diff --git a/README.md b/README.md index 08e33b272..5cb83d186 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,7 @@ or building work-precision diagrams for direct comparison of speed at given erro **If any of the code from any of the languages can be improved, please open a pull request**. + ## Results To view the results of the SciML Benchmarks, go to [benchmarks.sciml.ai](https://benchmarks.sciml.ai/stable/). By default, this diff --git a/benchmarks/Jumps/Diffusion_CTRW.jmd b/benchmarks/Jumps/Diffusion_CTRW.jmd index 71178e0d7..075b8add2 100644 --- a/benchmarks/Jumps/Diffusion_CTRW.jmd +++ b/benchmarks/Jumps/Diffusion_CTRW.jmd @@ -21,7 +21,7 @@ N = 256 h = 1 / N u0 = 10 * ones(Int64, N) tf = .01 -methods = (Direct(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve()) shortlabels = [string(leg)[15:end-2] for leg in methods] jprob = JumpProblemLibrary.prob_jump_diffnetwork rn = jprob.network(N) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 2b2433420..c1a264ecc 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -1,19 +1,19 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.1" +julia_version = "1.8.5" manifest_format = "2.0" project_hash = "013abde731b3d76e3dccfe35d36c5e64c73bb4e2" [[deps.AbstractAlgebra]] deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "ba2beb5f2a3170a0ef87953daefd97135cf46ecd" +git-tree-sha1 = "df23d15b1090a3332a09a7a51da45bd9f0a07f92" uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.27.4" +version = "0.27.8" [[deps.AbstractTrees]] -git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" +git-tree-sha1 = "52b3b436f8f73133d7bc3a6c71ee7ed6ab2ab754" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.2" +version = "0.4.3" [[deps.Adapt]] deps = ["LinearAlgebra"] @@ -38,15 +38,15 @@ version = "0.2.0" [[deps.ArrayInterface]] deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "Static"] -git-tree-sha1 = "d6173480145eb632d6571c148d94b9d3d773820e" +git-tree-sha1 = "6d0918cb9c0d3db7fe56bea2bc8638fc4014ac35" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "6.0.23" +version = "6.0.24" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "5bb0f8292405a516880a3809954cb832ae7a31c5" +git-tree-sha1 = "14c3f84a763848906ac681f94cf469a851601d92" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.20" +version = "0.1.28" [[deps.ArrayInterfaceGPUArrays]] deps = ["Adapt", "ArrayInterfaceCore", "GPUArraysCore", "LinearAlgebra"] @@ -56,21 +56,21 @@ version = "0.2.2" [[deps.ArrayInterfaceOffsetArrays]] deps = ["ArrayInterface", "OffsetArrays", "Static"] -git-tree-sha1 = "c49f6bad95a30defff7c637731f00934c7289c50" +git-tree-sha1 = "3d1a9a01976971063b3930d1aed1d9c4af0817f8" uuid = "015c0d05-e682-4f19-8f0a-679ce4c54826" -version = "0.1.6" +version = "0.1.7" [[deps.ArrayInterfaceStaticArrays]] -deps = ["Adapt", "ArrayInterface", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"] -git-tree-sha1 = "efb000a9f643f018d5154e56814e338b5746c560" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"] +git-tree-sha1 = "f12dc65aef03d0a49650b20b2fdaf184928fd886" uuid = "b0d46f97-bff5-4637-a19a-dd75974142cd" -version = "0.1.4" +version = "0.1.5" [[deps.ArrayInterfaceStaticArraysCore]] deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] -git-tree-sha1 = "a1e2cf6ced6505cbad2490532388683f1e88c3ed" +git-tree-sha1 = "93c8ba53d8d26e124a5a8d4ec914c3a16e6a0970" uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9" -version = "0.1.0" +version = "0.1.3" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -96,9 +96,9 @@ version = "0.1.1" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93" +git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.3.1" +version = "1.3.2" [[deps.Bijections]] git-tree-sha1 = "fe4f8c5ee7f76f2198d5c2a06d3961c249cce7bd" @@ -106,15 +106,15 @@ uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" version = "0.1.4" [[deps.BitFlags]] -git-tree-sha1 = "84259bb6172806304b9101094a7cc4bc6f56dbc6" +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.5" +version = "0.1.7" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "eaee37f76339077f86679787a71990c4e465477f" +git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.4" +version = "0.1.5" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -124,9 +124,9 @@ version = "1.0.8+0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "Static"] -git-tree-sha1 = "9bdd5aceea9fa109073ace6b430a24839d79315e" +git-tree-sha1 = "5b735f654bdfd7b6c18c49f1d3ebff34b4b8af43" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.1.27" +version = "0.2.1" [[deps.CSTParser]] deps = ["Tokenize"] @@ -135,7 +135,7 @@ uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f" version = "3.3.6" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -148,9 +148,9 @@ version = "0.5.1" [[deps.Catalyst]] deps = ["DataStructures", "DiffEqBase", "DocStringExtensions", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "SparseArrays", "Symbolics"] -git-tree-sha1 = "2a4249f749c3757c598449be016137201f288be0" +git-tree-sha1 = "5640db11beb77f24b712e3f922c1e780f6e85b5a" uuid = "479239e8-5488-4da2-87a7-35f2df7eef83" -version = "12.3.0" +version = "12.3.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -166,9 +166,9 @@ version = "0.1.4" [[deps.CloseOpenIntervals]] deps = ["ArrayInterface", "Static"] -git-tree-sha1 = "5522c338564580adf5d58d91e43a55db0fa5fb39" +git-tree-sha1 = "d61300b9895f129f4bd684b2aff97cf319b6c493" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.10" +version = "0.1.11" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -177,10 +177,10 @@ uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.0" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] +git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.19.0" +version = "3.20.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -190,15 +190,15 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.12.10" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -207,14 +207,14 @@ version = "1.0.2" [[deps.CommonMark]] deps = ["Crayons", "JSON", "URIs"] -git-tree-sha1 = "4cd7063c9bdebdbd55ede1af70f3c2f48fab4215" +git-tree-sha1 = "86cce6fd164c26bad346cc51ca736e692c9f553c" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.6" +version = "0.8.7" [[deps.CommonSolve]] -git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25" +git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.1" +version = "0.2.3" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -224,19 +224,19 @@ version = "0.3.0" [[deps.Compat]] deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "5856d3031cdb1f3b2b6340dfdc66b6d9a149a374" +git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.2.0" +version = "4.5.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.1+0" [[deps.CompositeTypes]] -git-tree-sha1 = "d5b014b216dc891e81fea299638e4c10c657b582" +git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.2" +version = "0.1.3" [[deps.CompositionsBase]] git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" @@ -272,15 +272,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "1106fa7e1256b402a86a8e7b15c00c85036fef49" +git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.11.0" +version = "1.14.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "db2a9cb664fcea7836da4b414c3278d71dd602d2" +deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.6" +version = "1.4.4" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -313,16 +313,16 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArrays", "Statistics", "Tricks", "ZygoteRules"] -git-tree-sha1 = "0f9f82671406d21f6275cb6e9336259f062e81fa" +deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "Static", "StaticArrays", "Statistics", "Tricks", "ZygoteRules"] +git-tree-sha1 = "b410f0b8a52752e1c1723b4316382203f914672c" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.105.0" +version = "6.113.1" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] -git-tree-sha1 = "f8cc1ad62a87988225a07524ef84c7df7264c232" +git-tree-sha1 = "485503846a90b59f3b79b39c2d818496bf50d197" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.24.1" +version = "2.24.3" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -332,9 +332,9 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "992a23afdb109d0d2f8802a30cf5ae4b1fe7ea68" +git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.11.1" +version = "1.12.2" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -348,21 +348,21 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "0d7d213133d948c56e8c2d9f4eab0293491d8e4a" +git-tree-sha1 = "74911ad88921455c6afcad1eefa12bd7b1724631" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.75" +version = "0.25.80" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.6" +version = "0.9.3" [[deps.DomainSets]] deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "dc45fbbe91d6d17a8e187abad39fb45963d97388" +git-tree-sha1 = "988e2db482abeb69efc76ae8b6eba2e93805ee70" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.5.13" +version = "0.5.15" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -381,6 +381,17 @@ git-tree-sha1 = "d0fa82f39c2a5cdb3ee385ad52bc05c42cb4b9f0" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" version = "0.4.5" +[[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" +uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" +version = "1.0.4" + [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" @@ -388,16 +399,21 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" [[deps.ExponentialUtilities]] -deps = ["ArrayInterfaceCore", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "b19c3f5001b11b71d0f970f354677d604f3a1a97" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"] +git-tree-sha1 = "9837d3f3a904c7a7ab9337759c0093d3abea1d81" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.19.0" +version = "1.22.0" [[deps.ExprTools]] git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.8" +[[deps.Extents]] +git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.1" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -405,16 +421,16 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.2+0" +version = "4.4.2+2" [[deps.FastBroadcast]] deps = ["ArrayInterface", "ArrayInterfaceCore", "LinearAlgebra", "Polyester", "Static", "StrideArraysCore"] -git-tree-sha1 = "21cdeff41e5a1822c2acd7fc7934c5f450588e00" +git-tree-sha1 = "4bef892787c972913d4d84e7255400759bb650e5" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.1" +version = "0.2.4" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -423,24 +439,24 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "14a6f7a21125f715d935fe8f83560ee833f7d79d" +git-tree-sha1 = "7fbaf9f73cd4c8561702ea9b16acf3f99d913fe4" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "1.2.7" +version = "1.2.8" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "87519eb762f85534445f5cda35be12e32759ee14" +git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.4" +version = "0.13.6" [[deps.FiniteDiff]] deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "5a2cff9b6b77b33b89f3d97a4d367747adce647e" +git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.15.0" +version = "2.17.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -462,9 +478,9 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "187198a4ed8ccd7b5d99c41b69c679269ea2b2d4" +git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.32" +version = "0.10.34" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -479,9 +495,9 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[deps.FunctionWrappers]] -git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" +git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" -version = "1.1.2" +version = "1.1.3" [[deps.FunctionWrappersWrappers]] deps = ["FunctionWrappers"] @@ -507,15 +523,15 @@ version = "0.1.2" [[deps.GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "0ac6f27e784059c68b987f42b909ade0bcfabe69" +git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.68.0" +version = "0.66.2" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "ad86229227847772bb985cc1dd3b842ff61317a7" +git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.69.0+0" +version = "0.69.1+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -523,6 +539,18 @@ git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" version = "0.5.3" +[[deps.GeoInterface]] +deps = ["Extents"] +git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" +uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" +version = "1.0.1" + +[[deps.GeometryBasics]] +deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] +git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" +uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" +version = "0.4.5" + [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" @@ -542,10 +570,15 @@ uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" version = "2.34.1+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+2" + +[[deps.Glob]] +git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2" +uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" +version = "1.3.0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -566,9 +599,9 @@ version = "1.0.2" [[deps.Groebner]] deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random"] -git-tree-sha1 = "144cd8158cce5b36614b9c95b8afab6911bd469b" +git-tree-sha1 = "47f0f03eddecd7ad59c42b1dd46d5f42916aff63" uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.2.10" +version = "0.2.11" [[deps.GroupsCore]] deps = ["Markdown", "Random"] @@ -578,9 +611,9 @@ version = "0.4.0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "4abede886fcba15cd5fd041fef776b230d004cee" +git-tree-sha1 = "752b7f2640a30bc991d37359d5fff50ce856ecde" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.4.0" +version = "1.7.1" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -590,15 +623,15 @@ version = "2.8.1+1" [[deps.Highlights]] deps = ["DocStringExtensions", "InteractiveUtils", "REPL"] -git-tree-sha1 = "f823a2d04fb233d52812c8024a6d46d9581904a4" +git-tree-sha1 = "0341077e8a6b9fc1c2ea5edc1e93a956d2aec0c7" uuid = "eafb193a-b7ab-5a9e-9068-77385905fa72" -version = "0.4.5" +version = "0.5.2" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "b7b88a4716ac33fe31d6556c02fc60017594343c" +git-tree-sha1 = "f64b890b2efa4de81520d2b0fbdc9aadb65bdf53" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.8" +version = "0.1.13" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] @@ -607,10 +640,10 @@ uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" version = "0.3.11" [[deps.IJulia]] -deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "98ab633acb0fe071b671f6c1785c46cd70bb86bd" +deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] +git-tree-sha1 = "59e19713542dd9dd02f31d59edbada69530d6a14" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.23.3" +version = "1.24.0" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -643,26 +676,31 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "076bb0da51a8c8d1229936a1af7bdfacd65037e1" +git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.2" +version = "0.7.3" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.7" +version = "0.1.8" [[deps.InvertedIndices]] -git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" +git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.2.0" [[deps.IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.1.1" +[[deps.IterTools]] +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" +version = "1.4.0" + [[deps.IterativeSolvers]] deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" @@ -674,12 +712,6 @@ git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" -[[deps.JLFzf]] -deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" -uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.5" - [[deps.JLLWrappers]] deps = ["Preferences"] git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" @@ -699,10 +731,10 @@ uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" version = "2.1.2+0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "CommonMark", "DataStructures", "Pkg", "Tokenize"] -git-tree-sha1 = "1ec2cb3b87d0c38e3b01c76d9b11639f1eaeec96" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "Tokenize"] +git-tree-sha1 = "447f5702b5271d99f064e924061bc05e26f52c4c" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.10" +version = "1.0.18" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -712,27 +744,27 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "5a6e6c522e8a7b39b24be8eebcc13cc7885c6f2c" +git-tree-sha1 = "09ed2720b2e343e48780a3156c4a6cef8dd54192" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.2.0" +version = "9.3.1" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0" +git-tree-sha1 = "764164ed65c30738750965d55652db9c94c59bfe" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.3.0" +version = "0.4.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "92256444f81fb094ff5aa742ed10835a621aef75" +git-tree-sha1 = "dd90aacbfb622f898a97c2a4411ac49101ebab8a" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.8.4" +version = "0.9.0" [[deps.KrylovKit]] -deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "49b0c1dd5c292870577b8f58c51072bd558febb9" +deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] +git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3" uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" -version = "0.5.4" +version = "0.6.0" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -758,22 +790,27 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" [[deps.LabelledArrays]] -deps = ["ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "3926535a04c12fb986028a4a86bf5a0a3cf88b91" +deps = ["ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] +git-tree-sha1 = "dae002226b59701dbafd7e2dd757df1bd83442fd" uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.12.0" +version = "1.12.5" + +[[deps.LambertW]] +git-tree-sha1 = "2d9f4009c486ef676646bca06419ac02061c088e" +uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" +version = "0.4.5" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "ab9aa169d2160129beb241cb2750ca499b4e90e9" +git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.17" +version = "0.15.18" [[deps.LayoutPointers]] deps = ["ArrayInterface", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] -git-tree-sha1 = "b67e749fb35530979839e7b4b606a97105fe4f1c" +git-tree-sha1 = "7e34177793212f6d64d045ee47d2883f09fffacc" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.10" +version = "0.1.12" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -811,9 +848,9 @@ version = "1.8.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf" +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.3.0+3" +version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -823,9 +860,9 @@ version = "1.42.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+1" +version = "1.16.1+2" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -856,37 +893,37 @@ deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"] -git-tree-sha1 = "c17007396b2ae56b8496f5a9857326dea0b7bb7b" +deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SnoopPrecompile", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] +git-tree-sha1 = "cf1227e369513687658476e466a5b73a7c3dfa1f" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.26.0" +version = "1.33.0" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" +git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.18" +version = "0.3.19" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" +git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.9" +version = "1.0.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "7b97cfe6e51e4fde195b7654425aa84e527d9657" +git-tree-sha1 = "155132d68bc33c826dbdeb452c5d0a79e2d0e586" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.128" +version = "0.12.146" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" +git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" +version = "0.5.10" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -899,9 +936,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "6872f9594ff273da6d13c7c1a1545d5a8c7d0c1c" +git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.6" +version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -909,9 +946,9 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.0+0" [[deps.Measures]] -git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" +git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.1" +version = "0.3.2" [[deps.Metatheory]] deps = ["AutoHashEquals", "DataStructures", "Dates", "DocStringExtensions", "Parameters", "Reexport", "TermInterface", "ThreadsX", "TimerOutputs"] @@ -921,33 +958,33 @@ version = "1.3.5" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "6bb7786e4f24d44b4e29df03c69add1b63d88f01" +git-tree-sha1 = "4d5917a26ca33c66c8e5ca3247bd163624d35493" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.2" +version = "0.1.3" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterfaceCore", "Combinatorics", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "NaNMath", "NonlinearSolve", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] -git-tree-sha1 = "9442dacd31424b624a8717867f4cebaf97f8480d" +deps = ["AbstractTrees", "ArrayInterfaceCore", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "NaNMath", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] +git-tree-sha1 = "86b5a6f7c95483eb8d98f7861e3f7c90113202b5" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.23.0" +version = "8.40.0" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2022.2.1" [[deps.MuladdMacro]] -git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68" +git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" -version = "0.2.2" +version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] @@ -963,15 +1000,15 @@ version = "1.0.14" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "4e675d6e9ec02061800d6cfb695812becbd03cdf" +git-tree-sha1 = "aa532179d4a643d4bd9f328589ca01fa20a0d197" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.0.4" +version = "1.1.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" +git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.2" +version = "7.8.3" [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -990,16 +1027,16 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterfaceCore", "FiniteDiff", "ForwardDiff", "IterativeSolvers", "LinearAlgebra", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "UnPack"] -git-tree-sha1 = "a754a21521c0ab48d37f44bbac1eefd1387bdcfc" +deps = ["ArrayInterfaceCore", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "7142ca5ab9bd7452cafb29f7d51f574a09d69052" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "0.3.22" +version = "1.1.1" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" +git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.7" +version = "1.12.8" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1019,15 +1056,15 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "f561403726db82fe98c0963a382b1b839e9287b1" +git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.1.2" +version = "1.3.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" +git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.17+0" +version = "1.1.19+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1047,22 +1084,16 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" [[deps.OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "eb86665fceb26f3db4123266c7b517146ad83d45" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "ArrayInterfaceStaticArraysCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "ca0c8939dbd3617ae3fdca13374d0b7501a2dd28" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.27.2" +version = "6.37.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" version = "10.40.0+0" -[[deps.PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" - [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" @@ -1076,15 +1107,10 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269" +deps = ["Dates", "SnoopPrecompile"] +git-tree-sha1 = "8175fc2b118a3755113c8e68084dc1a9e63c61ee" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.4.0" - -[[deps.Pipe]] -git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" -uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" -version = "1.3.0" +version = "2.5.3" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1099,39 +1125,39 @@ version = "1.8.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce" +git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.0.0" +version = "3.1.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "21303256d239f6b484977314674aef4bb1fe4420" +git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.1" +version = "1.3.2" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "6fae75c2178132582ea261d39f6da50cdd09c3c6" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "3f9b0706d6051d8edf9959e2422666703080722a" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.34.0" +version = "1.32.0" [[deps.PoissonRandom]] deps = ["Random"] -git-tree-sha1 = "9ac1bb7c15c39620685a3a7babc0651f5c64c35b" +git-tree-sha1 = "45f9da1ceee5078267eb273d065e8aa2f2515790" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.1" +version = "0.4.3" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "6ee5518f7baa05e154757a003bfb6936a174dbad" +git-tree-sha1 = "7f8dd47630b265df9e1d117137ee1894b195e032" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.6.15" +version = "0.7.1" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "b42fb2292fbbaed36f25d33a15c8cc0b4f287fcf" +git-tree-sha1 = "5d0a598c95f67ee0787723e38745cb954d143684" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.1.10" +version = "0.2.0" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -1141,9 +1167,9 @@ version = "1.4.2" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterfaceCore", "ForwardDiff"] -git-tree-sha1 = "3953d18698157e1d27a51678c89c88d53e071a42" +git-tree-sha1 = "758f3283aba57c53960c8e1900b4c724bf24ba74" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.4" +version = "0.4.8" [[deps.Preferences]] deps = ["TOML"] @@ -1152,10 +1178,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.3.0" [[deps.PrettyTables]] -deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5" +deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "1.3.1" +version = "2.2.2" [[deps.Primes]] deps = ["IntegerMathUtils"] @@ -1173,15 +1199,15 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" [[deps.Qt5Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "c6c0f690d0cc7caddb74cef7aa847b824a16b256" +git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+1" +version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241" +git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.5.0" +version = "2.6.0" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1204,27 +1230,28 @@ uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" version = "1.5.3" [[deps.RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.3" [[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "e7eac76a958f8664f2718508435d058168c7953d" +deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] +git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.3" +version = "0.6.11" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"] -git-tree-sha1 = "3004608dc42101a944e44c1c68b599fa7c669080" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "ZygoteRules"] +git-tree-sha1 = "fcf0962b399f3bc0fa13ae7274db7879c3ef9f1e" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.32.0" +version = "2.35.0" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "0a2dfb3358fcde3676beb75405e782faa8c9aded" +git-tree-sha1 = "0ab70c6cd81764d0047921cfc42741d2c2ff402e" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.12" +version = "0.2.15" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1239,9 +1266,9 @@ version = "0.1.2" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" +git-tree-sha1 = "cdbd3b1338c72ce29d9584fdbe9e9b70eeb5adca" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "1.0.0" +version = "0.1.3" [[deps.Requires]] deps = ["UUIDs"] @@ -1263,9 +1290,9 @@ version = "0.3.0+0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "cdc1e4278e91a6ad530770ebb327f9ed83cf10c4" +git-tree-sha1 = "50314d2ef65fce648975a8e80ae6d8409ebbf835" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.3" +version = "0.5.5" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1284,15 +1311,15 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "2ba4fee025f25d6711487b73e1ac177cbd127913" +git-tree-sha1 = "c8679919df2d3c71f74451321f1efea6433536cc" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.35" +version = "0.6.37" [[deps.SciMLBase]] -deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"] -git-tree-sha1 = "e6778c4d41f3d6213bf4d2803c4eb9ef12b6c0a7" +deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "RuntimeGeneratedFunctions", "StaticArraysCore", "Statistics", "Tables"] +git-tree-sha1 = "fe89a8113ea445bcff9ee570077830674babb534" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.59.3" +version = "1.81.0" [[deps.SciMLBenchmarks]] deps = ["Git", "IJulia", "InteractiveUtils", "Markdown", "Pkg", "Weave"] @@ -1300,6 +1327,12 @@ git-tree-sha1 = "a1d7791d68494b74fc0062cf63d8df7213dbd9dd" uuid = "31c91b34-3c75-11e9-0341-95557aab0344" version = "0.1.1" +[[deps.SciMLNLSolve]] +deps = ["LineSearches", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "b35d1f5d8afeee44e24915bb767e34fae867502f" +uuid = "e9a6253c-8580-4d32-9898-8661bb511710" +version = "0.1.1" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" @@ -1310,10 +1343,10 @@ version = "1.1.1" uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" [[deps.Setfield]] -deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "38d88503f695eb0301479bc9b0d4320b378bafe5" +deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] +git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.8.2" +version = "1.1.1" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -1330,6 +1363,12 @@ git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" +[[deps.SimpleNonlinearSolve]] +deps = ["ArrayInterfaceCore", "FiniteDiff", "ForwardDiff", "Reexport", "SciMLBase", "SnoopPrecompile", "StaticArraysCore"] +git-tree-sha1 = "fc4b9f81a033cf6879c91bb7f5b3ff59008c7dd2" +uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" +version = "0.1.4" + [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" @@ -1337,9 +1376,10 @@ uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" [[deps.SnoopPrecompile]] -git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.1" +version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1352,9 +1392,9 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" +git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.0.1" +version = "1.1.0" [[deps.SparseArrays]] deps = ["LinearAlgebra", "Random"] @@ -1362,9 +1402,15 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays", "VertexSafeGraphs"] -git-tree-sha1 = "5fb8ba9180f467885e87a2c99cae178b67934be1" +git-tree-sha1 = "4245283bee733122a9cb4545748d64e0c63337c0" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.26.2" +version = "1.30.0" + +[[deps.Sparspak]] +deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] +git-tree-sha1 = "4149bb50ccf65bc9c9d55e7001ca7aa4a7649603" +uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" +version = "0.3.4" [[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -1374,21 +1420,21 @@ version = "2.1.7" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] -git-tree-sha1 = "39c9f91521de844bad65049efd4f9223e7ed43f9" +git-tree-sha1 = "e08a62abc517eb79667d0a29dc08a3b589516bb5" uuid = "171d559e-b47b-412a-8079-5efa626c420e" -version = "0.1.14" +version = "0.1.15" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "de4f0a4f049a4c87e4948c04acff37baf1be01a6" +git-tree-sha1 = "c35b107b61e7f34fa3f124026f2a9be97dea9e1c" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.7.7" +version = "0.8.3" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "2189eb2c1f25cb3f43e5807f26aa864052e50c17" +git-tree-sha1 = "6954a456979f23d05085727adb17c4551c19ecd1" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.8" +version = "1.5.12" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1413,15 +1459,15 @@ version = "0.33.21" [[deps.StatsFuns]] deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" +git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.0.1" +version = "1.1.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "ThreadingUtilities"] -git-tree-sha1 = "ac730bd978bf35f9fe45daa0bd1f51e493e97eb4" +git-tree-sha1 = "70b6ee0e5cc1745a28dd9ba040b8e5ee28fffc69" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.3.15" +version = "0.4.5" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1429,6 +1475,17 @@ git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" version = "0.3.5" +[[deps.StringManipulation]] +git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.3.0" + +[[deps.StructArrays]] +deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" +uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" +version = "0.6.14" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1438,6 +1495,12 @@ deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "5.10.1+0" +[[deps.SymbolicIndexingInterface]] +deps = ["DocStringExtensions"] +git-tree-sha1 = "6b764c160547240d868be4e961a5037f47ad7379" +uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" +version = "0.2.1" + [[deps.SymbolicUtils]] deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "Metatheory", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "TermInterface", "TimerOutputs"] git-tree-sha1 = "027b43d312f6d52187bb16c2d4f0588ddb8c4bb2" @@ -1445,10 +1508,10 @@ uuid = "d1185830-fcd6-423d-90d6-eec64667417b" version = "0.19.11" [[deps.Symbolics]] -deps = ["ArrayInterfaceCore", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "Groebner", "IfElse", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "Markdown", "Metatheory", "NaNMath", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "TermInterface", "TreeViews"] -git-tree-sha1 = "873596ee5c98f913bcb2cbb2dc779d815c5aeb86" +deps = ["ArrayInterfaceCore", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "Markdown", "Metatheory", "NaNMath", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "TermInterface", "TreeViews"] +git-tree-sha1 = "111fbf43883d95989577133aeeb889f2040d0aea" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "4.10.4" +version = "4.14.0" [[deps.TOML]] deps = ["Dates"] @@ -1463,14 +1526,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "2d7164f7b8a066bcfa6224e67736ce0eb54aef5b" +git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.9.0" +version = "1.10.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.0" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1495,32 +1558,32 @@ version = "0.5.0" [[deps.ThreadsX]] deps = ["ArgCheck", "BangBang", "ConstructionBase", "InitialValues", "MicroCollections", "Referenceables", "Setfield", "SplittablesBase", "Transducers"] -git-tree-sha1 = "d223de97c948636a4f34d1f84d92fd7602dc555b" +git-tree-sha1 = "34e6bcf36b9ed5d56489600cf9f3c16843fa2aa2" uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" -version = "0.1.10" +version = "0.1.11" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "9dfcb767e17b0849d6aaf85997c98a5aea292513" +git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.21" +version = "0.5.22" [[deps.Tokenize]] -git-tree-sha1 = "2b3af135d85d7e70b863540160208fa612e736b9" +git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.24" +version = "0.5.25" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.9" +version = "0.9.11" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c76399a3bbe6f5a88faa33c8f8a65aa631d95013" +git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.73" +version = "0.4.75" [[deps.TreeViews]] deps = ["Test"] @@ -1530,9 +1593,9 @@ version = "0.3.0" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "Static", "VectorizationBase"] -git-tree-sha1 = "fdddcf6b2c7751cd97de69c18157aacc18fbc660" +git-tree-sha1 = "6cca884e0fe17916da63c62dc1bf5896ce5d723e" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.14" +version = "0.1.17" [[deps.Tricks]] git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" @@ -1540,9 +1603,9 @@ uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" version = "0.1.6" [[deps.URIs]] -git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" +git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.0" +version = "1.4.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1564,9 +1627,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d57a4ed70b6f9ff1da6719f5f2713706d57e0d66" +git-tree-sha1 = "d670a70dd3cdbe1c1186f2f17c9a68a7ec24838c" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.12.0" +version = "1.12.2" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1575,9 +1638,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] -git-tree-sha1 = "17b6042564eecf893aa893af94ec9ede4ddb307b" +git-tree-sha1 = "6b1dc4fc039d273abc247eba675ac1299380e5d9" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.49" +version = "0.21.57" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -1592,9 +1655,9 @@ version = "0.2.0" [[deps.Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1603,16 +1666,16 @@ uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" version = "1.25.0+0" [[deps.Weave]] -deps = ["Base64", "Dates", "Highlights", "JSON", "Markdown", "Mustache", "Pkg", "Printf", "REPL", "Requires", "Serialization", "YAML"] -git-tree-sha1 = "3095e0708dc274e3ce10fca14327d8d7e8de3d30" +deps = ["Base64", "Dates", "Highlights", "JSON", "Markdown", "Mustache", "Pkg", "Printf", "REPL", "RelocatableFolders", "Requires", "Serialization", "YAML"] +git-tree-sha1 = "6000515f13412fe1887792fbe1dc9306112af2ff" uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9" -version = "0.10.9" +version = "0.10.11" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" +git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.14+0" +version = "2.10.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1748,15 +1811,15 @@ version = "1.4.0+3" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "3c6e8b9f5cdaaa21340f841653942e1a6b6561e5" +git-tree-sha1 = "dbc7f1c0012a69486af79c8bcdb31be820670ba2" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.7" +version = "0.4.8" [[deps.ZMQ]] deps = ["FileWatching", "Sockets", "ZeroMQ_jll"] -git-tree-sha1 = "fc68e8a3719166950a0f3e390a14c7302c48f8de" +git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77" uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1" -version = "1.2.1" +version = "1.2.2" [[deps.ZeroMQ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "libsodium_jll"] @@ -1781,12 +1844,6 @@ git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" -[[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" -uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.29.0+0" - [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" diff --git a/benchmarks/Jumps/Mendes_multistate_example.jmd b/benchmarks/Jumps/Mendes_multistate_example.jmd index ccaa9794b..1c2fe2120 100644 --- a/benchmarks/Jumps/Mendes_multistate_example.jmd +++ b/benchmarks/Jumps/Mendes_multistate_example.jmd @@ -21,7 +21,7 @@ reactions(rn) # Plot solutions by each method ```julia -methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve()) shortlabels = [string(leg)[15:end-2] for leg in methods] tf = 10.0 * jprob.tstop prob = DiscreteProblem(rn, jprob.u0, (0.0, tf), jprob.rates) @@ -55,7 +55,7 @@ for (i,method) in enumerate(methods) end end push!(p, plot((1:4)', framestyle = :none, legend=:inside, labels=varlegs)) -plot(p..., layout=(4,2), format=fmt) +plot(p..., layout=(5,2), format=fmt) ``` # Benchmarking performance of the methods diff --git a/benchmarks/Jumps/NegFeedback_GeneExpr.jmd b/benchmarks/Jumps/NegFeedback_GeneExpr.jmd index 4f3f0cc02..794231ec2 100644 --- a/benchmarks/Jumps/NegFeedback_GeneExpr.jmd +++ b/benchmarks/Jumps/NegFeedback_GeneExpr.jmd @@ -20,7 +20,7 @@ reactions(rn) # Plot solutions by each method ```julia -methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve()) shortlabels = [string(leg)[15:end-2] for leg in methods] prob = prob_jump_dnarepressor.discrete_prob tf = prob_jump_dnarepressor.tstop diff --git a/benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd b/benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd index 38850048b..b99c8bb45 100644 --- a/benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd +++ b/benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd @@ -33,7 +33,7 @@ plot(solution, format=fmt) ```julia tf = 4000. -methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve()) shortlabels = [string(leg)[15:end-2] for leg in methods] prob = prob = DiscreteProblem(rn, u0, (0.0, tf), rnpar) ploth = plot(reuse=false)