From f3ebe81004fd53a5b1f8b702f475d2e8724f1627 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Mon, 17 Apr 2023 20:02:25 +0800 Subject: [PATCH 01/16] adds CoevolveSynced to benchmarks. --- benchmarks/Jumps/Diffusion_CTRW.jmd | 2 +- benchmarks/Jumps/Manifest.toml | 233 +++++++++--------- .../Jumps/Mendes_multistate_example.jmd | 4 +- benchmarks/Jumps/MultivariateHawkes.jmd | 20 +- benchmarks/Jumps/NegFeedback_GeneExpr.jmd | 2 +- .../Jumps/NegFeedback_GeneExpr_Marchetti.jmd | 2 +- 6 files changed, 137 insertions(+), 126 deletions(-) diff --git a/benchmarks/Jumps/Diffusion_CTRW.jmd b/benchmarks/Jumps/Diffusion_CTRW.jmd index 075b8add2..0b871c45e 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(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), CoevolveSynced()) 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 67848a803..213160b61 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -38,9 +38,9 @@ version = "0.2.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "a89acc90c551067cd84119ff018619a1a76c6277" +git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.2.1" +version = "7.4.3" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] @@ -64,9 +64,9 @@ version = "0.2.0" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "ee75410471c18f40d57eb53840bc705a74566f23" +git-tree-sha1 = "6ef8fc1d77b60f41041d59ce61ef9eb41ed97a83" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.16" +version = "0.17.18" [[deps.BangBang]] deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] @@ -206,9 +206,9 @@ version = "1.0.2" [[deps.CommonMark]] deps = ["Crayons", "JSON", "SnoopPrecompile", "URIs"] -git-tree-sha1 = "e2f4627b0d3f2c1876360e0b242a7c23923b469d" +git-tree-sha1 = "4a52799aee66e9528bd59e9c0bdd9322c0bf6998" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.10" +version = "0.8.11" [[deps.CommonSolve]] git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" @@ -302,10 +302,10 @@ uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" version = "0.1.2" [[deps.DelayDiffEq]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "UnPack"] -git-tree-sha1 = "dde3fa2cfc91fb5d39ba2a7dc7e4383e0a6665b3" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] +git-tree-sha1 = "89f3fbfe78f9d116d1ed0721d65b0b2cf9b36169" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.41.0" +version = "5.42.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -319,15 +319,15 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "a057a5fe2a6a05f28ef1092d5974a0c2986be23c" +git-tree-sha1 = "988bbd7283aaee5c34cd3cc09e78e7c45a931c5b" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.121.1" +version = "6.123.0" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "b497f63a13fe37e03ed7ac72d71b72aad17b46c4" +git-tree-sha1 = "63b6be7b396ad395825f3cc48c56b53bfaf7e69d" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.26.0" +version = "2.26.1" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArrays", "Statistics"] @@ -355,9 +355,9 @@ version = "7.7.0" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -365,9 +365,9 @@ 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 = "da9e1a9058f8d3eec3a8c9fe4faacfb89180066b" +git-tree-sha1 = "13027f188d26206b9e7b863036f87d2f2e7d013a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.86" +version = "0.25.87" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -416,9 +416,9 @@ uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" version = "1.24.0" [[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "0.1.9" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -454,15 +454,15 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "d3ba08ab64bdfd27234d3f61956c966266757fe6" +git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.7" +version = "0.13.11" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "ed1b56934a2f7a65035976985da71b6a65b4f2cf" +git-tree-sha1 = "03fcb1c42ec905d15b305359603888ec3e65f886" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.18.0" +version = "2.19.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -529,15 +529,15 @@ version = "0.1.4" [[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 = "660b2ea2ec2b010bb02823c6d0ff6afd9bdc5c16" +git-tree-sha1 = "0635807d28a496bb60bc15f465da0107fb29649c" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.71.7" +version = "0.72.0" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "d5e1fd17ac7f3aa4c5287a61ee28d4f8b8e98873" +git-tree-sha1 = "99e248f643b052a77d2766fe1a16fb32b661afd4" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.71.7+0" +version = "0.72.0+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -570,9 +570,9 @@ uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.74.0+2" [[deps.Glob]] -git-tree-sha1 = "4df9f7e06108728ebf00a0a11edee4b29a482bb2" +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" -version = "1.3.0" +version = "1.3.1" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -628,10 +628,10 @@ uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" version = "0.1.14" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] -git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "432b5b03176f8182bd6841fbfc42c718506a2d5f" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.11" +version = "0.3.15" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] @@ -687,9 +687,9 @@ uuid = "3587e190-3f89-42d0-90ee-14403ec27112" version = "0.1.8" [[deps.InvertedIndices]] -git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.2.0" +version = "1.3.0" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -721,9 +721,9 @@ version = "1.4.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -733,9 +733,9 @@ version = "2.1.91+0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "SnoopPrecompile", "Tokenize"] -git-tree-sha1 = "04c4f16ef537e7b5fe0998e507cfeedc5b95b01d" +git-tree-sha1 = "0f6545dd63fec03d0cfe0c1d28f851e2d804e942" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.24" +version = "1.0.25" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -745,9 +745,9 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "7af8d30e281ce558807917b69ba16575d05f412b" +path = "/home/gzagatti/.julia/dev/JumpProcesses/" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.5.1" +version = "9.6.1" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -918,10 +918,10 @@ deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SnoopPrecompile", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "fd65db5fff7238ba4c0b7a61de7e81748d73fa14" +deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SnoopPrecompile", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] +git-tree-sha1 = "4a4f8cc7a59fadbb02d1852d1e0cef5dca3a9460" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.38.0" +version = "1.42.0" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] @@ -940,9 +940,9 @@ version = "1.0.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "2acf6874142d05d5d1ad49e8d3786b8cd800936d" +git-tree-sha1 = "defbfba8ddbccdc8ca3edb4a96a6d6fd3cd33ebd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.152" +version = "0.12.157" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -983,9 +983,9 @@ version = "1.3.5" [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "4d5917a26ca33c66c8e5ca3247bd163624d35493" +git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.3" +version = "0.1.4" [[deps.Missings]] deps = ["DataAPI"] @@ -1019,9 +1019,9 @@ version = "0.4.7" [[deps.Mustache]] deps = ["Printf", "Tables"] -git-tree-sha1 = "1e566ae913a57d0062ff1af54d2697b9344b99cd" +git-tree-sha1 = "87c371d27dbf2449a5685652ab322be163269df0" uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.14" +version = "1.0.15" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] @@ -1052,10 +1052,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "3f856788ba532419c07ba2e0dc37b06e5d784992" +deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "a6000c813371cd3cd9cbbdf8a356fc3a97138d92" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.5.0" +version = "1.6.0" [[deps.OffsetArrays]] deps = ["Adapt"] @@ -1081,9 +1081,9 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" +git-tree-sha1 = "e9d68fe4b5f78f215aa2f0e6e6dc9e9911d33048" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.3" +version = "1.3.4" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1099,9 +1099,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "1903afc76b7d01719d9c30d3c7d501b61db96721" +git-tree-sha1 = "a89b11f0f354f06099e4001c151dffad7ebab015" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.4" +version = "1.7.5" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1110,15 +1110,15 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.0" [[deps.OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces", "UnPack"] -git-tree-sha1 = "d875f5fa389e8a35fb2ae8f39326cc97815d1075" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SimpleUnPack", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "b639e192c0422c849aeda7240382375961d0cb4b" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.49.0" +version = "6.50.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1179,15 +1179,15 @@ version = "1.3.4" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "da1d3fb7183e38603fcdd2061c47979d91202c97" +git-tree-sha1 = "186d38ea29d5c4f238b2d9fe6e1653264101944b" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.6" +version = "1.38.9" [[deps.PoissonRandom]] deps = ["Random"] -git-tree-sha1 = "45f9da1ceee5078267eb273d065e8aa2f2515790" +git-tree-sha1 = "a0f1159c33f846aa77c3f30ebbc69795e5327152" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.3" +version = "0.4.4" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] @@ -1227,9 +1227,9 @@ version = "1.3.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" +git-tree-sha1 = "548793c7859e28ef026dba514752275ee871169f" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.2" +version = "2.2.3" [[deps.Primes]] deps = ["IntegerMathUtils"] @@ -1259,9 +1259,9 @@ version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "786efa36b7eff813723c4849c90456609cf06661" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.8.1" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1302,10 +1302,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.11" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "ZygoteRules"] -git-tree-sha1 = "3dcb2a98436389c0aac964428a5fa099118944de" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "140cddd2c457e4ebb0cdc7c2fd14a7fbfbdf206e" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.0" +version = "2.38.3" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] @@ -1356,9 +1356,9 @@ version = "0.4.0+0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "50314d2ef65fce648975a8e80ae6d8409ebbf835" +git-tree-sha1 = "f139e81a81e6c29c40f1971c9e5309b09c03f2c3" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.5" +version = "0.5.6" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1377,9 +1377,9 @@ version = "0.6.38" [[deps.SciMLBase]] deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SnoopPrecompile", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "fdea92555855db1d86c3638f0a789d6e0a830e67" +git-tree-sha1 = "392d3e28b05984496af37100ded94dc46fa6c8de" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.89.0" +version = "1.91.7" [[deps.SciMLBenchmarks]] deps = ["Git", "IJulia", "InteractiveUtils", "Markdown", "Pkg", "Weave"] @@ -1389,9 +1389,9 @@ version = "0.1.1" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "66c7f901dbcad51791136e2d90ee67240256ecde" +git-tree-sha1 = "2e1606c282fae6bd9aed4f159695774a44b9c75f" uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.3" +version = "0.1.4" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1401,9 +1401,9 @@ version = "0.2.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.1" +version = "1.2.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] @@ -1437,9 +1437,9 @@ version = "1.1.0" [[deps.SimpleNonlinearSolve]] deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Reexport", "Requires", "SciMLBase", "SnoopPrecompile", "StaticArraysCore"] -git-tree-sha1 = "326789bbaa1b65b809bd4596b74e4fc3be5af6ac" +git-tree-sha1 = "54c78ac3cc0343a16785adabe5bbf4063c737967" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.13" +version = "0.1.14" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1447,6 +1447,11 @@ git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" +[[deps.SimpleUnPack]] +git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" +uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" +version = "1.1.0" + [[deps.SnoopPrecompile]] deps = ["Preferences"] git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" @@ -1498,9 +1503,9 @@ version = "0.1.15" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "d0435ba43ab5ad1cbb5f0d286ca4ba67029ed3ee" +git-tree-sha1 = "08be5ee09a7632c32695d954a602df96a877bf0d" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.4" +version = "0.8.6" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] @@ -1510,9 +1515,9 @@ version = "1.3.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "2d7d9e1ddadc8407ffd460e24218e37ef52dd9a3" +git-tree-sha1 = "63e84b7fdf5021026d0f17f76af7c57772313d99" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.16" +version = "1.5.21" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1525,9 +1530,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,21 +1548,21 @@ version = "1.3.0" [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "8998e426c1d49ef92d4c60cc81acb90ddf92c610" +git-tree-sha1 = "04a7d0bb1c824857ba0bb0c17bc5950dccbfdd5d" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.13.0" +version = "1.14.0" [[deps.StochasticDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "c6b4b802d4d830e0e958f5f2098d8dea0a935f4b" +git-tree-sha1 = "073da86200349ddf4ef8bc3e3f3acd62e1d554f7" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.58.0" +version = "6.60.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "2842f1dbd12d59f2728ba79f4002cd6b61808f8b" +git-tree-sha1 = "e2d60a1cd52d0583471f83bd5d2dcefa626d271f" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.8" +version = "0.4.10" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1581,9 +1586,9 @@ version = "5.10.1+0" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "c033830e3c6fb4260243fc907b1e7e93421e7ae8" +git-tree-sha1 = "a4e8491c163d74fb92905c6443e59558f5e609a4" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.15.1" +version = "4.16.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -1622,9 +1627,9 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1671,9 +1676,9 @@ version = "0.5.25" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" +git-tree-sha1 = "0b829474fed270a4b0ab07117dce9b9a2fa7581a" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.11" +version = "0.9.12" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] @@ -1694,15 +1699,15 @@ uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" version = "0.1.19" [[deps.Tricks]] -git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.6" +version = "0.1.7" [[deps.TruncatedStacktraces]] -deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "f7057ba94e63b269125c0db75dcdef913d956351" +deps = ["InteractiveUtils", "MacroTools", "Preferences"] +git-tree-sha1 = "7bc1632a4eafbe9bd94cf1a784a9a4eb5e040a91" uuid = "781d530d-4396-4725-bb49-402e4bee1e77" -version = "1.1.0" +version = "1.3.0" [[deps.URIs]] git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" @@ -1729,9 +1734,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "bb37ed24f338bc59b83e3fc9f32dd388e5396c53" +git-tree-sha1 = "dba3eba51b9512695b59e0bd8263ac074c5ed2d9" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.12.4" +version = "1.13.1" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1740,9 +1745,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "952ba509a61d1ebb26381ac459c5c6e838ed43c4" +git-tree-sha1 = "b182207d4af54ac64cbc71797765068fdeff475d" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.60" +version = "0.21.64" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" @@ -1936,15 +1941,15 @@ version = "1.2.12+3" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" +git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.4+0" +version = "1.5.5+0" [[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/benchmarks/Jumps/Mendes_multistate_example.jmd b/benchmarks/Jumps/Mendes_multistate_example.jmd index 1c2fe2120..a68145134 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(), Coevolve()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), CoevolveSynced()) 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=(5,2), format=fmt) +plot(p..., layout=(6,2), format=fmt) ``` # Benchmarking performance of the methods diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 42bddec2b..607e5767d 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -130,12 +130,12 @@ function hawkes_problem( end ``` -The `Coevolve()` aggregator knows how to handle the `SSAStepper`, so it accepts a `DiscreteProblem`. +The `Coevolve()` and `CoevolveSynced()` aggregator knows how to handle the `SSAStepper`, so it accepts a `DiscreteProblem`. ```julia function hawkes_problem( p, - agg::Coevolve; + agg::Union{Coevolve, CoevolveSynced}; u = [0.0], tspan = (0.0, 50.0), save_positions = (false, true), @@ -173,12 +173,15 @@ Now, we instantiate the problems, find their solutions and plot the results. algorithms = Tuple{Any, Any, Bool, String}[ (Direct(), Tsit5(), false, "Direct (brute-force)"), (Coevolve(), SSAStepper(), false, "Coevolve (brute-force)"), + (CoevolveSynced(), SSAStepper(), false, "CoevolveSynced (brute-force)"), (Direct(), Tsit5(), true, "Direct (recursive)"), (Coevolve(), SSAStepper(), true, "Coevolve (recursive)"), + (CoevolveSynced(), SSAStepper(), true, "CoevolveSynced (recursive)"), ] let fig = [] for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms) + @info label if use_recursion h = zeros(eltype(tspan), nv(G)) urate = zeros(eltype(tspan), nv(G)) @@ -193,7 +196,7 @@ let fig = [] sol = solve(jump_prob, stepper) push!(fig, plot(sol.t, sol[1:V, :]', title=label, legend=false, format=fmt)) end - fig = plot(fig..., layout=(2,2), format=fmt) + fig = plot(fig..., layout=(3,2), format=fmt, size=(width_px, 3*height_px/2)) end ``` @@ -270,8 +273,8 @@ push!(algorithms, (PDMPCHV(), CHV(Tsit5()), true, "PDMPCHV")); The Python `Tick` library can be accessed with the `PyCall.jl`. We install the required Python dependencies with `Conda.jl` and define a factory for the Multivariate Hawkes `PyTick` problem. ```julia -const BENCHMARK_PYTHON = false -const REBUILD_PYCALL = false +const BENCHMARK_PYTHON::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_PYTHON", "false")) +const REBUILD_PYCALL::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_REBUILD_PYCALL", "false")) struct PyTick end @@ -323,7 +326,8 @@ Now, we instantiate the problems, find their solutions and plot the results. ```julia let fig = [] - for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms[5:end]) + for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms[7:end]) + @info label if typeof(algo) <: PyTick _p = (p[1], p[2], p[3]) jump_prob = hawkes_problem(_p, algo; u, tspan, g, use_recursion) @@ -540,6 +544,7 @@ Now, we simulate all of the algorithms we defined in the previous Section $250$ ```julia let fig = [] for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms) + @info label if typeof(algo) <: PyTick _p = (p[1], p[2], p[3]) elseif typeof(algo) <: PDMPCHV @@ -579,7 +584,7 @@ let fig = [] qqs = qq(runs, Λ) push!(fig, qqplot(qqs..., legend = false, aspect_ratio = :equal, title=label, fmt=fmt)) end - fig = plot(fig..., layout = (3, 2), fmt=fmt, size=(width_px, 3*height_px/2)) + fig = plot(fig..., layout = (4, 2), fmt=fmt, size=(width_px, 4*height_px/2)) end ``` @@ -600,6 +605,7 @@ Gs = [erdos_renyi(V, 0.2, seed = 6221) for V in Vs] bs = Vector{Vector{BenchmarkTools.Trial}}() for (algo, stepper, use_recursion, label) in algorithms + @info label global _stepper = stepper push!(bs, Vector{BenchmarkTools.Trial}()) _bs = bs[end] diff --git a/benchmarks/Jumps/NegFeedback_GeneExpr.jmd b/benchmarks/Jumps/NegFeedback_GeneExpr.jmd index 794231ec2..db754c851 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(), Coevolve()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), CoevolveSynced()) 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 b99c8bb45..716fd19e0 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(), Coevolve()) +methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), CoevolveSynced()) shortlabels = [string(leg)[15:end-2] for leg in methods] prob = prob = DiscreteProblem(rn, u0, (0.0, tf), rnpar) ploth = plot(reuse=false) From 3f09032159a47c9fee956b4c35e8916430092578 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Wed, 26 Apr 2023 10:59:35 +0800 Subject: [PATCH 02/16] adds synapse benchmark --- benchmarks/Jumps/Manifest.toml | 430 ++++++++++++++++++++---- benchmarks/Jumps/MultivariateHawkes.jmd | 44 +-- benchmarks/Jumps/Project.toml | 1 + benchmarks/Jumps/Synapse.jmd | 138 ++++++++ 4 files changed, 521 insertions(+), 92 deletions(-) create mode 100644 benchmarks/Jumps/Synapse.jmd diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 213160b61..170ac00b4 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -1,8 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.5" +julia_version = "1.9.0-rc2" manifest_format = "2.0" -project_hash = "c42d2169376cc3fcf8f85135002943a271f20447" +project_hash = "90b531ee81678bcea6c6e8005bc34774fb1e8a5f" + +[[deps.ANSIColoredPrinters]] +git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" +uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" +version = "0.0.1" [[deps.AbstractAlgebra]] deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] @@ -11,15 +16,19 @@ uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" version = "0.27.10" [[deps.AbstractTrees]] -git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.4" +version = "0.3.4" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.6.1" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -42,6 +51,22 @@ git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" version = "7.4.3" + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" @@ -127,6 +152,18 @@ git-tree-sha1 = "2c144ddb46b552f72d7eafe7cc2f50746e41ea21" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" version = "0.2.2" +[[deps.CRlibm]] +deps = ["CRlibm_jll"] +git-tree-sha1 = "32abd86e3c2025db5172aa182b982debed519834" +uuid = "96374032-68de-5a5b-8d9e-752f78720389" +version = "1.0.1" + +[[deps.CRlibm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "e329286945d0cfc04456972ea732551869af1cfc" +uuid = "4e9b3aee-d8a1-5a3d-ad8b-7d824db253f0" +version = "1.0.1+0" + [[deps.CSTParser]] deps = ["Tokenize"] git-tree-sha1 = "3ddd48d200eb8ddf9cb3e0189fc059fd49b97c1f" @@ -157,18 +194,18 @@ git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" version = "1.15.7" -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.6" - [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.12" +[[deps.CodecBzip2]] +deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] +git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7" +uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" +version = "0.7.2" + [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" @@ -176,10 +213,10 @@ uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.1" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.21.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -222,15 +259,19 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] +deps = ["UUIDs"] git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" version = "4.6.1" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.1+0" +version = "1.0.2+0" [[deps.CompositeTypes]] git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" @@ -253,6 +294,11 @@ deps = ["LinearAlgebra"] git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" version = "1.5.1" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + IntervalSetsExt = "IntervalSets" + StaticArraysExt = "StaticArrays" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -309,20 +355,38 @@ version = "5.42.0" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.DensityInterface]] -deps = ["InverseFunctions", "Test"] -git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" -uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" -version = "0.4.0" +version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] git-tree-sha1 = "988bbd7283aaee5c34cd3cc09e78e7c45a931c5b" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" version = "6.123.0" + [deps.DiffEqBase.extensions] + DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" + DiffEqBaseMPIExt = "MPI" + DiffEqBaseMeasurementsExt = "Measurements" + DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" + DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseTrackerExt = "Tracker" + DiffEqBaseUnitfulExt = "Unitful" + DiffEqBaseZygoteExt = "Zygote" + + [deps.DiffEqBase.weakdeps] + Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + 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" + 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 = "63b6be7b396ad395825f3cc48c56b53bfaf7e69d" @@ -335,6 +399,12 @@ git-tree-sha1 = "2c4ed3eedb87579bfe9f20ecc2440de06b9f3b89" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" version = "5.16.0" + [deps.DiffEqNoiseProcess.extensions] + DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" + + [deps.DiffEqNoiseProcess.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + [[deps.DiffResults]] deps = ["StaticArraysCore"] git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" @@ -364,17 +434,31 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] git-tree-sha1 = "13027f188d26206b9e7b863036f87d2f2e7d013a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" version = "0.25.87" + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" +[[deps.Documenter]] +deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] +git-tree-sha1 = "58fea7c536acd71f3eef6be3b21c0df5f3df88fd" +uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +version = "0.27.24" + [[deps.DomainSets]] deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] git-tree-sha1 = "988e2db482abeb69efc76ae8b6eba2e93805ee70" @@ -403,6 +487,11 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" +[[deps.ErrorfreeArithmetic]] +git-tree-sha1 = "d6863c556f1142a061532e79f611aa46be201686" +uuid = "90fa49ef-747e-5e6f-a989-263ba693cf1a" +version = "0.5.2" + [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" @@ -449,6 +538,18 @@ git-tree-sha1 = "c1293a93193f0ae94be7cf338d33e162c39d8788" uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "1.2.9" +[[deps.FastRounding]] +deps = ["ErrorfreeArithmetic", "LinearAlgebra"] +git-tree-sha1 = "6344aa18f654196be82e62816935225b3b9abe44" +uuid = "fa42c844-2597-5d31-933b-ebd51ab2693f" +version = "0.3.1" + +[[deps.FileIO]] +deps = ["Pkg", "Requires", "UUIDs"] +git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +version = "1.16.0" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -470,6 +571,12 @@ git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" +[[deps.FlameGraphs]] +deps = ["AbstractTrees", "Colors", "FileIO", "FixedPointNumbers", "IndirectArrays", "LeftChildRightSiblingTrees", "Profile"] +git-tree-sha1 = "d9eee53657f6a13ee51120337f98684c9c702264" +uuid = "08572546-2f56-4bcf-ba4e-bab62c3a3f89" +version = "0.2.10" + [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" @@ -483,10 +590,14 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -521,6 +632,23 @@ git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" version = "3.3.8+0" +[[deps.GLPK]] +deps = ["GLPK_jll", "MathOptInterface"] +git-tree-sha1 = "b3e1aef8eddc38ce6f27d6166a5c8ba565463a7b" +uuid = "60bf3e95-4087-53dc-ae20-288a0d20c6a6" +version = "1.1.2" + +[[deps.GLPK_jll]] +deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "fe68622f32828aa92275895fdb324a85894a5b1b" +uuid = "e8aa6df9-e6ca-548a-97ff-1f85fc5b8b98" +version = "5.0.1+0" + +[[deps.GMP_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d" +version = "6.2.1+2" + [[deps.GPUArraysCore]] deps = ["Adapt"] git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" @@ -529,15 +657,15 @@ version = "0.1.4" [[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 = "0635807d28a496bb60bc15f465da0107fb29649c" +git-tree-sha1 = "db730189e3d250d97515a91886de7e33aa8833e6" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.0" +version = "0.72.2" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "99e248f643b052a77d2766fe1a16fb32b661afd4" +git-tree-sha1 = "47a2efe07729dd508a032e2f56c46c517481052a" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.0+0" +version = "0.72.2+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -639,11 +767,22 @@ git-tree-sha1 = "59e19713542dd9dd02f31d59edbada69530d6a14" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" version = "1.24.0" +[[deps.IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" + [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" +[[deps.IndirectArrays]] +git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f" +uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" +version = "1.0.0" + [[deps.Inflate]] git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" @@ -674,18 +813,18 @@ version = "0.1.0" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[deps.IntervalArithmetic]] +deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] +git-tree-sha1 = "c1c88395d09366dae431556bcb598ad08fa1392b" +uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" +version = "0.20.8" + [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" version = "0.7.3" -[[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" -uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" - [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" @@ -731,11 +870,17 @@ git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" version = "2.1.91+0" +[[deps.JuMP]] +deps = ["LinearAlgebra", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "Printf", "SnoopPrecompile", "SparseArrays"] +git-tree-sha1 = "4ec0e68fecbbe1b78db2ddf1ac573963ed5adebc" +uuid = "4076af6c-e467-56ae-b986-b466b2749572" +version = "1.10.0" + [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "SnoopPrecompile", "Tokenize"] -git-tree-sha1 = "0f6545dd63fec03d0cfe0c1d28f851e2d804e942" +git-tree-sha1 = "8bbb6ffe81a919b1a3e943d72fbe2f677bef6f77" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.25" +version = "1.0.26" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -747,7 +892,7 @@ version = "0.1.3" deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] path = "/home/gzagatti/.julia/dev/JumpProcesses/" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.6.1" +version = "9.6.2" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -815,9 +960,21 @@ version = "0.4.6" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" +git-tree-sha1 = "98dc144f1e0b299d49e8d23e56ad68d3e4f340a5" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.18" +version = "0.15.20" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + DiffEqBiologicalExt = "DiffEqBiological" + ParameterizedFunctionsExt = "DiffEqBase" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] @@ -831,6 +988,18 @@ git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" version = "0.15.1" +[[deps.LazySets]] +deps = ["Distributed", "GLPK", "IntervalArithmetic", "JuMP", "LinearAlgebra", "Random", "ReachabilityBase", "RecipesBase", "Reexport", "Requires", "SharedArrays", "SparseArrays", "StaticArraysCore"] +git-tree-sha1 = "00dabbd02d0503c21d3b48c7bf8b976cafb95f91" +uuid = "b4f0291d-fe17-52bc-9479-3d1a343d9043" +version = "2.7.4" + +[[deps.LeftChildRightSiblingTrees]] +deps = ["AbstractTrees"] +git-tree-sha1 = "b864cb409e8e445688bc478ef87c0afe4f6d1f8d" +uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" +version = "0.1.3" + [[deps.LevyArea]] deps = ["LinearAlgebra", "Random", "SpecialFunctions"] git-tree-sha1 = "56513a09b8e0ae6485f34401ea9e2f31357958ec" @@ -914,7 +1083,7 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] @@ -923,12 +1092,28 @@ git-tree-sha1 = "4a4f8cc7a59fadbb02d1852d1e0cef5dca3a9460" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" version = "1.42.0" + [deps.LinearSolve.extensions] + LinearSolveHYPRE = "HYPRE" + + [deps.LinearSolve.weakdeps] + HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" + [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" version = "0.3.23" + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -939,10 +1124,15 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] git-tree-sha1 = "defbfba8ddbccdc8ca3edb4a96a6d6fd3cd33ebd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" version = "0.12.157" +weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] + + [deps.LoopVectorization.extensions] + ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] + SpecialFunctionsExt = "SpecialFunctions" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -959,6 +1149,12 @@ version = "0.1.8" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MathOptInterface]] +deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] +git-tree-sha1 = "8e054675d393ce5866dcdd6a071075e25e21a39c" +uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" +version = "1.15.1" + [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" @@ -968,7 +1164,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1004,7 +1200,7 @@ version = "8.46.1" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1072,7 +1268,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1081,9 +1277,9 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "e9d68fe4b5f78f215aa2f0e6e6dc9e9911d33048" +git-tree-sha1 = "7fb975217aea8f1bb360cf1dde70bad2530622d2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.4" +version = "1.4.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1123,7 +1319,7 @@ version = "6.50.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1161,9 +1357,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.40.1+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1172,16 +1368,30 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.1.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.4" +version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "186d38ea29d5c4f238b2d9fe6e1653264101944b" +git-tree-sha1 = "5434b0ee344eaf2854de251f326df8720f6a7b55" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.9" +version = "1.38.10" + + [deps.Plots.extensions] + FileIOExt = "FileIO" + GeometryBasicsExt = "GeometryBasics" + IJuliaExt = "IJulia" + ImageInTerminalExt = "ImageInTerminal" + UnitfulExt = "Unitful" + + [deps.Plots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" + IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.PoissonRandom]] deps = ["Random"] @@ -1219,6 +1429,18 @@ git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" version = "0.4.12" + [deps.PreallocationTools.extensions] + PreallocationToolsReverseDiffExt = "ReverseDiff" + + [deps.PreallocationTools.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "bc2bda41d798c2e66e7c44a11007bb329b15941b" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.0.1" + [[deps.Preferences]] deps = ["TOML"] git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" @@ -1245,6 +1467,18 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" deps = ["Printf"] uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" +[[deps.ProfileSVG]] +deps = ["Colors", "FlameGraphs", "Profile", "UUIDs"] +git-tree-sha1 = "e4df82a5dadc26736f106f8d7fc97c42cc6c91ae" +uuid = "132c30aa-f267-4189-9183-c8a63c7e05e6" +version = "0.2.1" + +[[deps.ProgressMeter]] +deps = ["Distributed", "Printf"] +git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +uuid = "92933f4c-e287-5a05-a399-4b506db050ca" +version = "1.7.2" + [[deps.PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] git-tree-sha1 = "62f417f6ad727987c755549e9cd88c46578da562" @@ -1289,6 +1523,12 @@ git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" version = "1.5.3" +[[deps.ReachabilityBase]] +deps = ["ExprTools", "InteractiveUtils", "LinearAlgebra", "Random", "Requires", "SparseArrays"] +git-tree-sha1 = "65dd3407e52228aa5c6ae29d4998961043e131a4" +uuid = "379f33d0-9447-4353-bd03-d664070e549f" +version = "0.1.7" + [[deps.RecipesBase]] deps = ["SnoopPrecompile"] git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" @@ -1307,6 +1547,16 @@ git-tree-sha1 = "140cddd2c457e4ebb0cdc7c2fd14a7fbfbdf206e" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" version = "2.38.3" + [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsMeasurementsExt = "Measurements" + RecursiveArrayToolsTrackerExt = "Tracker" + RecursiveArrayToolsZygoteExt = "Zygote" + + [deps.RecursiveArrayTools.weakdeps] + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] git-tree-sha1 = "9088515ad915c99026beb5436d0a09cd8c18163e" @@ -1354,6 +1604,11 @@ git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.4.0+0" +[[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 = "f139e81a81e6c29c40f1971c9e5309b09c03f2c3" @@ -1414,6 +1669,11 @@ version = "1.3.18" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +[[deps.SetRounding]] +git-tree-sha1 = "d7a25e439d07a17b7cdf97eecee504c50fedf5f6" +uuid = "3cc68bcd-71a2-5612-b932-767ffbe40ab0" +version = "0.2.1" + [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" @@ -1441,6 +1701,12 @@ git-tree-sha1 = "54c78ac3cc0343a16785adabe5bbf4063c737967" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" version = "0.1.14" + [deps.SimpleNonlinearSolve.extensions] + SimpleBatchedNonlinearSolveExt = "NNlib" + + [deps.SimpleNonlinearSolve.weakdeps] + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" @@ -1474,7 +1740,7 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] @@ -1490,10 +1756,14 @@ uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" version = "0.3.9" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" version = "2.2.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1509,9 +1779,14 @@ version = "0.8.6" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "fd5f417fd7e103c121b0a0b4a6902f03991111f4" +git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.3.0" +version = "1.4.0" +weakdeps = ["OffsetArrays", "StaticArrays"] + + [deps.StaticArrayInterface.extensions] + StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" + StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] @@ -1527,6 +1802,7 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1541,11 +1817,19 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" version = "0.33.21" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] git-tree-sha1 = "04a7d0bb1c824857ba0bb0c17bc5950dccbfdd5d" @@ -1560,9 +1844,9 @@ version = "6.60.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "e2d60a1cd52d0583471f83bd5d2dcefa626d271f" +git-tree-sha1 = "f5a57d3c111c79fcc1f8fed6058a8753d061c6d2" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.10" +version = "0.4.12" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1582,7 +1866,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+0" +version = "5.10.1+6" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "Sundials_jll"] @@ -1614,10 +1898,16 @@ git-tree-sha1 = "111fbf43883d95989577133aeeb889f2040d0aea" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" version = "4.14.0" +[[deps.Synapse]] +deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] +path = "/home/gzagatti/.julia/dev/SynapseElife/" +uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" +version = "0.0.1" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1634,7 +1924,7 @@ version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1665,9 +1955,9 @@ version = "0.1.11" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" +version = "0.5.23" [[deps.Tokenize]] git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5" @@ -1937,7 +2227,7 @@ version = "4.3.4+0" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1970,9 +2260,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.4.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 607e5767d..f9e44cb4a 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -14,27 +14,27 @@ width_px, height_px = default(:size); # Model and example solutions -Let a graph with $V$ nodes, then the multivariate Hawkes process is characterized by $V$ point processes such that the conditional intensity rate of node $i$ connected to a set of nodes $E_i$ in the graph is given by: -$$ +Let a graph with ``V`` nodes, then the multivariate Hawkes process is characterized by ``V`` point processes such that the conditional intensity rate of node ``i`` connected to a set of nodes ``E_i`` in the graph is given by: +```math \lambda_i^\ast (t) = \lambda + \sum_{j \in E_i} \sum_{t_{n_j} < t} \alpha \exp \left[-\beta (t - t_{n_j}) \right] -$$ -This process is known as self-exciting, because the occurence of an event $ j $ at $t_{n_j}$ will increase the conditional intensity of all the processes connected to it by $\alpha$. The excited intensity then decreases at a rate proportional to $\beta$. +``` +This process is known as self-exciting, because the occurence of an event ``j `` at ``t_{n_j}`` will increase the conditional intensity of all the processes connected to it by ``\alpha``. The excited intensity then decreases at a rate proportional to ``\beta``. -The conditional intensity of this process has a recursive formulation which can significantly speed the simulation. The recursive formulation for the univariate case is derived in Laub et al. [2]. We derive the compound case here. Let $t_{N_i} = \max \{ t_{n_j} < t \mid j \in E_i \}$ and -$$ +The conditional intensity of this process has a recursive formulation which can significantly speed the simulation. The recursive formulation for the univariate case is derived in Laub et al. [2]. We derive the compound case here. Let ``t_{N_i} = \max \{ t_{n_j} < t \mid j \in E_i \}`` and +```math \begin{split} \phi_i^\ast (t) &= \sum_{j \in E_i} \sum_{t_{n_j} < t} \alpha \exp \left[-\beta (t - t_{N_i} + t_{N_i} - t_{n_j}) \right] \\ &= \exp \left[ -\beta (t - t_{N_i}) \right] \sum_{j \in E_i} \sum_{t_{n_j} \leq t_{N_i}} \alpha \exp \left[-\beta (t_{N_i} - t_{n_j}) \right] \\ &= \exp \left[ -\beta (t - t_{N_i}) \right] \left( \alpha + \phi^\ast (t_{N_i}) \right) \end{split} -$$ -Then the conditional intensity can be re-written in terms of $\phi_i^\ast (t_{N_i})$ -$$ +``` +Then the conditional intensity can be re-written in terms of ``\phi_i^\ast (t_{N_i})`` +```math \lambda_i^\ast (t) = \lambda + \phi_i^\ast (t) = \lambda + \exp \left[ -\beta (t - t_{N_i}) \right] \left( \alpha + \phi_i^\ast (t_{N_i}) \right) -$$ +``` -In Julia, we define a factory for the conditional intensity $\lambda_i$ which returns the brute-force or recursive versions of the intensity given node $i$ and network $g$. +In Julia, we define a factory for the conditional intensity ``\lambda_i`` which returns the brute-force or recursive versions of the intensity given node ``i`` and network ``g``. ```julia function hawkes_rate(i::Int, g; use_recursion = false) @@ -150,7 +150,7 @@ function hawkes_problem( end ``` -Lets solve the problems defined so far. We sample a random graph sampled from the Erdős-Rényi model. This model assumes that the probability of an edge between two nodes is independent of other edges, which we fix at $0.2$. For illustration purposes, we fix $V = 10$. +Lets solve the problems defined so far. We sample a random graph sampled from the Erdős-Rényi model. This model assumes that the probability of an edge between two nodes is independent of other edges, which we fix at ``0.2``. For illustration purposes, we fix ``V = 10``. ```julia V = 10 @@ -158,7 +158,7 @@ G = erdos_renyi(V, 0.2, seed = 9103) g = [neighbors(G, i) for i = 1:nv(G)] ``` -We fix the Hawkes parameters at $\lambda = 0.5 , \alpha = 0.1 , \beta = 2.0$ which ensures the process does not explode. +We fix the Hawkes parameters at ``\lambda = 0.5 , \alpha = 0.1 , \beta = 2.0`` which ensures the process does not explode. ```julia tspan = (0.0, 50.0) @@ -205,13 +205,13 @@ end We benchmark `JumpProcesses.jl` against `PiecewiseDeterministicMarkovProcesses.jl` and Python `Tick` library. In order to compare with the `PiecewiseDeterministicMarkovProcesses.jl`, we need to reformulate our jump problem as a Piecewise Deterministic Markov Process (PDMP). In this setting, we need to describe how the conditional intensity changes with time which we derive below: -$$ +```math \begin{split} \frac{d \lambda_i^\ast (t)}{d t} &= -\beta \sum_{j \in E_i} \sum_{t_{n_j} < t} \alpha \exp \left[-\beta (t - t_{n_j}) \right] \\ &= -\beta \left( \lambda_i^\ast (t) - \lambda \right) \end{split} -$$ +``` ```julia function hawkes_drate(dxc, xc, xd, p, t) @@ -350,10 +350,10 @@ end We check that the algorithms produce correct simulation by inspecting their QQ-plots. Point process theory says that transforming the simulated points using the compensator should produce points whose inter-arrival duration is distributed according to the exponential distribution (see Section 7.4 [1]). -The compensator of any point process is the integral of the conditional intensity $\Lambda_i^\ast(t) = \int_0^t \lambda_i^\ast(u) du$. The compensator for the Multivariate Hawkes process is defined below. -$$ +The compensator of any point process is the integral of the conditional intensity ``\Lambda_i^\ast(t) = \int_0^t \lambda_i^\ast(u) du``. The compensator for the Multivariate Hawkes process is defined below. +```math \Lambda_i^\ast(t) = \lambda t + \frac{\alpha}{\beta} \sum_{j \in E_i} \sum_{t_{n_j} < t} ( 1 - \exp \left[-\beta (t - t_{n_j}) \right]) -$$ +``` ```julia function hawkes_Λ(i::Int, g, p) @@ -539,7 +539,7 @@ We can construct QQ-plots with a Plot recipe as following. end ``` -Now, we simulate all of the algorithms we defined in the previous Section $250$ times to produce their QQ-plots. +Now, we simulate all of the algorithms we defined in the previous Section ``250`` times to produce their QQ-plots. ```julia let fig = [] @@ -592,9 +592,9 @@ end In this Section we benchmark all the algorithms introduced in the first Section. -We generate networks in the range from $1$ to $95$ nodes and simulate the Multivariate Hawkes process $25$ units of time. +We generate networks in the range from ``1`` to ``95`` nodes and simulate the Multivariate Hawkes process ``25`` units of time. - and simulate models in the range from $1$ to $95$ nodes for $25$ units of time. We fix the Hawkes parameters at $\lambda = 0.5 , \alpha = 0.1 , \beta = 5.0$ which ensures the process does not explode. We simulate $50$ trajectories with a limit of ten seconds to complete execution for each configuration. + and simulate models in the range from ``1`` to ``95`` nodes for ``25`` units of time. We fix the Hawkes parameters at ``\lambda = 0.5 , \alpha = 0.1 , \beta = 5.0`` which ensures the process does not explode. We simulate ``50`` trajectories with a limit of ten seconds to complete execution for each configuration. ```julia tspan = (0.0, 25.0) @@ -677,7 +677,7 @@ for (algo, stepper, use_recursion, label) in algorithms median_time = length(trial) > 0 ? "$(BenchmarkTools.prettytime(median(trial.times)))" : "nan" - println("algo=$(label), V = $(nv(G)), length = $(length(trial.times)), median time = $median_time") + println("algo=``(label), V = ``(nv(G)), length = ``(length(trial.times)), median time = ``median_time") end end end diff --git a/benchmarks/Jumps/Project.toml b/benchmarks/Jumps/Project.toml index 3b1fecbad..c6e75ac26 100644 --- a/benchmarks/Jumps/Project.toml +++ b/benchmarks/Jumps/Project.toml @@ -16,6 +16,7 @@ PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +Synapse = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" [compat] BenchmarkTools = "1.3.1" diff --git a/benchmarks/Jumps/Synapse.jmd b/benchmarks/Jumps/Synapse.jmd new file mode 100644 index 000000000..fcc91cc2b --- /dev/null +++ b/benchmarks/Jumps/Synapse.jmd @@ -0,0 +1,138 @@ +--- +title: Synapse model +author: Yuri Rodrigues, Cian O'Donnel, Romain Veltz, Guilherme Zagatti +weave_options: + fig_ext: ".png" +--- + +```julia +using Synapse +using PiecewiseDeterministicMarkovProcesses, JumpProcesses, OrdinaryDiffEq, Plots +using BenchmarkTools +``` + +# Parameters and initial conditions + +```julia +p_synapse = SynapseParams(t_end = 1000.0); +glu = 0.0; +events_sorted_times = [500.0]; +is_pre_or_post_event = [true]; +events_bap = events_sorted_times[is_pre_or_post_event.==false]; +bap_by_epsp = Float64[]; +t1 = 0.0; +t2 = 500.0; +nu = buildTransitionMatrix(); +``` + +```julia +xc0 = initial_conditions_continuous_temp(p_synapse); +xd0 = initial_conditions_discrete(p_synapse); +``` + +# Algorithms to benchmark + +```julia +solver = AutoTsit5(Rosenbrock23()); +algorithms = [ + ( + label = "PDMP", + agg = nothing, + solver = (CHV(solver), CHV(solver)), + save_positions = (false, true), # necessary to save at regular intervals + saveat = [], + ), + ( + label = "Coevolve", + agg = CoevolveSynced(), + solver = (solver, solver), + save_positions = (false, false), + saveat = 0.05, # similar rate as the PDMP problem + ), +]; +``` + +# Model and example solutions + +```julia +results = [] + +for algo in algorithms + push!( + results, + evolveSynapse( + xc0, + xd0, + p_synapse, + events_sorted_times, + is_pre_or_post_event, + bap_by_epsp, + [true], + nu, + algo.solver, + algo.agg; + save_positions = algo.save_positions, + saveat = algo.saveat, + save_everystep = false, + ), + ) +end +``` + +```julia +fig = plot(xlabel = "Voltage", ylabel = "Time"); +for (i, algo) in enumerate(algorithms) + res = results[i] + plot!(res.t, res.Vsp, label = algo.label) +end +title!("Vsp") +``` + +```julia +fig = plot(xlabel = "N", ylabel = "Time"); +for (i, algo) in enumerate(algorithms) + res = results[i] + plot!(res.t, res.XD[1, :], label = algo.label) +end +title!("2line-Go, AMPA") +``` + +# Benchmarking perfomance + +```julia +bs = Vector{BenchmarkTools.Trial}() + +for algo in algorithms + push!( + bs, + @benchmark( + evolveSynapse( + xc0, + xd0, + p_synapse, + events_sorted_times, + is_pre_or_post_event, + bap_by_epsp, + [true], + nu, + $(algo).solver, + $(algo).agg; + save_positions = $(algo).save_positions, + saveat = $(algo).saveat, + save_everystep = false, + ), + samples = 50, + evals = 1, + seconds = 500, + ) + ) +end +``` + +```julia +``` + +# References + +[1] Y. E. Rodrigues, C. M. Tigaret, H. Marie, C. O’Donnell, and R. Veltz, "A stochastic model of hippocampal synaptic plasticity with geometrical readout of enzyme dynamics." bioRxiv, p. 2021.03.30.437703, Mar. 30, 2021. doi: 10.1101/2021.03.30.437703. + From 3e231cbdd70d6b8a21963e5a4a2d1f9cd0aeec8c Mon Sep 17 00:00:00 2001 From: gzagatti Date: Wed, 26 Apr 2023 12:31:56 +0800 Subject: [PATCH 03/16] adds synapse benchmark --- benchmarks/Jumps/Manifest.toml | 8 ++++++-- benchmarks/Jumps/Synapse.jmd | 30 ++++++++++++++++++++++++++---- 2 files changed, 32 insertions(+), 6 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 170ac00b4..82638220f 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -890,7 +890,9 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -path = "/home/gzagatti/.julia/dev/JumpProcesses/" +git-tree-sha1 = "c3c4979515513fa23269b1edd6bd255830a808d2" +repo-rev = "coevolve-ii" +repo-url = "https://github.com/gzagatti/JumpProcesses.jl" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" version = "9.6.2" @@ -1900,7 +1902,9 @@ version = "4.14.0" [[deps.Synapse]] deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] -path = "/home/gzagatti/.julia/dev/SynapseElife/" +git-tree-sha1 = "d5c494549b0e8839ce7351f1f9f56a4d448f91e3" +repo-rev = "coevolve-ii" +repo-url = "https://github.com/gzagatti/SynapseElife" uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" version = "0.0.1" diff --git a/benchmarks/Jumps/Synapse.jmd b/benchmarks/Jumps/Synapse.jmd index fcc91cc2b..3d9e52707 100644 --- a/benchmarks/Jumps/Synapse.jmd +++ b/benchmarks/Jumps/Synapse.jmd @@ -9,9 +9,15 @@ weave_options: using Synapse using PiecewiseDeterministicMarkovProcesses, JumpProcesses, OrdinaryDiffEq, Plots using BenchmarkTools +fmt = :png ``` -# Parameters and initial conditions +# Model and example solutions + +Here we implement the stochastic model of hippocampal synaptic plasticity with geometrical readount of enzyme dinamics from Rodrigues et al. [1]. + + +## Parameters and initial conditions ```julia p_synapse = SynapseParams(t_end = 1000.0); @@ -30,7 +36,9 @@ xc0 = initial_conditions_continuous_temp(p_synapse); xd0 = initial_conditions_discrete(p_synapse); ``` -# Algorithms to benchmark +## Algorithms to benchmark + +`CoevolveSynced` allow us to save at regular intervals. Thus, rather than saving when a jump occurs, we save at the same average frequency as obtained with `PDMP`. ```julia solver = AutoTsit5(Rosenbrock23()); @@ -43,7 +51,7 @@ algorithms = [ saveat = [], ), ( - label = "Coevolve", + label = "CoevolveSynced", agg = CoevolveSynced(), solver = (solver, solver), save_positions = (false, false), @@ -52,7 +60,7 @@ algorithms = [ ]; ``` -# Model and example solutions +## Example solutions ```julia results = [] @@ -130,6 +138,20 @@ end ``` ```julia +labels = [a.label for a in algorithms] +medtimes = [text(string(round(median(b).time/1e9, digits=3),"s"), :center, 12) for b in bs] +relmedtimes = [median(b).time for b in bs] +relmedtimes ./= relmedtimes[1] +bar(labels, relmedtimes, markeralpha=0, series_annotation=medtimes, fmt=fmt) +title!("evolveSynapse (Median time)") +``` + +```julia +medmem = [text(string(round(median(b).memory/1e6, digits=3),"Mb"), :center, 12) for b in bs] +relmedmem = Float64[median(b).memory for b in bs] +relmedmem ./= relmedmem[1] +bar(labels, relmedmem, markeralpha=0, series_annotation=medmem, fmt=fmt) +title!("evolveSynapse (Median memory)") ``` # References From 30709914c11c4bd4ee7c355342517a002489c278 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Wed, 26 Apr 2023 23:54:40 +0800 Subject: [PATCH 04/16] downgrade julia version --- benchmarks/Jumps/Manifest.toml | 236 +++++++-------------------------- benchmarks/Jumps/Project.toml | 2 + 2 files changed, 50 insertions(+), 188 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 82638220f..48bd038fd 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.0-rc2" +julia_version = "1.8.5" manifest_format = "2.0" -project_hash = "90b531ee81678bcea6c6e8005bc34774fb1e8a5f" +project_hash = "fe02b3e1f7cde4a2759c65ebc5bbc3e19172cd42" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -25,10 +25,6 @@ deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.6.1" -weakdeps = ["StaticArrays"] - - [deps.Adapt.extensions] - AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -51,22 +47,6 @@ git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" version = "7.4.3" - [deps.ArrayInterface.extensions] - ArrayInterfaceBandedMatricesExt = "BandedMatrices" - ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" - ArrayInterfaceCUDAExt = "CUDA" - ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" - ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" - ArrayInterfaceTrackerExt = "Tracker" - - [deps.ArrayInterface.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" - BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" @@ -194,6 +174,12 @@ git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" version = "1.15.7" +[[deps.ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.6" + [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" @@ -259,19 +245,15 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["UUIDs"] +deps = ["Dates", "LinearAlgebra", "UUIDs"] git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" version = "4.6.1" -weakdeps = ["Dates", "LinearAlgebra"] - - [deps.Compat.extensions] - CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.0.1+0" [[deps.CompositeTypes]] git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" @@ -294,11 +276,6 @@ deps = ["LinearAlgebra"] git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" version = "1.5.1" -weakdeps = ["IntervalSets", "StaticArrays"] - - [deps.ConstructionBase.extensions] - IntervalSetsExt = "IntervalSets" - StaticArraysExt = "StaticArrays" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -355,38 +332,20 @@ version = "5.42.0" [[deps.DelimitedFiles]] deps = ["Mmap"] -git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -version = "1.9.1" + +[[deps.DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] git-tree-sha1 = "988bbd7283aaee5c34cd3cc09e78e7c45a931c5b" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" version = "6.123.0" - [deps.DiffEqBase.extensions] - DiffEqBaseDistributionsExt = "Distributions" - DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" - DiffEqBaseMPIExt = "MPI" - DiffEqBaseMeasurementsExt = "Measurements" - DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" - DiffEqBaseReverseDiffExt = "ReverseDiff" - DiffEqBaseTrackerExt = "Tracker" - DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" - - [deps.DiffEqBase.weakdeps] - Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" - 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" - 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 = "63b6be7b396ad395825f3cc48c56b53bfaf7e69d" @@ -399,12 +358,6 @@ git-tree-sha1 = "2c4ed3eedb87579bfe9f20ecc2440de06b9f3b89" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" version = "5.16.0" - [deps.DiffEqNoiseProcess.extensions] - DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" - - [deps.DiffEqNoiseProcess.weakdeps] - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - [[deps.DiffResults]] deps = ["StaticArraysCore"] git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" @@ -434,19 +387,11 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] git-tree-sha1 = "13027f188d26206b9e7b863036f87d2f2e7d013a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" version = "0.25.87" - [deps.Distributions.extensions] - DistributionsChainRulesCoreExt = "ChainRulesCore" - DistributionsDensityInterfaceExt = "DensityInterface" - - [deps.Distributions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" - [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -590,14 +535,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" version = "0.10.35" -weakdeps = ["StaticArrays"] - - [deps.ForwardDiff.extensions] - ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -825,6 +766,12 @@ git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" version = "0.7.3" +[[deps.InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.8" + [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" @@ -890,9 +837,9 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "c3c4979515513fa23269b1edd6bd255830a808d2" +git-tree-sha1 = "d45ba4ee7b0847dc9707111dfe800ef08dbb900c" repo-rev = "coevolve-ii" -repo-url = "https://github.com/gzagatti/JumpProcesses.jl" +repo-url = "https://github.com/gzagatti/JumpProcesses.jl.git" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" version = "9.6.2" @@ -966,18 +913,6 @@ git-tree-sha1 = "98dc144f1e0b299d49e8d23e56ad68d3e4f340a5" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" version = "0.15.20" - [deps.Latexify.extensions] - DataFramesExt = "DataFrames" - DiffEqBiologicalExt = "DiffEqBiological" - ParameterizedFunctionsExt = "DiffEqBase" - SymEngineExt = "SymEngine" - - [deps.Latexify.weakdeps] - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" - DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0" - SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" - [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" @@ -1085,7 +1020,7 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] +deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] @@ -1094,28 +1029,12 @@ git-tree-sha1 = "4a4f8cc7a59fadbb02d1852d1e0cef5dca3a9460" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" version = "1.42.0" - [deps.LinearSolve.extensions] - LinearSolveHYPRE = "HYPRE" - - [deps.LinearSolve.weakdeps] - HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" - [[deps.LogExpFunctions]] -deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" version = "0.3.23" - [deps.LogExpFunctions.extensions] - LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" - LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" - LogExpFunctionsInverseFunctionsExt = "InverseFunctions" - - [deps.LogExpFunctions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1126,15 +1045,10 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] git-tree-sha1 = "defbfba8ddbccdc8ca3edb4a96a6d6fd3cd33ebd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" version = "0.12.157" -weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] - - [deps.LoopVectorization.extensions] - ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] - SpecialFunctionsExt = "SpecialFunctions" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1166,7 +1080,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.0+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1202,7 +1116,7 @@ version = "8.46.1" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2022.2.1" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1270,7 +1184,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.20+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1321,7 +1235,7 @@ version = "6.50.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+0" +version = "10.40.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1359,9 +1273,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.40.1+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.0" +version = "1.8.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1381,20 +1295,6 @@ git-tree-sha1 = "5434b0ee344eaf2854de251f326df8720f6a7b55" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.38.10" - [deps.Plots.extensions] - FileIOExt = "FileIO" - GeometryBasicsExt = "GeometryBasics" - IJuliaExt = "IJulia" - ImageInTerminalExt = "ImageInTerminal" - UnitfulExt = "Unitful" - - [deps.Plots.weakdeps] - FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" - GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" - IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" - ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - [[deps.PoissonRandom]] deps = ["Random"] git-tree-sha1 = "a0f1159c33f846aa77c3f30ebbc69795e5327152" @@ -1431,12 +1331,6 @@ git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" version = "0.4.12" - [deps.PreallocationTools.extensions] - PreallocationToolsReverseDiffExt = "ReverseDiff" - - [deps.PreallocationTools.weakdeps] - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - [[deps.PrecompileTools]] deps = ["Preferences"] git-tree-sha1 = "bc2bda41d798c2e66e7c44a11007bb329b15941b" @@ -1549,16 +1443,6 @@ git-tree-sha1 = "140cddd2c457e4ebb0cdc7c2fd14a7fbfbdf206e" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" version = "2.38.3" - [deps.RecursiveArrayTools.extensions] - RecursiveArrayToolsMeasurementsExt = "Measurements" - RecursiveArrayToolsTrackerExt = "Tracker" - RecursiveArrayToolsZygoteExt = "Zygote" - - [deps.RecursiveArrayTools.weakdeps] - Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" - [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] git-tree-sha1 = "9088515ad915c99026beb5436d0a09cd8c18163e" @@ -1703,12 +1587,6 @@ git-tree-sha1 = "54c78ac3cc0343a16785adabe5bbf4063c737967" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" version = "0.1.14" - [deps.SimpleNonlinearSolve.extensions] - SimpleBatchedNonlinearSolveExt = "NNlib" - - [deps.SimpleNonlinearSolve.weakdeps] - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" - [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" @@ -1742,7 +1620,7 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] +deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] @@ -1758,14 +1636,10 @@ uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" version = "0.3.9" [[deps.SpecialFunctions]] -deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" version = "2.2.0" -weakdeps = ["ChainRulesCore"] - - [deps.SpecialFunctions.extensions] - SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1784,11 +1658,6 @@ deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "Snoo git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" version = "1.4.0" -weakdeps = ["OffsetArrays", "StaticArrays"] - - [deps.StaticArrayInterface.extensions] - StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" - StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] @@ -1804,7 +1673,6 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1819,19 +1687,11 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" version = "0.33.21" [[deps.StatsFuns]] -deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" - [deps.StatsFuns.extensions] - StatsFunsChainRulesCoreExt = "ChainRulesCore" - StatsFunsInverseFunctionsExt = "InverseFunctions" - - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] git-tree-sha1 = "04a7d0bb1c824857ba0bb0c17bc5950dccbfdd5d" @@ -1846,9 +1706,9 @@ version = "6.60.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "f5a57d3c111c79fcc1f8fed6058a8753d061c6d2" +git-tree-sha1 = "b3e9c174a9df77ed7b66fc0aa605def3351a0653" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.12" +version = "0.4.13" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1868,7 +1728,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "5.10.1+0" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "Sundials_jll"] @@ -1904,14 +1764,14 @@ version = "4.14.0" deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] git-tree-sha1 = "d5c494549b0e8839ce7351f1f9f56a4d448f91e3" repo-rev = "coevolve-ii" -repo-url = "https://github.com/gzagatti/SynapseElife" +repo-url = "https://github.com/gzagatti/SynapseElife.git" uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" version = "0.0.1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.3" +version = "1.0.0" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1928,7 +1788,7 @@ version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.0" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -2231,7 +2091,7 @@ version = "4.3.4+0" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.12+3" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2264,9 +2124,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.4.0+0" +version = "5.1.1+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/benchmarks/Jumps/Project.toml b/benchmarks/Jumps/Project.toml index c6e75ac26..2561b284c 100644 --- a/benchmarks/Jumps/Project.toml +++ b/benchmarks/Jumps/Project.toml @@ -3,6 +3,7 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" JumpProblemLibrary = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e" @@ -16,6 +17,7 @@ PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" Synapse = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" [compat] From 807afa0f1fc254595f5470415ff3c665115c43f3 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Thu, 27 Apr 2023 12:47:07 +0800 Subject: [PATCH 05/16] uses comparable saving routine --- benchmarks/Jumps/Synapse.jmd | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/benchmarks/Jumps/Synapse.jmd b/benchmarks/Jumps/Synapse.jmd index 3d9e52707..7f33ab772 100644 --- a/benchmarks/Jumps/Synapse.jmd +++ b/benchmarks/Jumps/Synapse.jmd @@ -47,15 +47,13 @@ algorithms = [ label = "PDMP", agg = nothing, solver = (CHV(solver), CHV(solver)), - save_positions = (false, true), # necessary to save at regular intervals saveat = [], ), ( label = "CoevolveSynced", agg = CoevolveSynced(), solver = (solver, solver), - save_positions = (false, false), - saveat = 0.05, # similar rate as the PDMP problem + saveat = p_synapse.sampling_rate, ), ]; ``` @@ -79,7 +77,7 @@ for algo in algorithms nu, algo.solver, algo.agg; - save_positions = algo.save_positions, + save_positions = (false, true), saveat = algo.saveat, save_everystep = false, ), @@ -125,7 +123,7 @@ for algo in algorithms nu, $(algo).solver, $(algo).agg; - save_positions = $(algo).save_positions, + save_positions = (false, true), saveat = $(algo).saveat, save_everystep = false, ), From 1cfae2590d5cfe54b91d740bf771965ee9e9de1d Mon Sep 17 00:00:00 2001 From: gzagatti Date: Thu, 27 Apr 2023 13:22:36 +0800 Subject: [PATCH 06/16] update dependencies --- benchmarks/Jumps/Manifest.toml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index 48bd038fd..cb463c7f5 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -824,10 +824,10 @@ uuid = "4076af6c-e467-56ae-b986-b466b2749572" version = "1.10.0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "SnoopPrecompile", "Tokenize"] -git-tree-sha1 = "8bbb6ffe81a919b1a3e943d72fbe2f677bef6f77" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] +git-tree-sha1 = "536ef70e17d2f5b0dcbe5411002721c9bbdfaa05" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.26" +version = "1.0.27" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -837,7 +837,7 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "d45ba4ee7b0847dc9707111dfe800ef08dbb900c" +git-tree-sha1 = "1471ea7d5dc77904af550626bbe7f80ebe68e97d" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/JumpProcesses.jl.git" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" @@ -1762,7 +1762,7 @@ version = "4.14.0" [[deps.Synapse]] deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] -git-tree-sha1 = "d5c494549b0e8839ce7351f1f9f56a4d448f91e3" +git-tree-sha1 = "b5f5cc6d26a2065022055aac68e5ce7ae1d03b2d" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/SynapseElife.git" uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" From 6c8753fcacb6cb85ef8ae1868857d6c1e7cb0b2c Mon Sep 17 00:00:00 2001 From: gzagatti Date: Sat, 29 Apr 2023 13:45:23 +0800 Subject: [PATCH 07/16] fix saving callback --- benchmarks/Jumps/Manifest.toml | 61 +++++++++++++++++----------------- benchmarks/Jumps/Synapse.jmd | 4 +-- 2 files changed, 32 insertions(+), 33 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index cb463c7f5..a199fc73e 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -228,10 +228,10 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" version = "1.0.2" [[deps.CommonMark]] -deps = ["Crayons", "JSON", "SnoopPrecompile", "URIs"] -git-tree-sha1 = "4a52799aee66e9528bd59e9c0bdd9322c0bf6998" +deps = ["Crayons", "JSON", "PrecompileTools", "URIs"] +git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.11" +version = "0.8.12" [[deps.CommonSolve]] git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" @@ -265,6 +265,12 @@ git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.1" +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "b306df2650947e9eb100ec125ff8c65ca2053d30" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.1.1" + [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] git-tree-sha1 = "e32a90da027ca45d84678b826fffd3110bb3fc90" @@ -598,15 +604,15 @@ version = "0.1.4" [[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 = "db730189e3d250d97515a91886de7e33aa8833e6" +git-tree-sha1 = "efaac003187ccc71ace6c755b197284cd4811bfe" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.2" +version = "0.72.4" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "47a2efe07729dd508a032e2f56c46c517481052a" +git-tree-sha1 = "4486ff47de4c18cb511a0da420efebb314556316" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.2+0" +version = "0.72.4+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -673,10 +679,10 @@ uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" version = "0.4.0" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "69182f9a2d6add3736b7a06ab6416aafdeec2196" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.7.4" +version = "1.8.0" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -729,11 +735,6 @@ git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.3" -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" - [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" @@ -1333,9 +1334,9 @@ version = "0.4.12" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "bc2bda41d798c2e66e7c44a11007bb329b15941b" +git-tree-sha1 = "2e47054ffe7d0a8872e977c0d09eb4b3d162ebde" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.0.1" +version = "1.0.2" [[deps.Preferences]] deps = ["TOML"] @@ -1403,9 +1404,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Random123]] deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b" +git-tree-sha1 = "552f30e847641591ba3f39fd1bed559b9deb0ef3" uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.0" +version = "1.6.1" [[deps.RandomExtensions]] deps = ["Random", "SparseArrays"] @@ -1426,22 +1427,22 @@ uuid = "379f33d0-9447-4353-bd03-d664070e549f" version = "0.1.7" [[deps.RecipesBase]] -deps = ["SnoopPrecompile"] -git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.3.3" +version = "1.3.4" [[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] -git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" +deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] +git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.11" +version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "140cddd2c457e4ebb0cdc7c2fd14a7fbfbdf206e" +git-tree-sha1 = "68078e9fa9130a6a768815c48002d0921a232c11" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.3" +version = "2.38.4" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] @@ -1661,9 +1662,9 @@ version = "1.4.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "63e84b7fdf5021026d0f17f76af7c57772313d99" +git-tree-sha1 = "c8c6fee2ecfeae4dae754d2b69926d03478d5a1d" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.21" +version = "1.5.23" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1762,7 +1763,7 @@ version = "4.14.0" [[deps.Synapse]] deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] -git-tree-sha1 = "b5f5cc6d26a2065022055aac68e5ce7ae1d03b2d" +git-tree-sha1 = "29945123e7e4fcf83e3966b76a9b22e68a3d4b53" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/SynapseElife.git" uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" diff --git a/benchmarks/Jumps/Synapse.jmd b/benchmarks/Jumps/Synapse.jmd index 7f33ab772..87748c6f5 100644 --- a/benchmarks/Jumps/Synapse.jmd +++ b/benchmarks/Jumps/Synapse.jmd @@ -26,8 +26,6 @@ events_sorted_times = [500.0]; is_pre_or_post_event = [true]; events_bap = events_sorted_times[is_pre_or_post_event.==false]; bap_by_epsp = Float64[]; -t1 = 0.0; -t2 = 500.0; nu = buildTransitionMatrix(); ``` @@ -53,7 +51,7 @@ algorithms = [ label = "CoevolveSynced", agg = CoevolveSynced(), solver = (solver, solver), - saveat = p_synapse.sampling_rate, + saveat = 1 / p_synapse.sampling_rate, ), ]; ``` From ef8026752970eec3a97ed57b74c630835ab21563 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Mon, 1 May 2023 13:11:40 +0800 Subject: [PATCH 08/16] fix MultivaraiteHawkes.jmd. --- benchmarks/Jumps/MultivariateHawkes.jmd | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index f9e44cb4a..234cc48c9 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -273,8 +273,8 @@ push!(algorithms, (PDMPCHV(), CHV(Tsit5()), true, "PDMPCHV")); The Python `Tick` library can be accessed with the `PyCall.jl`. We install the required Python dependencies with `Conda.jl` and define a factory for the Multivariate Hawkes `PyTick` problem. ```julia -const BENCHMARK_PYTHON::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_PYTHON", "false")) -const REBUILD_PYCALL::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_REBUILD_PYCALL", "false")) +const BENCHMARK_PYTHON::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_PYTHON", "true")) +const REBUILD_PYCALL::Bool = tryparse(Bool, get(ENV, "SCIMLBENCHMARK_REBUILD_PYCALL", "true")) struct PyTick end @@ -294,7 +294,9 @@ if BENCHMARK_PYTHON Conda.pip("install", "tick", Conda.ROOTENV) end + ENV["PYTHON"] = "" using PyCall + @info "PyCall" PyCall.libpython PyCall.pyversion PyCall.conda function hawkes_problem( p, @@ -677,7 +679,7 @@ for (algo, stepper, use_recursion, label) in algorithms median_time = length(trial) > 0 ? "$(BenchmarkTools.prettytime(median(trial.times)))" : "nan" - println("algo=``(label), V = ``(nv(G)), length = ``(length(trial.times)), median time = ``median_time") + println("algo=$(label), V = $(nv(G)), length = $(length(trial.times)), median time = $median_time") end end end From fcd18cb487a2aa6924f1a7442aefe3e3be72eef8 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Mon, 1 May 2023 13:13:06 +0800 Subject: [PATCH 09/16] inverts call to Conda. --- benchmarks/Jumps/MultivariateHawkes.jmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 234cc48c9..374781ff1 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -282,16 +282,16 @@ if BENCHMARK_PYTHON if REBUILD_PYCALL using Pkg, Conda - # rebuild PyCall to ensure it links to the python provided by Conda.jl - ENV["PYTHON"] = "" - Pkg.build("PyCall") - # PyCall only works with Conda.ROOTENV # tick requires python=3.8 Conda.add("python=3.8", Conda.ROOTENV) Conda.add("numpy", Conda.ROOTENV) Conda.pip_interop(true, Conda.ROOTENV) Conda.pip("install", "tick", Conda.ROOTENV) + + # rebuild PyCall to ensure it links to the python provided by Conda.jl + ENV["PYTHON"] = "" + Pkg.build("PyCall") end ENV["PYTHON"] = "" From ba0827aca9f1da1c83d11805f2e50405d3847e0e Mon Sep 17 00:00:00 2001 From: gzagatti Date: Wed, 3 May 2023 22:20:04 +0800 Subject: [PATCH 10/16] tweak rate interval and update dependencies --- benchmarks/Jumps/Manifest.toml | 54 ++++++++++++------------- benchmarks/Jumps/MultivariateHawkes.jmd | 2 +- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index a199fc73e..69351ec98 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -175,10 +175,10 @@ uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" version = "1.15.7" [[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "f84967c4497e0e1955f9a582c232b02847c5f589" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.6" +version = "0.1.7" [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] @@ -394,9 +394,9 @@ 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 = "13027f188d26206b9e7b863036f87d2f2e7d013a" +git-tree-sha1 = "180538ef4e3aa02b01413055a7a9e8b6047663e1" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.87" +version = "0.25.88" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -497,9 +497,9 @@ version = "0.3.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -769,9 +769,9 @@ version = "0.7.3" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.9" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -820,9 +820,9 @@ version = "2.1.91+0" [[deps.JuMP]] deps = ["LinearAlgebra", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "Printf", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "4ec0e68fecbbe1b78db2ddf1ac573963ed5adebc" +git-tree-sha1 = "1cccd3598a08951e6fa243ca0512376f8f8aab63" uuid = "4076af6c-e467-56ae-b986-b466b2749572" -version = "1.10.0" +version = "1.11.0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] @@ -838,11 +838,11 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "1471ea7d5dc77904af550626bbe7f80ebe68e97d" +git-tree-sha1 = "93f0ebfab440e35fd2ba8b9342d9ecd50c4e3f41" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/JumpProcesses.jl.git" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.6.2" +version = "9.6.3" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -910,9 +910,9 @@ version = "0.4.6" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "98dc144f1e0b299d49e8d23e56ad68d3e4f340a5" +git-tree-sha1 = "8c57307b5d9bb3be1ff2da469063628631d4d51e" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.20" +version = "0.15.21" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] @@ -1046,10 +1046,10 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "defbfba8ddbccdc8ca3edb4a96a6d6fd3cd33ebd" +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "e7ce3cdc520da8135e73d7cb303e0617a19f582b" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.157" +version = "0.12.158" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1291,10 +1291,10 @@ uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" version = "1.3.5" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "5434b0ee344eaf2854de251f326df8720f6a7b55" +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", "Unzip"] +git-tree-sha1 = "6c7f47fd112001fc95ea1569c2757dffd9e81328" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.10" +version = "1.38.11" [[deps.PoissonRandom]] deps = ["Random"] @@ -1662,9 +1662,9 @@ version = "1.4.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "c8c6fee2ecfeae4dae754d2b69926d03478d5a1d" +git-tree-sha1 = "c262c8e978048c2b095be1672c9bee55b4619521" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.23" +version = "1.5.24" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1695,9 +1695,9 @@ version = "1.3.0" [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "04a7d0bb1c824857ba0bb0c17bc5950dccbfdd5d" +git-tree-sha1 = "564451a262696334a3bab19108a99dd90d5a22c8" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.14.0" +version = "1.15.0" [[deps.StochasticDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] @@ -1831,9 +1831,9 @@ version = "0.5.25" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "0b829474fed270a4b0ab07117dce9b9a2fa7581a" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.12" +version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 374781ff1..e8f514435 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -76,7 +76,7 @@ Given the rate factory, we can create a jump factory which will create all the j function hawkes_jump(i::Int, g; use_recursion = false) rate = hawkes_rate(i, g; use_recursion) urate = rate - @inbounds rateinterval(u, p, t) = p[5][i] == p[1] ? typemax(t) : 1 / (2*p[5][i]) + @inbounds rateinterval(u, p, t) = p[5][i] == p[1] ? typemax(t) : 2 / p[5][i] @inbounds lrate(u, p, t) = p[1] @inbounds function affect_recursion!(integrator) λ, α, β, h, _, ϕ = integrator.p From d92c7a9e9260be94186c867af9cada25a982d661 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Wed, 17 May 2023 17:01:30 +0800 Subject: [PATCH 11/16] removes references to CoevolveSynced after moving CoevolveSynced to Coevolve, remos the original Coevolve from benchmarks --- benchmarks/Jumps/Diffusion_CTRW.jmd | 2 +- benchmarks/Jumps/Manifest.toml | 169 +++++++++--------- .../Jumps/Mendes_multistate_example.jmd | 2 +- benchmarks/Jumps/MultivariateHawkes.jmd | 12 +- benchmarks/Jumps/NegFeedback_GeneExpr.jmd | 2 +- .../Jumps/NegFeedback_GeneExpr_Marchetti.jmd | 2 +- benchmarks/Jumps/Synapse.jmd | 4 +- 7 files changed, 96 insertions(+), 97 deletions(-) diff --git a/benchmarks/Jumps/Diffusion_CTRW.jmd b/benchmarks/Jumps/Diffusion_CTRW.jmd index 0b871c45e..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(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), CoevolveSynced()) +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 69351ec98..ce9617d9d 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -22,9 +22,9 @@ version = "0.3.4" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.6.1" +version = "3.6.2" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -42,10 +42,10 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.2.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "38911c7737e123b28182d89027f4216cfc8a9da7" +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "917286faa2abb288796e75b88ca67edc016f3219" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.3" +version = "7.4.5" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] @@ -74,10 +74,10 @@ uuid = "aae01518-5342-5314-be14-df237901396f" version = "0.17.18" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] +git-tree-sha1 = "54b00d1b93791f8e19e31584bd30f2cb6004614b" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.3.38" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -170,9 +170,9 @@ version = "12.3.2" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.7" +version = "1.16.0" [[deps.ChangesOfVariables]] deps = ["LinearAlgebra", "Test"] @@ -261,15 +261,15 @@ uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" version = "0.1.3" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "b306df2650947e9eb100ec125ff8c65ca2053d30" +git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.1.1" +version = "2.2.0" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] @@ -279,9 +279,9 @@ version = "1.8.0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" +git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.1" +version = "1.5.2" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -300,9 +300,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataFrames]] deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] @@ -338,6 +338,7 @@ version = "5.42.0" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[deps.DensityInterface]] @@ -347,10 +348,10 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "988bbd7283aaee5c34cd3cc09e78e7c45a931c5b" +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "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 = "1c03e389a28be70cd9049f98ff0b84cf7539d959" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.123.0" +version = "6.125.0" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] @@ -393,10 +394,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "180538ef4e3aa02b01413055a7a9e8b6047663e1" +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "4f59fe4eb1308011bd33b390369cbad74e46eea4" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.88" +version = "0.25.92" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -512,9 +513,9 @@ version = "0.13.11" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "03fcb1c42ec905d15b305359603888ec3e65f886" +git-tree-sha1 = "6604e18a0220650dbbea7854938768f15955dd8e" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.19.0" +version = "2.20.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -680,9 +681,9 @@ version = "0.4.0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "69182f9a2d6add3736b7a06ab6416aafdeec2196" +git-tree-sha1 = "41f7dfb2b20e7e8bf64f6b6fae98f4d2df027b06" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.8.0" +version = "1.9.4" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -704,9 +705,9 @@ version = "0.1.14" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "432b5b03176f8182bd6841fbfc42c718506a2d5f" +git-tree-sha1 = "84204eae2dd237500835990bcade263e27674a93" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.15" +version = "0.3.16" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] @@ -826,9 +827,9 @@ version = "1.11.0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "536ef70e17d2f5b0dcbe5411002721c9bbdfaa05" +git-tree-sha1 = "01ab91fcce19c965b3c68a82eb26260a3a7af271" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.27" +version = "1.0.29" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -838,7 +839,7 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "93f0ebfab440e35fd2ba8b9342d9ecd50c4e3f41" +git-tree-sha1 = "7fc52bc22fa69aee9237f05b2a4823c756b01346" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/JumpProcesses.jl.git" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" @@ -852,9 +853,9 @@ version = "0.4.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "dd90aacbfb622f898a97c2a4411ac49101ebab8a" +git-tree-sha1 = "0356a64062656b0cbb43c504ad5de338251f4bda" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.0" +version = "0.9.1" [[deps.KrylovKit]] deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] @@ -928,9 +929,9 @@ version = "0.15.1" [[deps.LazySets]] deps = ["Distributed", "GLPK", "IntervalArithmetic", "JuMP", "LinearAlgebra", "Random", "ReachabilityBase", "RecipesBase", "Reexport", "Requires", "SharedArrays", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "00dabbd02d0503c21d3b48c7bf8b976cafb95f91" +git-tree-sha1 = "479438df8028221919ca256a3be33cd22fff8460" uuid = "b4f0291d-fe17-52bc-9479-3d1a343d9043" -version = "2.7.4" +version = "2.7.6" [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] @@ -1047,9 +1048,9 @@ version = "1.0.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "e7ce3cdc520da8135e73d7cb303e0617a19f582b" +git-tree-sha1 = "3bb62b5003bc7d2d49f26663484267dc49fa1bf5" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.158" +version = "0.12.159" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1068,9 +1069,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "8e054675d393ce5866dcdd6a071075e25e21a39c" +git-tree-sha1 = "6ba094e471106981b278f60179170d8b10985052" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.15.1" +version = "1.16.0" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] @@ -1138,9 +1139,9 @@ version = "1.0.15" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "3295d296288ab1a0a2528feb424b854418acff57" +git-tree-sha1 = "964cb1a7069723727025ae295408747a0b36a854" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.2.3" +version = "1.3.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1194,9 +1195,9 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "7fb975217aea8f1bb360cf1dde70bad2530622d2" +git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.0" +version = "1.4.1" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1228,10 +1229,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.0" [[deps.OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SimpleUnPack", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "b639e192c0422c849aeda7240382375961d0cb4b" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "6ffebfa8971546bace3fc312f9a703795f79f5b9" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.50.0" +version = "6.51.2" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1251,10 +1252,10 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "a5aef8d4a6e8d81f171b2bd4be5265b01384c74c" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.8" +version = "2.5.10" [[deps.PiecewiseDeterministicMarkovProcesses]] deps = ["DifferentialEquations", "Distributions", "ForwardDiff", "JumpProcesses", "LSODA", "LinearAlgebra", "Parameters", "PreallocationTools", "Random", "RecursiveArrayTools", "SciMLBase", "SparseArrays", "StatsBase", "Sundials", "Test"] @@ -1292,9 +1293,9 @@ version = "1.3.5" [[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", "Unzip"] -git-tree-sha1 = "6c7f47fd112001fc95ea1569c2757dffd9e81328" +git-tree-sha1 = "d03ef538114b38f89d66776f2d8fdc0280f90621" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.11" +version = "1.38.12" [[deps.PoissonRandom]] deps = ["Random"] @@ -1334,21 +1335,21 @@ version = "0.4.12" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "2e47054ffe7d0a8872e977c0d09eb4b3d162ebde" +git-tree-sha1 = "259e206946c293698122f63e2b513a7c99a244e8" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.0.2" +version = "1.1.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "548793c7859e28ef026dba514752275ee871169f" +git-tree-sha1 = "213579618ec1f42dea7dd637a42785a608b1ea9c" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.3" +version = "2.2.4" [[deps.Primes]] deps = ["IntegerMathUtils"] @@ -1440,9 +1441,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "68078e9fa9130a6a768815c48002d0921a232c11" +git-tree-sha1 = "02ef02926f30d53b94be443bfaea010c47f6b556" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.4" +version = "2.38.5" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] @@ -1498,9 +1499,9 @@ version = "0.2.1" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "f139e81a81e6c29c40f1971c9e5309b09c03f2c3" +git-tree-sha1 = "d7d9ebe28062161c1e314ed643097b0c6fe657d9" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.6" +version = "0.5.7" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1518,10 +1519,10 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.38" [[deps.SciMLBase]] -deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SnoopPrecompile", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "392d3e28b05984496af37100ded94dc46fa6c8de" +deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "e803672f8d58e9937f59923dd3b159c9b7e1838b" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.91.7" +version = "1.92.0" [[deps.SciMLBenchmarks]] deps = ["Git", "IJulia", "InteractiveUtils", "Markdown", "Pkg", "Weave"] @@ -1531,15 +1532,15 @@ version = "0.1.1" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "2e1606c282fae6bd9aed4f159695774a44b9c75f" +git-tree-sha1 = "a8eb97c56cac50c21096582afb2a0110784dc36e" uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.4" +version = "0.1.6" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "e61e48ef909375203092a6e83508c8416df55a83" +git-tree-sha1 = "90163ebc767cba9f126ea00aeef1d75ed74fe7b0" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.2.0" +version = "0.2.8" [[deps.Scratch]] deps = ["Dates"] @@ -1650,9 +1651,9 @@ version = "0.1.15" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "08be5ee09a7632c32695d954a602df96a877bf0d" +git-tree-sha1 = "dbde6766fc677423598138a5951269432b0fcc90" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.6" +version = "0.8.7" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] @@ -1662,9 +1663,9 @@ version = "1.4.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "c262c8e978048c2b095be1672c9bee55b4619521" +git-tree-sha1 = "8982b3607a212b070a5e46eea83eb62b4744ae12" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.24" +version = "1.5.25" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1707,9 +1708,9 @@ version = "6.60.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "b3e9c174a9df77ed7b66fc0aa605def3351a0653" +git-tree-sha1 = "5ffcee1813efc849f188dce82ca1553bd5f3a476" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.13" +version = "0.4.14" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -1732,10 +1733,10 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "5.10.1+0" [[deps.Sundials]] -deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "a4e8491c163d74fb92905c6443e59558f5e609a4" +deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] +git-tree-sha1 = "ace8080f882c5181d61c8dbb749ac9aa72a49bd0" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.16.0" +version = "4.17.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -1763,7 +1764,7 @@ version = "4.14.0" [[deps.Synapse]] deps = ["BenchmarkTools", "Catalyst", "DataFrames", "DataStructures", "DiffEqCallbacks", "DifferentialEquations", "Distributions", "DocStringExtensions", "Documenter", "JumpProcesses", "LSODA", "LabelledArrays", "LazySets", "LinearAlgebra", "OrdinaryDiffEq", "Parameters", "PiecewiseDeterministicMarkovProcesses", "Plots", "Printf", "Profile", "ProfileSVG", "ProgressMeter", "RecursiveArrayTools", "SparseArrays", "StaticArrays", "StatsBase", "Sundials"] -git-tree-sha1 = "29945123e7e4fcf83e3966b76a9b22e68a3d4b53" +git-tree-sha1 = "82c1f5b460c1886da8a6578b2c6d691abac69f29" repo-rev = "coevolve-ii" repo-url = "https://github.com/gzagatti/SynapseElife.git" uuid = "7cc9ea39-daa9-4846-be95-d8a08c9e3c85" @@ -1837,9 +1838,9 @@ version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" +git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.75" +version = "0.4.76" [[deps.TreeViews]] deps = ["Test"] @@ -1889,9 +1890,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "dba3eba51b9512695b59e0bd8263ac074c5ed2d9" +git-tree-sha1 = "ba4aa36b2d5c98d6ed1f149da916b3ba46527b2b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.13.1" +version = "1.14.0" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" diff --git a/benchmarks/Jumps/Mendes_multistate_example.jmd b/benchmarks/Jumps/Mendes_multistate_example.jmd index a68145134..d207423d0 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(), Coevolve(), CoevolveSynced()) +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) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index e8f514435..cbef4e17d 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -130,12 +130,12 @@ function hawkes_problem( end ``` -The `Coevolve()` and `CoevolveSynced()` aggregator knows how to handle the `SSAStepper`, so it accepts a `DiscreteProblem`. +The `Coevolve()` aggregator knows how to handle the `SSAStepper`, so it accepts a `DiscreteProblem`. ```julia function hawkes_problem( p, - agg::Union{Coevolve, CoevolveSynced}; + agg::Coevolve; u = [0.0], tspan = (0.0, 50.0), save_positions = (false, true), @@ -173,10 +173,8 @@ Now, we instantiate the problems, find their solutions and plot the results. algorithms = Tuple{Any, Any, Bool, String}[ (Direct(), Tsit5(), false, "Direct (brute-force)"), (Coevolve(), SSAStepper(), false, "Coevolve (brute-force)"), - (CoevolveSynced(), SSAStepper(), false, "CoevolveSynced (brute-force)"), (Direct(), Tsit5(), true, "Direct (recursive)"), (Coevolve(), SSAStepper(), true, "Coevolve (recursive)"), - (CoevolveSynced(), SSAStepper(), true, "CoevolveSynced (recursive)"), ] let fig = [] @@ -196,7 +194,7 @@ let fig = [] sol = solve(jump_prob, stepper) push!(fig, plot(sol.t, sol[1:V, :]', title=label, legend=false, format=fmt)) end - fig = plot(fig..., layout=(3,2), format=fmt, size=(width_px, 3*height_px/2)) + fig = plot(fig..., layout=(2,2), format=fmt, size=(width_px, 2*height_px/2)) end ``` @@ -328,7 +326,7 @@ Now, we instantiate the problems, find their solutions and plot the results. ```julia let fig = [] - for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms[7:end]) + for (i, (algo, stepper, use_recursion, label)) in enumerate(algorithms[5:end]) @info label if typeof(algo) <: PyTick _p = (p[1], p[2], p[3]) @@ -586,7 +584,7 @@ let fig = [] qqs = qq(runs, Λ) push!(fig, qqplot(qqs..., legend = false, aspect_ratio = :equal, title=label, fmt=fmt)) end - fig = plot(fig..., layout = (4, 2), fmt=fmt, size=(width_px, 4*height_px/2)) + fig = plot(fig..., layout = (3, 2), fmt=fmt, size=(width_px, 3*height_px/2)) end ``` diff --git a/benchmarks/Jumps/NegFeedback_GeneExpr.jmd b/benchmarks/Jumps/NegFeedback_GeneExpr.jmd index db754c851..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(), Coevolve(), CoevolveSynced()) +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 716fd19e0..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(), Coevolve(), CoevolveSynced()) +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) diff --git a/benchmarks/Jumps/Synapse.jmd b/benchmarks/Jumps/Synapse.jmd index 87748c6f5..d13a2db5c 100644 --- a/benchmarks/Jumps/Synapse.jmd +++ b/benchmarks/Jumps/Synapse.jmd @@ -48,8 +48,8 @@ algorithms = [ saveat = [], ), ( - label = "CoevolveSynced", - agg = CoevolveSynced(), + label = "Coevolve", + agg = Coevolve(), solver = (solver, solver), saveat = 1 / p_synapse.sampling_rate, ), From e1725019661c9c0200f566ddb4d538c8d1381665 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Tue, 18 Jul 2023 13:14:13 +0800 Subject: [PATCH 12/16] bump JumpProcesses.jl to 9.7 --- benchmarks/Jumps/Manifest.toml | 756 +++++++++++++++++++++------------ benchmarks/Jumps/Project.toml | 2 +- 2 files changed, 488 insertions(+), 270 deletions(-) diff --git a/benchmarks/Jumps/Manifest.toml b/benchmarks/Jumps/Manifest.toml index ce9617d9d..deb5e6fb5 100644 --- a/benchmarks/Jumps/Manifest.toml +++ b/benchmarks/Jumps/Manifest.toml @@ -1,8 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.5" +julia_version = "1.9.2" manifest_format = "2.0" -project_hash = "fe02b3e1f7cde4a2759c65ebc5bbc3e19172cd42" +project_hash = "9b07b1a633980f322bdc19e461c407d9a51da856" + +[[deps.ADTypes]] +git-tree-sha1 = "e58c18d2312749847a74f5be80bb0fa53da102bd" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "0.1.5" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -25,6 +30,10 @@ deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -43,9 +52,25 @@ version = "0.2.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "917286faa2abb288796e75b88ca67edc016f3219" +git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.5" +version = "7.4.11" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] @@ -55,9 +80,9 @@ version = "0.1.29" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "4aff5fa660eb95c2e0deb6bcdabe4d9a96bc4667" +git-tree-sha1 = "e0da03c52673bc0ab5138d1381b4dbc48ea343b9" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "0.8.18" +version = "1.0.12" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -68,16 +93,30 @@ uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" version = "0.2.0" [[deps.BandedMatrices]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "6ef8fc1d77b60f41041d59ce61ef9eb41ed97a83" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools", "SparseArrays"] +git-tree-sha1 = "206e78eb10c9aaee4e73962b1cbd0ecf688d4b49" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.18" +version = "0.17.30" [[deps.BangBang]] deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] -git-tree-sha1 = "54b00d1b93791f8e19e31584bd30f2cb6004614b" +git-tree-sha1 = "e28912ce94077686443433c2800104b061a827ed" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.38" +version = "0.3.39" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -127,10 +166,10 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" [[deps.CPUSummary]] -deps = ["CpuId", "IfElse", "Static"] -git-tree-sha1 = "2c144ddb46b552f72d7eafe7cc2f50746e41ea21" +deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] +git-tree-sha1 = "89e0654ed8c7aebad6d5ad235d6242c2d737a928" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.2" +version = "0.2.3" [[deps.CRlibm]] deps = ["CRlibm_jll"] @@ -174,12 +213,6 @@ git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" version = "1.16.0" -[[deps.ChangesOfVariables]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "f84967c4497e0e1955f9a582c232b02847c5f589" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.7" - [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" @@ -194,9 +227,9 @@ version = "0.7.2" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.1" +version = "0.7.2" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] @@ -234,9 +267,9 @@ uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" version = "0.8.12" [[deps.CommonSolve]] -git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" +git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.3" +version = "0.2.4" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -245,15 +278,19 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" +deps = ["UUIDs"] +git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.6.1" +version = "4.7.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.1+0" +version = "1.0.5+0" [[deps.CompositeTypes]] git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" @@ -265,23 +302,34 @@ git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.2" + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + + [deps.CompositionsBase.weakdeps] + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" +git-tree-sha1 = "5372dbbf8f0bdb8c700db5367132925c0771ef7e" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.2.0" +version = "2.2.1" [[deps.Conda]] deps = ["Downloads", "JSON", "VersionParsing"] -git-tree-sha1 = "e32a90da027ca45d84678b826fffd3110bb3fc90" +git-tree-sha1 = "915ebe6f0e7302693bdd8eac985797dba1d25662" uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d" -version = "1.8.0" +version = "1.9.0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" +git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.2" +version = "1.5.3" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -305,16 +353,16 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.15.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" +deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "089d29c0fc00a190661517e4f3cba5dcb3fd0c08" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.5.0" +version = "1.6.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "cf25ccb972fec4e4817764d01c82386ae94f77b4" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.14" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -340,18 +388,35 @@ version = "5.42.0" deps = ["Mmap"] git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.DensityInterface]] -deps = ["InverseFunctions", "Test"] -git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" -uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" -version = "0.4.0" +version = "1.9.1" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "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 = "1c03e389a28be70cd9049f98ff0b84cf7539d959" +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 = "62c41421bd0facc43dfe4e9776135fe21fd1e1b9" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.125.0" +version = "6.126.0" + + [deps.DiffEqBase.extensions] + DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" + DiffEqBaseMPIExt = "MPI" + DiffEqBaseMeasurementsExt = "Measurements" + DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" + DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseTrackerExt = "Tracker" + DiffEqBaseUnitfulExt = "Unitful" + DiffEqBaseZygoteExt = "Zygote" + + [deps.DiffEqBase.weakdeps] + Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + 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" + 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"] @@ -360,10 +425,16 @@ uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" version = "2.26.1" [[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArrays", "Statistics"] -git-tree-sha1 = "2c4ed3eedb87579bfe9f20ecc2440de06b9f3b89" +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "26594c6ec8416fb6ef3ed8828fd29c98b10bfaad" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.16.0" +version = "5.17.2" + + [deps.DiffEqNoiseProcess.extensions] + DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" + + [deps.DiffEqNoiseProcess.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -373,15 +444,15 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.13.0" +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 = "ac145e3d718157c679fc4febf2fcef73ec77b067" +git-tree-sha1 = "1cfe0178410e1bb4b14058c537d0f347eb9d95dc" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.7.0" +version = "7.8.0" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -394,10 +465,18 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "4f59fe4eb1308011bd33b390369cbad74e46eea4" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "e76a3281de2719d7c81ed62c6ea7057380c87b1d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.92" +version = "0.25.98" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -407,9 +486,9 @@ version = "0.9.3" [[deps.Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "58fea7c536acd71f3eef6be3b21c0df5f3df88fd" +git-tree-sha1 = "39fd748a73dce4c05a9655475e437170d8fb1b67" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.24" +version = "0.27.25" [[deps.DomainSets]] deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] @@ -444,11 +523,17 @@ git-tree-sha1 = "d6863c556f1142a061532e79f611aa46be201686" uuid = "90fa49ef-747e-5e6f-a989-263ba693cf1a" version = "0.5.2" +[[deps.ExceptionUnwrapping]] +deps = ["Test"] +git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96" +uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" +version = "0.1.9" + [[deps.Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.8+0" +version = "2.5.0+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SnoopPrecompile", "SparseArrays", "libblastrampoline_jll"] @@ -486,9 +571,9 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "c1293a93193f0ae94be7cf338d33e162c39d8788" +git-tree-sha1 = "b12f05108e405dadcc2aff0008db7f831374e051" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "1.2.9" +version = "2.0.0" [[deps.FastRounding]] deps = ["ErrorfreeArithmetic", "LinearAlgebra"] @@ -507,15 +592,25 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" +git-tree-sha1 = "192cee6de045c39e26f4ce4b7e0f00a9dae14dd1" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.11" +version = "1.4.1" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "6604e18a0220650dbbea7854938768f15955dd8e" +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.20.0" +version = "2.21.1" + + [deps.FiniteDiff.extensions] + FiniteDiffBandedMatricesExt = "BandedMatrices" + FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffStaticArraysExt = "StaticArrays" + + [deps.FiniteDiff.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -542,16 +637,20 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" version = "0.10.35" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] -deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" +deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.4+0" +version = "2.13.1+0" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -599,21 +698,21 @@ version = "6.2.1+2" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.4" +version = "0.1.5" [[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 = "efaac003187ccc71ace6c755b197284cd4811bfe" +git-tree-sha1 = "8e2d86e06ceb4580110d9e716be26658effc5bfd" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.4" +version = "0.72.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "4486ff47de4c18cb511a0da420efebb314556316" +git-tree-sha1 = "da121cbdc95b065da07fbb93638367737969693f" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.4+0" +version = "0.72.8+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -680,10 +779,10 @@ uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" version = "0.4.0" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "41f7dfb2b20e7e8bf64f6b6fae98f4d2df027b06" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "cb56ccdd481c0dd7f975ad2b3b62d9eda088f7e2" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.9.4" +version = "1.9.14" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -699,27 +798,27 @@ version = "0.5.2" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "734fd90dd2f920a2f1921d5388dcebe805b262dc" +git-tree-sha1 = "d38bd0d9759e3c6cfa19bdccc314eccf8ce596cc" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.14" +version = "0.1.15" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "84204eae2dd237500835990bcade263e27674a93" +git-tree-sha1 = "83e95aaab9dc184a6dcd9c4c52aa0dc26cd14a1d" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.16" +version = "0.3.21" [[deps.IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] -git-tree-sha1 = "59e19713542dd9dd02f31d59edbada69530d6a14" +git-tree-sha1 = "47ac8cc196b81001a711f4b2c12c97372338f00c" uuid = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -version = "1.24.0" +version = "1.24.2" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.2" +version = "0.2.3" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -748,9 +847,9 @@ uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" version = "1.4.0" [[deps.IntegerMathUtils]] -git-tree-sha1 = "f366daebdfb079fd1fe4e3d560f99a0c892e15bc" +git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" -version = "0.1.0" +version = "0.1.2" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -758,9 +857,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.IntervalArithmetic]] deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] -git-tree-sha1 = "c1c88395d09366dae431556bcb598ad08fa1392b" +git-tree-sha1 = "5ab7744289be503d76a944784bac3f2df7b809af" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.20.8" +version = "0.20.9" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] @@ -768,12 +867,6 @@ git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" version = "0.7.3" -[[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" -uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.9" - [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" @@ -784,12 +877,6 @@ git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" -[[deps.IterativeSolvers]] -deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" -uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.2" - [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" @@ -821,15 +908,15 @@ version = "2.1.91+0" [[deps.JuMP]] deps = ["LinearAlgebra", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "Printf", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "1cccd3598a08951e6fa243ca0512376f8f8aab63" +git-tree-sha1 = "b0ded4f36829f7cfd4400b11289faf9b4f0b795a" uuid = "4076af6c-e467-56ae-b986-b466b2749572" -version = "1.11.0" +version = "1.12.0" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "01ab91fcce19c965b3c68a82eb26260a3a7af271" +git-tree-sha1 = "60567b51bd9e1e19ae2fd8a54dcd6bc5994727f0" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.29" +version = "1.0.34" [[deps.JumpProblemLibrary]] deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"] @@ -839,11 +926,9 @@ version = "0.1.3" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "7fc52bc22fa69aee9237f05b2a4823c756b01346" -repo-rev = "coevolve-ii" -repo-url = "https://github.com/gzagatti/JumpProcesses.jl.git" +git-tree-sha1 = "6f1e0f4364022ea2cd9e324cc9b851bc5434d41c" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.6.3" +version = "9.7.0" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -853,15 +938,9 @@ version = "0.4.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "0356a64062656b0cbb43c504ad5de338251f4bda" +git-tree-sha1 = "6dc4ad9cd74ad4ca0a8e219e945dbd22039f2125" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.1" - -[[deps.KrylovKit]] -deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] -git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3" -uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" -version = "0.6.0" +version = "0.9.2" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -875,17 +954,23 @@ git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "3.0.0+1" +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" + [[deps.LSODA]] deps = ["Compat", "DiffEqBase", "LSODA_jll", "LinearAlgebra", "Parameters", "Printf", "SciMLBase"] -git-tree-sha1 = "4114813bdff2041da3f2e403385b8b2ccf570ee3" +git-tree-sha1 = "96a6ff0be7ebda67e35af1e6937a68141dd59e70" uuid = "7f56f5a3-f504-529b-bc02-0b1fe5e64312" -version = "0.7.3" +version = "0.7.4" [[deps.LSODA_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a19962a454cf319151cee31219dd5eb3434a37d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "3c5277e990a9026f31a35ca6c4acddc8a706a38c" uuid = "aae0fff6-70f8-51e1-979a-8150c7cc74bd" -version = "0.1.1+0" +version = "0.1.2+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -915,6 +1000,18 @@ git-tree-sha1 = "8c57307b5d9bb3be1ff2da469063628631d4d51e" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" version = "0.15.21" + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + DiffEqBiologicalExt = "DiffEqBiological" + ParameterizedFunctionsExt = "DiffEqBase" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" + [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" @@ -929,9 +1026,9 @@ version = "0.15.1" [[deps.LazySets]] deps = ["Distributed", "GLPK", "IntervalArithmetic", "JuMP", "LinearAlgebra", "Random", "ReachabilityBase", "RecipesBase", "Reexport", "Requires", "SharedArrays", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "479438df8028221919ca256a3be33cd22fff8460" +git-tree-sha1 = "d173eaf9b7e2d0003750e56357a6a3fc3b6c8b5f" uuid = "b4f0291d-fe17-52bc-9479-3d1a343d9043" -version = "2.7.6" +version = "2.8.0" [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] @@ -1022,20 +1119,44 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SnoopPrecompile", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "4a4f8cc7a59fadbb02d1852d1e0cef5dca3a9460" +deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LinearAlgebra", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] +git-tree-sha1 = "1b55771f2c211583ad52af5a5ca6475be374c961" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.42.0" +version = "2.4.1" + + [deps.LinearSolve.extensions] + LinearSolveCUDAExt = "CUDA" + LinearSolveHYPREExt = "HYPRE" + LinearSolveIterativeSolversExt = "IterativeSolvers" + LinearSolveKrylovKitExt = "KrylovKit" + LinearSolvePardisoExt = "Pardiso" + + [deps.LinearSolve.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" + IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" + KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.23" +version = "0.3.24" + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1047,10 +1168,15 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "3bb62b5003bc7d2d49f26663484267dc49fa1bf5" +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "24e6c5697a6c93b5e10af2acf95f0b2e15303332" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.159" +version = "0.12.163" +weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] + + [deps.LoopVectorization.extensions] + ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] + SpecialFunctionsExt = "SpecialFunctions" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1069,9 +1195,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "6ba094e471106981b278f60179170d8b10985052" +git-tree-sha1 = "5c5cd501ae1d76d3ccd7c7e6b4325a15dde7f31c" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.16.0" +version = "1.18.0" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] @@ -1082,7 +1208,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1118,7 +1244,7 @@ version = "8.46.1" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1133,9 +1259,9 @@ version = "0.4.7" [[deps.Mustache]] deps = ["Printf", "Tables"] -git-tree-sha1 = "87c371d27dbf2449a5685652ab322be163269df0" +git-tree-sha1 = "821e918c170ead5298ff84bffee41dd28929a681" uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70" -version = "1.0.15" +version = "1.0.17" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] @@ -1166,16 +1292,16 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "a6000c813371cd3cd9cbbdf8a356fc3a97138d92" +deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "2a7f28c62eb2c16b9c375c38f664cdcf22313cf5" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.6.0" +version = "1.8.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" +git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.9" +version = "1.12.10" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1186,7 +1312,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1200,10 +1326,10 @@ uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" version = "1.4.1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1aa4b74f80b01c6bc2b89992b861b5f210e665b5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.20+0" +version = "1.1.21+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1213,9 +1339,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "a89b11f0f354f06099e4001c151dffad7ebab015" +git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.5" +version = "1.7.6" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1229,15 +1355,15 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.0" [[deps.OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "6ffebfa8971546bace3fc312f9a703795f79f5b9" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "4f1ab68f236fa846d0c30718c6b29c1665b019c0" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.51.2" +version = "6.53.3" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1253,9 +1379,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "a5aef8d4a6e8d81f171b2bd4be5265b01384c74c" +git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.10" +version = "2.7.1" [[deps.PiecewiseDeterministicMarkovProcesses]] deps = ["DifferentialEquations", "Distributions", "ForwardDiff", "JumpProcesses", "LSODA", "LinearAlgebra", "Parameters", "PreallocationTools", "Random", "RecursiveArrayTools", "SciMLBase", "SparseArrays", "StatsBase", "Sundials", "Test"] @@ -1269,15 +1395,15 @@ uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" version = "1.3.0" [[deps.Pixman_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] +git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.1+0" +version = "0.42.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.2" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1292,10 +1418,24 @@ uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" version = "1.3.5" [[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", "Unzip"] -git-tree-sha1 = "d03ef538114b38f89d66776f2d8fdc0280f90621" +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 = "75ca67b2c6512ad2d0c767a7cfc55e75075f8bbc" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.12" +version = "1.38.16" + + [deps.Plots.extensions] + FileIOExt = "FileIO" + GeometryBasicsExt = "GeometryBasics" + IJuliaExt = "IJulia" + ImageInTerminalExt = "ImageInTerminal" + UnitfulExt = "Unitful" + + [deps.Plots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" + IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.PoissonRandom]] deps = ["Random"] @@ -1333,11 +1473,17 @@ git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" version = "0.4.12" + [deps.PreallocationTools.extensions] + PreallocationToolsReverseDiffExt = "ReverseDiff" + + [deps.PreallocationTools.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "259e206946c293698122f63e2b513a7c99a244e8" +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.1" +version = "1.1.2" [[deps.Preferences]] deps = ["TOML"] @@ -1347,15 +1493,15 @@ version = "1.4.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "213579618ec1f42dea7dd637a42785a608b1ea9c" +git-tree-sha1 = "331cc8048cba270591eab381e7aa3e2e3fef7f5e" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.4" +version = "2.2.5" [[deps.Primes]] deps = ["IntegerMathUtils"] -git-tree-sha1 = "311a2aa90a64076ea0fac2ad7492e914e6feeb81" +git-tree-sha1 = "4c9f306e5d6603ae203c2000dd460d81a5251489" uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" -version = "0.5.3" +version = "0.5.4" [[deps.Printf]] deps = ["Unicode"] @@ -1379,9 +1525,9 @@ version = "1.7.2" [[deps.PyCall]] deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"] -git-tree-sha1 = "62f417f6ad727987c755549e9cd88c46578da562" +git-tree-sha1 = "43d304ac6f0354755f1d60730ece8c499980f7ba" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" -version = "1.95.1" +version = "1.96.1" [[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"] @@ -1441,9 +1587,19 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "02ef02926f30d53b94be443bfaea010c47f6b556" +git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.5" +version = "2.38.7" + + [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsMeasurementsExt = "Measurements" + RecursiveArrayToolsTrackerExt = "Tracker" + RecursiveArrayToolsZygoteExt = "Zygote" + + [deps.RecursiveArrayTools.weakdeps] + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] @@ -1499,9 +1655,9 @@ version = "0.2.1" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "d7d9ebe28062161c1e314ed643097b0c6fe657d9" +git-tree-sha1 = "237edc1563bbf078629b4f8d194bd334e97907cf" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.7" +version = "0.5.11" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1514,33 +1670,33 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "cda0aece8080e992f6370491b08ef3909d1c04e7" +git-tree-sha1 = "4b8586aece42bee682399c4c4aee95446aa5cd19" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.38" +version = "0.6.39" [[deps.SciMLBase]] -deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "e803672f8d58e9937f59923dd3b159c9b7e1838b" +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "ddf8d14762bac98d035453b33b9c5952f36c3b79" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.92.0" +version = "1.93.2" [[deps.SciMLBenchmarks]] deps = ["Git", "IJulia", "InteractiveUtils", "Markdown", "Pkg", "Weave"] -git-tree-sha1 = "a1d7791d68494b74fc0062cf63d8df7213dbd9dd" +git-tree-sha1 = "f4076dd5a103010d48bb6c4e50c5526f6622fa96" uuid = "31c91b34-3c75-11e9-0341-95557aab0344" -version = "0.1.1" +version = "0.1.3" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "a8eb97c56cac50c21096582afb2a0110784dc36e" +git-tree-sha1 = "9dfc8e9e3d58c0c74f1a821c762b5349da13eccf" uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.6" +version = "0.1.8" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] -git-tree-sha1 = "90163ebc767cba9f126ea00aeef1d75ed74fe7b0" +git-tree-sha1 = "b1fe33c9984c6789b58419e62e7a2b92f9aa813e" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.2.8" +version = "0.3.3" [[deps.Scratch]] deps = ["Dates"] @@ -1550,9 +1706,9 @@ version = "1.2.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "77d3c4726515dca71f6d80fbb5e251088defe305" +git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.18" +version = "1.4.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1584,10 +1740,16 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Reexport", "Requires", "SciMLBase", "SnoopPrecompile", "StaticArraysCore"] -git-tree-sha1 = "54c78ac3cc0343a16785adabe5bbf4063c737967" +deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PrecompileTools", "Reexport", "Requires", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "56aa73a93cdca493af5155a0338a864ed314222b" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.14" +version = "0.1.16" + + [deps.SimpleNonlinearSolve.extensions] + SimpleBatchedNonlinearSolveExt = "NNlib" + + [deps.SimpleNonlinearSolve.weakdeps] + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1617,19 +1779,25 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" +git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.0" +version = "1.1.1" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] -deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays", "VertexSafeGraphs"] -git-tree-sha1 = "e19ac47477c9a8fcca06dab5e5471417d5d9d723" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Reexport", "Requires", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "VertexSafeGraphs"] +git-tree-sha1 = "4c1a57bcbc0b795fbfdc2009e70f9c2fd2815bfe" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.31.0" +version = "2.4.1" + + [deps.SparseDiffTools.extensions] + SparseDiffToolsZygoteExt = "Zygote" + + [deps.SparseDiffTools.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -1638,10 +1806,14 @@ uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" version = "0.3.9" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.2.0" +version = "2.3.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1660,21 +1832,31 @@ deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "Snoo git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" version = "1.4.0" +weakdeps = ["OffsetArrays", "StaticArrays"] + + [deps.StaticArrayInterface.extensions] + StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" + StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "8982b3607a212b070a5e46eea83eb62b4744ae12" +deps = ["LinearAlgebra", "Random", "StaticArraysCore"] +git-tree-sha1 = "fffc14c695c17bfdbfa92a2a01836cdc542a1e46" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.25" +version = "1.6.1" +weakdeps = ["Statistics"] + + [deps.StaticArrays.extensions] + StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.2" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1689,34 +1871,42 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" version = "0.33.21" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "564451a262696334a3bab19108a99dd90d5a22c8" +git-tree-sha1 = "6e801d0da4c81d9cd6a05d97340404f9892fba85" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.15.0" +version = "1.16.0" [[deps.StochasticDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "073da86200349ddf4ef8bc3e3f3acd62e1d554f7" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "ccf744171b3a83879158a4b3f3a430c1bc585123" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.60.0" +version = "6.61.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "5ffcee1813efc849f188dce82ca1553bd5f3a476" +git-tree-sha1 = "f02eb61eb5c97b48c153861c72fbbfdddc607e06" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.14" +version = "0.4.17" [[deps.StringEncodings]] deps = ["Libiconv_jll"] -git-tree-sha1 = "33c0da881af3248dafefb939a21694b97cfece76" +git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" -version = "0.3.6" +version = "0.3.7" [[deps.StringManipulation]] git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" @@ -1730,13 +1920,13 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+0" +version = "5.10.1+6" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "ace8080f882c5181d61c8dbb749ac9aa72a49bd0" +git-tree-sha1 = "4931f9013c53128337ce8df54a2d38c79fe58d4c" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.17.0" +version = "4.19.3" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -1773,7 +1963,7 @@ version = "0.0.1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1790,7 +1980,7 @@ version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1809,9 +1999,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "c97f60dd4f2331e1a495527f80d242501d2f9865" +git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.5.1" +version = "0.5.2" [[deps.ThreadsX]] deps = ["ArgCheck", "BangBang", "ConstructionBase", "InitialValues", "MicroCollections", "Referenceables", "Setfield", "SplittablesBase", "Transducers"] @@ -1838,9 +2028,23 @@ version = "0.9.13" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "25358a5f2384c490e98abd565ed321ffae2cbb37" +git-tree-sha1 = "a66fb81baec325cf6ccafa243af573b031e87b00" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.76" +version = "0.4.77" + + [deps.Transducers.extensions] + TransducersBlockArraysExt = "BlockArrays" + TransducersDataFramesExt = "DataFrames" + TransducersLazyArraysExt = "LazyArrays" + TransducersOnlineStatsBaseExt = "OnlineStatsBase" + TransducersReferenceablesExt = "Referenceables" + + [deps.Transducers.weakdeps] + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" + Referenceables = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" [[deps.TreeViews]] deps = ["Test"] @@ -1861,9 +2065,9 @@ version = "0.1.7" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] -git-tree-sha1 = "7bc1632a4eafbe9bd94cf1a784a9a4eb5e040a91" +git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" uuid = "781d530d-4396-4725-bb49-402e4bee1e77" -version = "1.3.0" +version = "1.4.0" [[deps.URIs]] git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" @@ -1889,10 +2093,24 @@ uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" [[deps.Unitful]] -deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "ba4aa36b2d5c98d6ed1f149da916b3ba46527b2b" +deps = ["Dates", "LinearAlgebra", "Random"] +git-tree-sha1 = "c4d2a349259c8eba66a00a540d550f122a3ab228" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.14.0" +version = "1.15.0" + + [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" +uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" +version = "1.6.3" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -1947,16 +2165,16 @@ uuid = "aed1982a-8fda-507f-9586-7b0439959a61" version = "1.1.34+0" [[deps.Xorg_libX11_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.6.9+4" +version = "1.8.6+0" [[deps.Xorg_libXau_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.9+4" +version = "1.0.11+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -1965,10 +2183,10 @@ uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.3+4" +version = "1.1.4+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -2007,22 +2225,22 @@ uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" version = "0.9.10+4" [[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" +version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" +version = "1.15.0+0" [[deps.Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.0+4" +version = "1.1.2+0" [[deps.Xorg_xcb_util_image_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] @@ -2055,28 +2273,28 @@ uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" version = "0.4.1+1" [[deps.Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" +version = "1.4.6+0" [[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" +version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" +version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "dbc7f1c0012a69486af79c8bcdb31be820670ba2" +git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.8" +version = "0.4.9" [[deps.ZMQ]] deps = ["FileWatching", "Sockets", "ZeroMQ_jll"] @@ -2093,7 +2311,7 @@ version = "4.3.4+0" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2126,9 +2344,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/benchmarks/Jumps/Project.toml b/benchmarks/Jumps/Project.toml index 2561b284c..9dd6adc66 100644 --- a/benchmarks/Jumps/Project.toml +++ b/benchmarks/Jumps/Project.toml @@ -25,7 +25,7 @@ BenchmarkTools = "1.3.1" Catalyst = "12.2" DataFrames = "1.3.4" JumpProblemLibrary = "0.1" -JumpProcesses = "9.1" +JumpProcesses = "9.7" ModelingToolkit = "8.18" OrdinaryDiffEq = "6.20" Plots = "1.31" From 121815291012793f35843c1370e3772ff228a6d3 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Fri, 21 Jul 2023 21:30:09 +0800 Subject: [PATCH 13/16] adds PDMPCHVSimple to benchmarks --- benchmarks/Jumps/MultivariateHawkes.jmd | 178 +++++++++++++++++++++--- 1 file changed, 157 insertions(+), 21 deletions(-) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index cbef4e17d..9b6591b4d 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -202,7 +202,100 @@ end We benchmark `JumpProcesses.jl` against `PiecewiseDeterministicMarkovProcesses.jl` and Python `Tick` library. -In order to compare with the `PiecewiseDeterministicMarkovProcesses.jl`, we need to reformulate our jump problem as a Piecewise Deterministic Markov Process (PDMP). In this setting, we need to describe how the conditional intensity changes with time which we derive below: +In order to compare with the `PiecewiseDeterministicMarkovProcesses.jl`, we need to reformulate our jump problem as a Piecewise Deterministic Markov Process (PDMP). In this setting, we have two options. + +The simple version only requires the conditional intensity. Like above, we define a brute-force and recursive approach. Following the library's specification we define the following functions. + +```julia +function hawkes_rate_simple_recursion(rate, xc, xd, p, t, issum::Bool) + λ, _, β, h, ϕ, g = p + for i in 1:length(g) + rate[i] = λ + exp(-β * (t - h[i])) * ϕ[i] + end + if issum + return sum(rate) + end + return 0.0 +end + +function hawkes_rate_simple_brute(rate, xc, xd, p, t, issum::Bool) + λ, α, β, h, g = p + for i in 1:length(g) + x = zero(typeof(t)) + for j in g[i] + for _t in reverse(h[j]) + ϕij = α * exp(-β * (t - _t)) + if ϕij ≈ 0 + break + end + x += ϕij + end + end + rate[i] = λ + x + end + if issum + return sum(rate) + end + return 0.0 +end + +function hawkes_affect_simple_recursion!(xc, xd, p, t, i::Int64) + _, α, β, h, ϕ, g = p + for j in g[i] + ϕ[j] *= exp(-β * (t - h[j])) + ϕ[j] += α + h[j] = t + end +end + +function hawkes_affect_simple_brute!(xc, xd, p, t, i::Int64) + push!(p[4][i], t) +end +``` + +Since this is a library for PDMP, we also need to define the ODE problem. In the simple version, we simply set it to zero. + +```julia +function hawkes_drate_simple(dxc, xc, xd, p, t) + dxc .= 0 +end + +``` + +Next, we create a factory for the Multivariate Hawkes `PDMPCHVSimple` problem. + +```julia +import LinearAlgebra: I +using PiecewiseDeterministicMarkovProcesses +const PDMP = PiecewiseDeterministicMarkovProcesses + +struct PDMPCHVSimple end + +function hawkes_problem(p, + agg::PDMPCHVSimple; + u = [0.0], + tspan = (0.0, 50.0), + save_positions = (false, true), + g = [[1]], + use_recursion = true) + xd0 = Array{Int}(u) + xc0 = copy(u) + nu = one(eltype(xd0)) * I(length(xd0)) + if use_recursion + jprob = PDMPProblem(hawkes_drate_simple, hawkes_rate_simple_recursion, + hawkes_affect_simple_recursion!, nu, xc0, xd0, p, tspan) + else + jprob = PDMPProblem(hawkes_drate_simple, hawkes_rate_simple_brute, + hawkes_affect_simple_brute!, nu, xc0, xd0, p, tspan) + end + return jprob +end + +push!(algorithms, (PDMPCHVSimple(), CHV(Tsit5()), false, "PDMPCHVSimple (brute-force)")); +push!(algorithms, (PDMPCHVSimple(), CHV(Tsit5()), true, "PDMPCHVSimple (recursive)")); +``` + +The full version requires that we describe how the conditional intensity changes with time which we derive below: ```math \begin{split} \frac{d \lambda_i^\ast (t)}{d t} @@ -212,7 +305,7 @@ In order to compare with the `PiecewiseDeterministicMarkovProcesses.jl`, we need ``` ```julia -function hawkes_drate(dxc, xc, xd, p, t) +function hawkes_drate_full(dxc, xc, xd, p, t) λ, α, β, _, _, g = p for i = 1:length(g) dxc[i] = -β * (xc[i] - λ) @@ -223,7 +316,7 @@ end Next, we need to define the intensity rate and the jumps according to library's specification. ```julia -function hawkes_rate(rate, xc, xd, p, t, issum::Bool) +function hawkes_rate_full(rate, xc, xd, p, t, issum::Bool) λ, α, β, _, _, g = p if issum return sum(@view(xc[1:length(g)])) @@ -232,7 +325,7 @@ function hawkes_rate(rate, xc, xd, p, t, issum::Bool) return 0.0 end -function hawkes_affect!(xc, xd, p, t, i::Int64) +function hawkes_affect_full!(xc, xd, p, t, i::Int64) λ, α, β, _, _, g = p for j in g[i] xc[i] += α @@ -240,18 +333,14 @@ function hawkes_affect!(xc, xd, p, t, i::Int64) end ``` -Finally, we create a factory for the Multivariate Hawkes `PDMPCHV` problem. +Finally, we create a factory for the Multivariate Hawkes `PDMPCHVFull` problem. ```julia -import LinearAlgebra: I -using PiecewiseDeterministicMarkovProcesses -const PDMP = PiecewiseDeterministicMarkovProcesses - -struct PDMPCHV end +struct PDMPCHVFull end function hawkes_problem( p, - agg::PDMPCHV; + agg::PDMPCHVFull; u = [0.0], tspan = (0.0, 50.0), save_positions = (false, true), @@ -261,11 +350,11 @@ function hawkes_problem( xd0 = Array{Int}(u) xc0 = [p[1] for i = 1:length(u)] nu = one(eltype(xd0)) * I(length(xd0)) - jprob = PDMPProblem(hawkes_drate, hawkes_rate, hawkes_affect!, nu, xc0, xd0, p, tspan) + jprob = PDMPProblem(hawkes_drate_full, hawkes_rate_full, hawkes_affect_full!, nu, xc0, xd0, p, tspan) return jprob end -push!(algorithms, (PDMPCHV(), CHV(Tsit5()), true, "PDMPCHV")); +push!(algorithms, (PDMPCHVFull(), CHV(Tsit5()), true, "PDMPCHVFull")); ``` The Python `Tick` library can be accessed with the `PyCall.jl`. We install the required Python dependencies with `Conda.jl` and define a factory for the Multivariate Hawkes `PyTick` problem. @@ -336,16 +425,29 @@ let fig = [] t = tspan[1]:0.1:tspan[2] N = [[sum(jumps .< _t) for _t in t] for jumps in jump_prob.timestamps] push!(fig, plot(t, N, title=label, legend=false, format=fmt)) - elseif typeof(algo) <: PDMPCHV + elseif typeof(algo) <: PDMPCHVSimple + if use_recursion + h = zeros(eltype(tspan), nv(g)) + ϕ = zeros(eltype(tspan), nv(g)) + _p = (p[1], p[2], p[3], h, ϕ, g) + else + h = [eltype(tspan)[] for _ in 1:nv(g)] + _p = (p[1], p[2], p[3], h, g) + end + jump_prob = hawkes_problem(_p, algo; u, tspan, g, use_recursion) + sol = solve(jump_prob, stepper) + push!(fig, plot(sol.time, sol.xd[1:V, :]', title=label, legend=false, format=fmt)) + elseif typeof(algo) <: PDMPCHVFull _p = (p[1], p[2], p[3], nothing, nothing, g) jump_prob = hawkes_problem(_p, algo; u, tspan, g, use_recursion) sol = solve(jump_prob, stepper) push!(fig, plot(sol.time, sol.xd[1:V, :]', title=label, legend=false, format=fmt)) end end - fig = plot(fig..., layout=(1,2), format=fmt, size=(width_px, height_px/2)) + fig = plot(fig..., layout=(2,2), format=fmt, size=(width_px, 2*height_px/2)) end ``` + # Correctness: QQ-Plots We check that the algorithms produce correct simulation by inspecting their QQ-plots. Point process theory says that transforming the simulated points using the compensator should produce points whose inter-arrival duration is distributed according to the exponential distribution (see Section 7.4 [1]). @@ -547,7 +649,16 @@ let fig = [] @info label if typeof(algo) <: PyTick _p = (p[1], p[2], p[3]) - elseif typeof(algo) <: PDMPCHV + elseif typeof(algo) <: PDMPCHVSimple + if use_recursion + h = zeros(eltype(tspan), nv(g)) + ϕ = zeros(eltype(tspan), nv(g)) + _p = (p[1], p[2], p[3], h, ϕ, g) + else + h = [eltype(tspan)[] for _ in 1:nv(g)] + _p = (p[1], p[2], p[3], h, g) + end + elseif typeof(algo) <: PDMPCHVFull _p = (p[1], p[2], p[3], nothing, nothing, g) else if use_recursion @@ -569,14 +680,16 @@ let fig = [] jump_prob.simulate() runs[n] = jump_prob.timestamps else - if ~(typeof(algo) <: PDMPCHV) + if ~(typeof(algo) <: PDMPCHVFull) if use_recursion h .= 0 ϕ .= 0 else for _h in h empty!(_h) end end - urate .= 0 + if ~(typeof(algo) <: PDMPCHVSimple) + urate .= 0 + end end runs[n] = histories(solve(jump_prob, stepper)) end @@ -584,7 +697,7 @@ let fig = [] qqs = qq(runs, Λ) push!(fig, qqplot(qqs..., legend = false, aspect_ratio = :equal, title=label, fmt=fmt)) end - fig = plot(fig..., layout = (3, 2), fmt=fmt, size=(width_px, 3*height_px/2)) + fig = plot(fig..., layout = (4, 2), fmt=fmt, size=(width_px, 4*height_px/2)) end ``` @@ -614,7 +727,16 @@ for (algo, stepper, use_recursion, label) in algorithms local u = [0.0 for i = 1:nv(G)] if typeof(algo) <: PyTick _p = (p[1], p[2], p[3]) - elseif typeof(algo) <: PDMPCHV + elseif typeof(algo) <: PDMPCHVSimple + if use_recursion + global h = zeros(eltype(tspan), nv(G)) + global ϕ = zeros(eltype(tspan), nv(G)) + _p = (p[1], p[2], p[3], h, ϕ, g) + else + global h = [eltype(tspan)[] for _ in 1:nv(G)] + _p = (p[1], p[2], p[3], h, g) + end + elseif typeof(algo) <: PDMPCHVFull _p = (p[1], p[2], p[3], nothing, nothing, g) else if use_recursion @@ -639,7 +761,7 @@ for (algo, stepper, use_recursion, label) in algorithms seconds = 10, ) else - if typeof(algo) <: PDMPCHV + if typeof(algo) <: PDMPCHVFull @benchmark( solve(jump_prob, _stepper), setup = (), @@ -647,6 +769,20 @@ for (algo, stepper, use_recursion, label) in algorithms evals = 1, seconds = 10, ) + elseif typeof(algo) <: PDMPCHVSimple + if use_recursion + @benchmark(solve(jump_prob, _stepper), + setup=(h .= 0; ϕ .= 0), + samples=50, + evals=1, + seconds=10,) + else + @benchmark(solve(jump_prob, _stepper), + setup=(reset_history!(h)), + samples=50, + evals=1, + seconds=10,) + end else if use_recursion @benchmark( From 4692fb09eda04ddae7cec7a9e711d5f521134a49 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Sun, 23 Jul 2023 12:36:25 +0800 Subject: [PATCH 14/16] fix typo --- benchmarks/Jumps/MultivariateHawkes.jmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 9b6591b4d..20272870b 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -427,11 +427,11 @@ let fig = [] push!(fig, plot(t, N, title=label, legend=false, format=fmt)) elseif typeof(algo) <: PDMPCHVSimple if use_recursion - h = zeros(eltype(tspan), nv(g)) - ϕ = zeros(eltype(tspan), nv(g)) + h = zeros(eltype(tspan), nv(G)) + ϕ = zeros(eltype(tspan), nv(G)) _p = (p[1], p[2], p[3], h, ϕ, g) else - h = [eltype(tspan)[] for _ in 1:nv(g)] + h = [eltype(tspan)[] for _ in 1:nv(G)] _p = (p[1], p[2], p[3], h, g) end jump_prob = hawkes_problem(_p, algo; u, tspan, g, use_recursion) @@ -651,11 +651,11 @@ let fig = [] _p = (p[1], p[2], p[3]) elseif typeof(algo) <: PDMPCHVSimple if use_recursion - h = zeros(eltype(tspan), nv(g)) - ϕ = zeros(eltype(tspan), nv(g)) + h = zeros(eltype(tspan), nv(G)) + ϕ = zeros(eltype(tspan), nv(G)) _p = (p[1], p[2], p[3], h, ϕ, g) else - h = [eltype(tspan)[] for _ in 1:nv(g)] + h = [eltype(tspan)[] for _ in 1:nv(G)] _p = (p[1], p[2], p[3], h, g) end elseif typeof(algo) <: PDMPCHVFull From 1037e68efa89dfe655eaed0ea5e788c2fb633b61 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Sun, 23 Jul 2023 00:50:31 -0400 Subject: [PATCH 15/16] Update run_benchmark.yml --- .buildkite/run_benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/run_benchmark.yml b/.buildkite/run_benchmark.yml index 48e3b5004..a8f285069 100644 --- a/.buildkite/run_benchmark.yml +++ b/.buildkite/run_benchmark.yml @@ -15,7 +15,7 @@ steps: - BUILDKITE_S3_SECRET_ACCESS_KEY="U2FsdGVkX19MkMLkCxkclrpxYMfzHvYlUJssaSbX/wkdNiL+H5/aHwiYiTsBXyXh2m/1pcIUMHCR0nerHevB8g==" - BUILDKITE_S3_DEFAULT_REGION="U2FsdGVkX18ccoE9FmtkwsCm1x0MLMBlN/FLcAyKkY4=" - JuliaCI/julia#v1: - version: 1.8 + version: 1.9 - staticfloat/sandbox: rootfs_url: "https://github.com/ven-k/Placeholder/releases/download/v0.23.0/aws_uploader.x86_64.tar.gz" rootfs_treehash: "d46b35aa927024de8729d63fde18442a0a590e62" From 3bf650c1aae7b10e49cbd10e8f626d2a517f3e79 Mon Sep 17 00:00:00 2001 From: gzagatti Date: Sun, 23 Jul 2023 08:16:41 -0700 Subject: [PATCH 16/16] fix calling inexistant function --- benchmarks/Jumps/MultivariateHawkes.jmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/Jumps/MultivariateHawkes.jmd b/benchmarks/Jumps/MultivariateHawkes.jmd index 20272870b..eedfa2804 100644 --- a/benchmarks/Jumps/MultivariateHawkes.jmd +++ b/benchmarks/Jumps/MultivariateHawkes.jmd @@ -778,7 +778,7 @@ for (algo, stepper, use_recursion, label) in algorithms seconds=10,) else @benchmark(solve(jump_prob, _stepper), - setup=(reset_history!(h)), + setup=([empty!(_h) for _h in h]), samples=50, evals=1, seconds=10,)