e-8, reltol=1e-8, - maxiters=1000000, termination_condition=AbsNormTerminationMode()) + maxiters=1000000, + termination_condition=NonlinearSolve.AbsNormTerminationMode(Base.Fix1(maximum, abs))) if norm(sol.resid, Inf) < 1e-6 Base.printstyled("[Info] Solver $(solver.name) returned retcode $(sol.retcode) \ with an residual norm = $(norm(sol.resid, Inf)).\n"; color=:green) diff --git a/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd b/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd index 6c7b1e4f4..9129ee964 100644 --- a/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd +++ b/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd @@ -7,9 +7,10 @@ This is a test of a simple small nonlinear rootfinding problem. ```julia using NonlinearSolve, StaticArrays, DiffEqDevTools, Sundials, CairoMakie, LinearSolve, - LinearAlgebra, StableRNGs, BenchmarkTools, Setfield + LinearAlgebra, StableRNGs, BenchmarkTools, Setfield, RecursiveFactorization import PolyesterForwardDiff, MINPACK, NLsolve, SpeedMapping -RUS = RadiusUpdateSchemes; + +const RUS = RadiusUpdateSchemes; BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.5; f_oop(u, p) = u .* u .- p @@ -18,7 +19,8 @@ f_iip(du, u, p) = @. du = u * u - p function generate_prob(::Val{N}, ::Val{static}) where {N, static} u0_ = ones(N) .+ randn(StableRNG(0), N) * 0.01 u0 = static ? SVector{N, Float64}(u0_) : u0_ - prob = static ? NonlinearProblem{false}(f_oop, u0, 2.0) : + prob = static ? + NonlinearProblem{false}(f_oop, u0, 2.0) : NonlinearProblem{true}(f_iip, u0, 2.0) return prob end @@ -207,46 +209,28 @@ save("regular_arrays_quadratic.svg", fig) ## Comparison against SimpleNonlinearSolve ```julia -function __set_ad_chunksize(solver::GeneralizedFirstOrderAlgorithm{CJ, N}, ck) where {CJ, N} - ad = AutoForwardDiff(; chunksize = ck) - return GeneralizedFirstOrderAlgorithm{CJ, N}(; solver.descent, solver.linesearch, - solver.trustregion, jacobian_ad = ad, solver.max_shrink_times, solver.forward_ad, - solver.reverse_ad) -end -function __set_ad_chunksize(solver::SimpleNewtonRaphson, ck) - solver.autodiff === nothing || return solver - autodiff = AutoForwardDiff(; chunksize = ck) - return SimpleNewtonRaphson(; autodiff) -end -function __set_ad_chunksize(solver::SimpleTrustRegion, ck) - solver.autodiff === nothing || return solver - autodiff = AutoForwardDiff(; chunksize = ck) - return SimpleTrustRegion(; autodiff) -end -__set_ad_chunksize(solver, _) = solver - function benchmark_combinations(solvers, probs) return map(Iterators.product(solvers, probs)) do (solver, prob) try - solver_concrete = prob.u0 isa SArray ? solver.solver[:alg] : - __set_ad_chunksize(solver.solver[:alg], - min(NonlinearSolve.pickchunksize(prob.u0), 6)) - + solver_concrete = solver.solver[:alg] + termination_condition = NonlinearSolveBase.AbsNormTerminationMode( + Base.Fix1(maximum, abs)) sol = solve(prob, solver_concrete; abstol = 1e-10, reltol = 1e-10, - maxiters = 1000, termination_condition = AbsNormTerminationMode()) + maxiters = 1000, termination_condition) @info "Solver $(solver.name) successfully solved the problem with norm = \ $(norm(sol.resid, Inf))." if norm(sol.resid, Inf) ≤ 1e-10 tt = @belapsed solve($prob, $solver_concrete; abstol = 1e-10, - reltol = 1e-10, maxiters = 1000) + reltol = 1e-10, maxiters = 1000, + termination_condition = $termination_condition) @info "Solver $(solver.name) took $(tt) seconds." return tt else return NaN end catch e - @error "Solver $(solver.name) threw an error." + @error "Solver $(solver.name) threw an error $(e)." return NaN end end @@ -299,15 +283,14 @@ fig = begin ax = Axis(fig[1, i]; ylabel = "", - title = L"N = %$(length(probs_sa[i].u0))$", + title = L"$N = %$(length(probs_sa[i].u0))$", titlegap = 10, xticksvisible = false, yticksvisible = true, xticklabelsvisible = false, yticklabelsvisible = true, titlesize = 22, spinewidth = STROKEWIDTH, xlabelsize = 22, ylabelsize = 22, xticklabelrotation = π / 4, xticklabelsize = 20, yticklabelsize = 20) axs[1, i] = ax - barplot!(ax, xs, ys; dogde = dodge, color = dodge, colormap = :seaborn_bright, - strokewidth = 2) + barplot!(ax, xs, ys; color = dodge, colormap = :seaborn_bright, strokewidth = 2) hlines!(ax, [1.0], color = :black, linestyle = :dash, linewidth = 2) end @@ -324,7 +307,7 @@ fig = begin ax = Axis(fig[2, i]; ylabel = "", - title = L"N = %$(length(probs_reg[i].u0))$", + title = L"$N = %$(length(probs_reg[i].u0))$", titlegap = 10, xticksvisible = true, yticksvisible = true, xticklabelsvisible = true, yticklabelsvisible = true, titlesize = 22, spinewidth = STROKEWIDTH, xlabelsize = 22, ylabelsize = 22, diff --git a/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd b/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd new file mode 100644 index 000000000..0d90762b0 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd @@ -0,0 +1,141 @@ +--- +title: CUTEst Bounded Constrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + @info "here 1" + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + @info "here 2" + + for prob_name in problems + @info prob_name + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Equality/Inequality constrained problems with bounded variables + +Now we analyze the subset of problems with equality/inequality constraints and whose +variables are bounded. There are 666 such problems. + +The following figure shows the results of the same benchmarks previously described for the +problems on this section. + +```julia +@info "before" +eq_bou_problems = CUTEst.select(min_con=1, only_equ_con=true, only_free_var=false) +@info "after1" + +# Analysis +eq_bou_results = run_benchmarks(eq_bou_problems, optimizers) +@info "after2" + +@df eq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +@info "after3" +``` + +Next, we examine the same relationship for problems with inequality-constrained problems, +of which there are 244. + +```julia +@info "after4" +neq_bou_problems = CUTEst.select(min_con=1, only_ineq_con=true, only_free_var=false) +@info "after5" + +# Analysis +neq_bou_results = run_benchmarks(neq_bou_problems, optimizers) +@info "after6" + +@df neq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` diff --git a/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd b/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd new file mode 100644 index 000000000..263180fe2 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd @@ -0,0 +1,109 @@ +--- +title: CUTEst Quadratic Programming with Linear Constraints Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +# Quadratic programs with linear constraints + +Lastly, we examine the problems with a quadratic objective function and only linear +constraints. There are 252 such problems in the suite. + +```julia +quad_problems = CUTEst.select(objtype="quadratic", contype="linear") + +# Analysis +quad_results = run_benchmarks(quad_problems, optimizers) + +@df neq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd b/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd new file mode 100644 index 000000000..70e1f7003 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd @@ -0,0 +1,130 @@ +--- +title: CUTEst Unbounded Constrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Equality/Inequality constrained problems with unbounded variables + +These problems have a constraint function that's subject to either equality or inequality +constraints, but the variables themselves are free. CUTEst contains 285 problems with +equality constraints and 114 with inequality constraints for a total of 299. + +We start by analyzing the equality-constrained problems, of which there are 285. The +following figure shows the time to solution as a function of number of variables by +optimizer. + +```julia +eq_unb_problems = CUTEst.select(min_con=1, only_equ_con=true, only_free_var=true) + +# Analysis +eq_unb_results = run_benchmarks(eq_unb_problems, optimizers) + +@df eq_unb_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +Next, we examine the same relationship for problems with inequality-constrained problems. + +```julia +neq_unb_problems = CUTEst.select(min_con=1, only_ineq_con=true, only_free_var=true) + +# Analysis +neq_unb_results = run_benchmarks(neq_unb_problems, optimizers) + +@df neq_unb_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd b/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd new file mode 100644 index 000000000..da2fe781f --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd @@ -0,0 +1,109 @@ +--- +title: CUTEst Unconstrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Unconstrained problems + +CUTEst contains 286 unconstrained problems. We will compare how the optimizers behave in +terms of the time to solution with respect to the number of variables. + +```julia +unc_problems = CUTEst.select(contype="unc") + +# Analysis +unc_results = run_benchmarks(unc_problems, optimizers) + +@df unc_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/Manifest.toml b/benchmarks/OptimizationCUTEst/Manifest.toml new file mode 100644 index 000000000..18d7957b1 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/Manifest.toml @@ -0,0 +1,3000 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.5" +manifest_format = "2.0" +project_hash = "8e523feffcd9fa77d38f37602ee0cd7ccacee285" + 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b/benchmarks/OptimizationCUTEst/Project.toml new file mode 100644 index 000000000..a117214b4 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/Project.toml @@ -0,0 +1,11 @@ +[deps] +CUTEst = "1b53aba6-35b6-5f92-a507-53c67d53f819" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9" +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +OptimizationMOI = "fd9f6733-72f4-499f-8506-86b2bdd0dea1" +OptimizationNLPModels = "064b21be-54cf-11ef-1646-cdfee32b588f" +OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" \ No newline at end of file diff --git a/benchmarks/SimpleHandwrittenPDE/Project.toml b/benchmarks/SimpleHandwrittenPDE/Project.toml index fb9735020..32801ff6d 100644 --- a/benchmarks/SimpleHandwrittenPDE/Project.toml +++ b/benchmarks/SimpleHandwrittenPDE/Project.toml @@ -10,6 +10,7 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -24,5 +25,6 @@ ModelingToolkit = "8" ODEInterfaceDiffEq = "3.7" OrdinaryDiffEq = "5.41, 6" Plots = "1.4" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4.2" diff --git a/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd index 1c736ce6b..b2de3efee 100644 --- a/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd index e2b2b05a6..a4b423a76 100644 --- a/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd index 00ec2785a..0f100f351 100644 --- a/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd index 2c46dd471..502ebf658 100644 --- a/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd index 136543791..4a862dfe8 100644 --- a/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd index 109b0fd93..f285c417f 100644 --- a/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd index 9c58f8852..224929e14 100644 --- a/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd index 80ff66386..f096e90f0 100644 --- a/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/StiffBVP/Manifest.toml b/benchmarks/StiffBVP/Manifest.toml new file mode 100644 index 000000000..5c85c872e --- /dev/null +++ b/benchmarks/StiffBVP/Manifest.toml @@ -0,0 +1,3105 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.5" +manifest_format = "2.0" +project_hash = "1f65927f64cdcfcfc4cd6b8b25512abab1ed81c7" + +[[deps.ADTypes]] +git-tree-sha1 = "30bb95a372787af850addf28ac937f1be7b79173" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.10.0" 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"764a87c0-6b3e-53db-9096-fe964310641d" +BracketingNonlinearSolve = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" +Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" +ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" +OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" +StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + +[compat] +BenchmarkTools = "1" +BoundaryValueDiffEq = "5.12" +BracketingNonlinearSolve = "1.1.0" +CairoMakie = "0.12" +DiffEqDevTools = "2.42.0" +Interpolations = "0.15.1" +ODEInterface = "0.5" +OrdinaryDiffEq = "6.90.1" +Plots = "1.4" +SciMLBenchmarks = "0.1" +StaticArrays = "1.9.8" diff --git a/benchmarks/StiffBVP/ionic_liquid_dehumidifier.jmd b/benchmarks/StiffBVP/ionic_liquid_dehumidifier.jmd new file mode 100644 index 000000000..95017802a --- /dev/null +++ b/benchmarks/StiffBVP/ionic_liquid_dehumidifier.jmd @@ -0,0 +1,241 @@ +--- +title: Ionic Liquid Dehumidifier Benchmarks +author: Qingyu Qu and maysam-gholampour +--- + +This benchmark compares the runtime and error of BVP solvers, including FIRK solvers and FORTRAN BVP solvers on ionic liquid dehumidifier problem. +For this problem, we test the following solvers: + +- BoundaryValueDiffEq.jl's FIRK nested solvers(including `RadauIIa3`, `RadauIIa5`, `RadauIIa7`, `LobattoIIIa3`, `LobattoIIIa4`, `LobattoIIIa5`, `LobattoIIIb3`, `LobattoIIIb4`, `LobattoIIIb5`, `LobattoIIIc3`, `LobattoIIIc4`, `LobattoIIIc5`). +- FORTRAN BVP solvers from ODEInterface.jl(including `BVPM2` and `COLNEW`). + +# Setup + +Fetch required packages. + +```julia +using BoundaryValueDiffEq, BracketingNonlinearSolve, ODEInterface, DiffEqDevTools, BenchmarkTools, + Interpolations, StaticArrays, CairoMakie +``` + +Set up the benchmarked solvers. + +```julia +solvers_all = [ + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa3", solver = Dict(:alg => RadauIIa3(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa5", solver = Dict(:alg => RadauIIa5(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "RadauIIa7", solver = Dict(:alg => RadauIIa7(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIa3", solver = Dict(:alg => LobattoIIIa3(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIa4", solver = Dict(:alg => LobattoIIIa4(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIa5", solver = Dict(:alg => LobattoIIIa5(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb3", solver = Dict(:alg => LobattoIIIb3(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb4", solver = Dict(:alg => LobattoIIIb4(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb5", solver = Dict(:alg => LobattoIIIb5(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb3", solver = Dict(:alg => LobattoIIIc3(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb4", solver = Dict(:alg => LobattoIIIc4(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :boundaryvaluediffeq, type = :firk, name = "LobattoIIIb5", solver = Dict(:alg => LobattoIIIc5(; nested_nlsolve = true), :dts=>1.0 ./ 10.0 .^ (2:4))), + (; pkg = :wrapper, type = :general, name = "COLNEW", solver = Dict(:alg => COLNEW(), :dts=>1.0 ./ 10.0 .^ (2:4))), +]; +``` + +Set tolerances. + +```julia +abstols = 1.0 ./ 10.0 .^ (1:3) +reltols = 1.0 ./ 10.0 .^ (1:3); +``` + +# Benchmarks + +```julia +iᵥ_ₛₐₜ(T) = 10^(6.697227966814859 - 273.8702703951898 / + (T + 642.1729733423742)) + +begin + "Properties Interpolations and Extrapolations" + + const Tⁿᵒᵈᵉˢ = @SVector[x + 273.15 for x in [25.0, 35.0, 60.0, 80.0]] + const ξⁿᵒᵈᵉˢ_2 = @SVector[x * 0.01 for x in [0.0, 50.0, 70.0, 80.0, 85.0, 90.0, 95.0]] + const nodes = (Tⁿᵒᵈᵉˢ, ξⁿᵒᵈᵉˢ_2) + + const Δh_data = @SMatrix[ + 0.0 -58000.0 -75000.0 -74000.0 -68000.0 -55000.0 -34000.0 + 0.0 -57000.0 -72000.0 -72000.0 -67000.0 -54000.0 -33000.0 + 0.0 -52000.0 -67000.0 -67000.0 -62000.0 -51000.0 -31000.0 + 0.0 -48000.0 -62000.0 -64000.0 -59000.0 -49000.0 -30000.0 + ] + # # ================== Interpolation and Extrapolation P_ν ================== + const a0_p = 12.10 + const a1_p = -28.01 + const a2_p = 50.34 + const a3_p = -24.63 + const b0_p = 1212.67 + const b1_p = 772.37 + const b2_p = 614.59 + const b3_p = 493.33 + + @inline function _Pᵥₐₚₒᵣ_ₛₒₗ(T, ξ) + A = a0_p + a1_p * ξ + a2_p * ξ^2 + a3_p * ξ^3 + B = b0_p + b1_p * ξ + b2_p * ξ^2 + b3_p * ξ^3 + return 10^(A - B / T) * 100.0 + end + # ================== Interpolation and Extrapolation cp ==================== + function _cpₛₒₗ(T, ξ) + return ((0.00476 * T - 4.01) * ξ + 4.21) * 1e3 + end + + @inline function _Δh(T, ξ) + Δh_interpolated = interpolate(nodes, Δh_data, Gridded(Linear())) + Δh_extrapolated = extrapolate(Δh_interpolated, Line()) + return Δh_extrapolated(T, ξ) + end + + @inline function _iₛₒₗ(T, ξ) + Δh = _Δh(T, ξ) + i = _cpₛₒₗ(T, ξ) * (T - 273.15) + Δh + return i + end + + # ================== Find T given i_sol and ξ ==================== + # Function to find the root, given i_sol and ξ + @inline function calculate_T_sol(iᵛₛₒₗ, ξ; T_lower = -150.0 + 273.15, T_upper = 95.0 + 273.15) + f(T, p) = _iₛₒₗ(T, p[2]) - p[1] + p = @SVector[iᵛₛₒₗ, ξ] + T_span = (T_lower, T_upper) + prob = IntervalNonlinearProblem{false}(f, T_span, p) + result = solve(prob, BracketingNonlinearSolve.ITP()) + return result.u + end +end + +function ionic_liquid_coil_ode!(du, u, p, t) + # ωₐᵢᵣ, iₐᵢᵣ, ṁₛₒₗ,ξₛₒₗ, iₛₒₗ = u + # ======================================== + Le = p[1] + ∂Qᵣ = p[2] + ṁₐᵢᵣ = p[3] + NTUᴰₐᵢᵣ = p[4] + σ = p[5] + ṁₛₒₗ_ᵢₙ = p[6] + ξₛₒₗ_ᵢₙ = p[7] + iₛₒₗ_ᵢₙ = p[8] + ωₐ_ᵢₙ = p[9] + iₐ_ᵢₙ = p[10] + MR = ṁₛₒₗ_ᵢₙ / ṁₐᵢᵣ + ER = iₛₒₗ_ᵢₙ / iₐ_ᵢₙ + # ======================================== + Tₛₒₗ = calculate_T_sol(u[5] * iₛₒₗ_ᵢₙ, u[4] * ξₛₒₗ_ᵢₙ) + Pᵥₐₚₒᵣ_ₛₒₗ = _Pᵥₐₚₒᵣ_ₛₒₗ(Tₛₒₗ, u[4] * ξₛₒₗ_ᵢₙ) + ωₑ = 0.622 * Pᵥₐₚₒᵣ_ₛₒₗ / (101325.0 - Pᵥₐₚₒᵣ_ₛₒₗ) / ωₐ_ᵢₙ + iₑ = (1.005 * (Tₛₒₗ - 273.15) + ωₑ * ωₐ_ᵢₙ * (2500.9 + 1.82 * (Tₛₒₗ - 273.15))) / iₐ_ᵢₙ + iₑ *= 1000 + iᵥₐₚₒᵣ_ₜₛ = iᵥ_ₛₐₜ(Tₛₒₗ) / iₐ_ᵢₙ + + du[1] = σ * NTUᴰₐᵢᵣ * (u[1] - ωₑ) + du[2] = σ * NTUᴰₐᵢᵣ * Le * ((u[2] - iₑ) + (ωₐ_ᵢₙ * iᵥₐₚₒᵣ_ₜₛ * (1 / Le - 1) * (u[1] - ωₑ))) + du[3] = σ * ωₐ_ᵢₙ * du[1] / MR + du[4] = (-u[4] / u[3]) * du[3] + du[5] = (1 / u[3]) * (σ * (1.0 / (MR * ER)) * du[2] - u[5] * du[3] - ∂Qᵣ / (ṁₛₒₗ_ᵢₙ * iₛₒₗ_ᵢₙ)) + nothing +end + +function bca!(res_a, u_a, p) + res_a[1] = u_a[3] - 1.0 + res_a[2] = u_a[4] - 1.0 + res_a[3] = u_a[5] - 1.0 + nothing +end + +function bcb!(res_b, u_b, p) + res_b[1] = u_b[1] - 1.0 + res_b[2] = u_b[2] - 1.0 + nothing +end + + +dt = 0.05 +tspan = (0.0, 1.0) + +Le = 0.85 +σ = 1.0 +ṁₛₒₗ_ᵢₙ = 7.466666666666666e-5 +ξₛₒₗ_ᵢₙ = 0.8 +iₛₒₗ_ᵢₙ = -30235.4128 +ωₐ_ᵢₙ = 0.022800264832054707 +iₐ_ᵢₙ = 88436.57753410653 +∂Qᵣ = -12.416666666666666 +ṁₐᵢᵣ_ᵢₙ = 0.0003733333333333333 +NTUᴰₐᵢᵣ = 4.678477517542263 + +p = @SVector[Le, ∂Qᵣ, ṁₐᵢᵣ_ᵢₙ, NTUᴰₐᵢᵣ, σ, ṁₛₒₗ_ᵢₙ, ξₛₒₗ_ᵢₙ, iₛₒₗ_ᵢₙ, ωₐ_ᵢₙ, iₐ_ᵢₙ] + +u0 = [0.1, 0.1, 1.0001, 0.9, 1.01] + +bvp_fun = BVPFunction( + ionic_liquid_coil_ode!, (bca!, bcb!); + bcresid_prototype = (zeros(3), zeros(2)), twopoint = Val(true), +) + +prob = TwoPointBVProblem(bvp_fun, u0, tspan, p) +sol = solve(prob, RadauIIa7(nested_nlsolve = true, nest_tol = 1e-3), dt = dt, abstol = 1e-5) +testsol = TestSolution(sol) +wp_set = WorkPrecisionSet(prob, abstols, reltols, getfield.(solvers_all, :solver); names = getfield.(solvers_all, :name), appxsol = testsol, maxiters=Int(1e4)) +``` + +Plot the result + +```julia +fig = begin + LINESTYLES = Dict(:boundaryvaluediffeq => :solid, :simpleboundaryvaluediffeq => :dash, :wrapper => :dot) + ASPECT_RATIO = 0.7 + WIDTH = 1200 + HEIGHT = round(Int, WIDTH * ASPECT_RATIO) + STROKEWIDTH = 2.5 + + colors = cgrad(:seaborn_bright, length(solvers_all); categorical = true) + cycle = Cycle([:marker], covary = true) + plot_theme = Theme(Lines = (; cycle), Scatter = (; cycle)) + + with_theme(plot_theme) do + fig = Figure(; size = (WIDTH, HEIGHT)) + ax = Axis(fig[1, 1], ylabel = L"Time $\mathbf{(s)}$", + xlabelsize = 22, ylabelsize = 22, + xlabel = L"Error: $\mathbf{||f(u^\ast)||_\infty}$", + xscale = log10, yscale = log10, xtickwidth = STROKEWIDTH, + ytickwidth = STROKEWIDTH, spinewidth = STROKEWIDTH, + xticklabelsize = 20, yticklabelsize = 20) + + idxs = sortperm(median.(getfield.(wp_set.wps, :times))) + + ls, scs = [], [] + + for (i, (wp, solver)) in enumerate(zip(wp_set.wps[idxs], solvers_all[idxs])) + (; name, times, errors) = wp + errors = [err.l∞ for err in errors] + l = lines!(ax, errors, times; linestyle = LINESTYLES[solver.pkg], label = name, + linewidth = 5, color = colors[i]) + sc = scatter!(ax, errors, times; label = name, markersize = 16, strokewidth = 2, + color = colors[i]) + push!(ls, l) + push!(scs, sc) + end + + xlims!(ax; high=1) + ylims!(ax; low=1e-4) + + axislegend(ax, [[l, sc] for (l, sc) in zip(ls, scs)], + [solver.name for solver in solvers_all[idxs]], "BVP Solvers"; + framevisible=true, framewidth = STROKEWIDTH, position = :rb, + titlesize = 20, labelsize = 16, patchsize = (40.0f0, 20.0f0)) + + fig[0, :] = Label(fig, "Ionic Liquid Dehumidifier Benchmark", + fontsize = 24, tellwidth = false, font = :bold) + fig + end +end +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` diff --git a/benchmarks/StiffODE/Bruss.jmd b/benchmarks/StiffODE/Bruss.jmd index 59530f22c..07d0e6b7d 100644 --- a/benchmarks/StiffODE/Bruss.jmd +++ b/benchmarks/StiffODE/Bruss.jmd @@ -6,7 +6,8 @@ author: Chris Rackauckas and Utkarsh ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, SparseArrays, LinearSolve, - LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit + LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit, + RecursiveFactorization gr() const N = 8 diff --git a/benchmarks/StiffODE/Hires.jmd b/benchmarks/StiffODE/Hires.jmd index f888ebb14..c4028347b 100644 --- a/benchmarks/StiffODE/Hires.jmd +++ b/benchmarks/StiffODE/Hires.jmd @@ -5,7 +5,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, DiffEqDevTools, Sundials -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization gr() #gr(fmt=:png) diff --git a/benchmarks/StiffODE/Orego.jmd b/benchmarks/StiffODE/Orego.jmd index e113ab9c9..f5974a1c9 100644 --- a/benchmarks/StiffODE/Orego.jmd +++ b/benchmarks/StiffODE/Orego.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, Sundials gr() #gr(fmt=:png) -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization f = @ode_def Orego begin dy1 = p1*(y2+y1*(1-p2*y1-y2)) diff --git a/benchmarks/StiffODE/Pollution.jmd b/benchmarks/StiffODE/Pollution.jmd index ea7ae39f9..730bb9943 100644 --- a/benchmarks/StiffODE/Pollution.jmd +++ b/benchmarks/StiffODE/Pollution.jmd @@ -7,7 +7,7 @@ author: Chris Rackauckas using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, LinearSolve using ProfileSVG, BenchmarkTools, Profile gr() # gr(fmt=:png) -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization const k1=.35e0 const k2=.266e2 diff --git a/benchmarks/StiffODE/Project.toml b/benchmarks/StiffODE/Project.toml index 3f08d98e4..59bf75ab7 100644 --- a/benchmarks/StiffODE/Project.toml +++ b/benchmarks/StiffODE/Project.toml @@ -15,6 +15,7 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" ParameterizedFunctions = "65888b18-ceab-5e60-b2b9-181511a3b968" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" ProfileSVG = "132c30aa-f267-4189-9183-c8a63c7e05e6" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" @@ -30,7 +31,7 @@ DomainSets = "0.7" GeometricIntegratorsDiffEq = "0.2" IncompleteLU = "0.2" LSODA = "0.7" -LinearSolve = "1, 2" +LinearSolve = "3" MethodOfLines = "0.11" ModelingToolkit = "9" ODEInterfaceDiffEq = "3.10" @@ -38,6 +39,7 @@ OrdinaryDiffEq = "6.19" ParameterizedFunctions = "5.3" Plots = "1.4" ProfileSVG = "0.2" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" StaticArrays = "1" Sundials = "4.2" diff --git a/benchmarks/StiffODE/ROBER.jmd b/benchmarks/StiffODE/ROBER.jmd index 6f9b4c9c5..5f04a4cb3 100644 --- a/benchmarks/StiffODE/ROBER.jmd +++ b/benchmarks/StiffODE/ROBER.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA gr() -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization rober = @ode_def begin dy₁ = -k₁*y₁+k₃*y₂*y₃ diff --git a/benchmarks/StiffODE/VanDerPol.jmd b/benchmarks/StiffODE/VanDerPol.jmd index e1f76ae53..5f62fe4d3 100644 --- a/benchmarks/StiffODE/VanDerPol.jmd +++ b/benchmarks/StiffODE/VanDerPol.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA gr() -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization van = @ode_def begin dy = μ*((1-x^2)*y - x) diff --git a/docs/pages.jl b/docs/pages.jl index ffdba8fca..67c8b21f3 100644 --- a/docs/pages.jl +++ b/docs/pages.jl @@ -40,7 +40,7 @@ end # The result is in alphabetical order, change to the wanted order permute!(pages, - [1, 17, 14, 12, 23, 4, 5, 21, 31, 7, 3, 9, 19, 16, 29, 8, 10, 18, 22, 32, 20, 30, 13, 11, 25, 24, 28, 6, 15, 26, 27, 2, 33] + [1, 17, 14, 12, 23, 4, 5, 21, 32, 7, 3, 9, 19, 30, 16, 29, 8, 10, 18, 22, 33, 20, 31, 13, 11, 25, 24, 28, 6, 15, 26, 27, 2, 34] ) names = [ @@ -56,7 +56,8 @@ names = [ "Biological Differential Equations", "Astrochemistry Differential Equations", "Differential-Algebraic Equations (DAEs)", - "Boundary Value Problems (BVPs)", + "Non-Stiff Boundary Value Problems (BVPs)", + "Stiff Boundary Value Problems (BVPs)", "ModelingToolkit Acausal Modeling / Symbolic-Numeric Benchmarks", "Simple Handwritten Partial Differential Equations (PDEs) as ODEs", "Complicated Partial Differential Equations (PDEs)",