diff --git a/Manifest.toml b/Manifest.toml index 7ff792f..7175674 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,13 +1,19 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.1" +julia_version = "1.9.2" manifest_format = "2.0" -project_hash = "283a566a5d05e4589a1b5859a995461386be0bc3" +project_hash = "767c093e67fdab416f979f052b06bf048b75f0ac" + +[[deps.ACSets]] +deps = ["CompTime", "JSON", "MLStyle", "OrderedCollections", "Pkg", "PrettyTables", "Reexport", "StaticArrays", "StructEquality", "Tables"] +git-tree-sha1 = "935a09f5a40d199ac9c7fb55357e2164b1ef8671" +uuid = "227ef7b5-1206-438b-ac65-934d6da304b8" +version = "0.2.3" [[deps.ADTypes]] -git-tree-sha1 = "dcfdf328328f2645531c4ddebf841228aef74130" +git-tree-sha1 = "e58c18d2312749847a74f5be80bb0fa53da102bd" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.3" +version = "0.1.5" [[deps.AMQPClient]] deps = ["Logging", "MbedTLS", "Sockets"] @@ -22,16 +28,16 @@ uuid = "ae81ac8f-d209-56e5-92de-9978fef736f9" version = "0.1.3+0" [[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "3ee5c58774f4487a5bf2bb05e39d91ff5022b4cc" +deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] +git-tree-sha1 = "1bd8a536c949eb3de9b58042d57790ded6b70fa6" uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.29.4" +version = "0.30.9" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] -git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" +git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.3.1" +version = "1.4.0" weakdeps = ["ChainRulesCore"] [deps.AbstractFFTs.extensions] @@ -39,9 +45,9 @@ weakdeps = ["ChainRulesCore"] [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "a21654aa796bcc993284dace0d17d1022774c0a3" +git-tree-sha1 = "87e63dcb990029346b091b170252f3c416568afc" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.4.1" +version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] @@ -54,6 +60,24 @@ git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.4" +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] +git-tree-sha1 = "954634616d5846d8e216df1298be2298d55280b2" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.32" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" @@ -66,9 +90,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "25d38b80e29533f5f85af19692a39e4275047a51" +git-tree-sha1 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.4.5" +version = "0.4.6" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -105,21 +129,26 @@ uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" version = "0.1.6" [[deps.AlgebraicPetri]] -deps = ["Catlab", "DataStructures", "GeneralizedGenerated", "LabelledArrays", "StatsBase"] -git-tree-sha1 = "3607af61f8ab68825b3ad37cdd166b756fb688ef" +deps = ["Catlab", "GeneralizedGenerated", "LabelledArrays"] +git-tree-sha1 = "d798c838e065927a09edf431791d34fd5a709023" uuid = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b" -version = "0.8.11" +version = "0.9.0" [deps.AlgebraicPetri.extensions] AlgebraicPetriCatalystExt = "Catalyst" AlgebraicPetriModelingToolkitExt = "ModelingToolkit" - AlgebraicPetriPetriExt = "Petri" + AlgebraicPetriOrdinaryDiffEqExt = "OrdinaryDiffEq" [deps.AlgebraicPetri.weakdeps] Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" - Petri = "4259d249-1051-49fa-8328-3f8ab9391c33" - Requires = "ae029012-a4dd-5104-9daa-d747884805df" + OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" + +[[deps.AlphaStableDistributions]] +deps = ["Distributions", "FileIO", "Interpolations", "JLD2", "LinearAlgebra", "Random", "SpecialFunctions", "StaticArrays", "Statistics", "StatsBase", "ToeplitzMatrices"] +git-tree-sha1 = "ad5789d4d1a7e38a9fb1e5e02369eeb799833b2e" +uuid = "f20549b4-2d50-407f-863c-cdd202ba59a3" +version = "1.1.6" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -138,9 +167,9 @@ 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" @@ -166,9 +195,9 @@ version = "0.1.29" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "4aff5fa660eb95c2e0deb6bcdabe4d9a96bc4667" +git-tree-sha1 = "9e5ad0f651c1be8a355e4d327e9cb3bc135d1b73" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "0.8.18" +version = "1.0.8" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -192,16 +221,16 @@ uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" version = "0.4.6" [[deps.BandedMatrices]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "6ef8fc1d77b60f41041d59ce61ef9eb41ed97a83" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools", "SparseArrays"] +git-tree-sha1 = "3c63ab5fb851444fb018b97883cfd79ae044e888" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.18" +version = "0.17.29" [[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" @@ -277,16 +306,28 @@ 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.CPUTime]] git-tree-sha1 = "2dcc50ea6a0a1ef6440d6eecd0fe3813e5671f45" uuid = "a9c8d775-2e2e-55fc-8582-045d282d599e" version = "1.0.0" +[[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" @@ -295,9 +336,9 @@ version = "3.3.6" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "ed28c86cbde3dc3f53cf76643c2e9bc11d56acc7" +git-tree-sha1 = "44dbf560808d49041989b8a96cae4cffbeb7966a" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.10" +version = "0.10.11" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] @@ -312,16 +353,34 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.Catlab]] -deps = ["Colors", "CompTime", "Compose", "DataStructures", "GeneralizedGenerated", "JSON", "LightXML", "LinearAlgebra", "Logging", "MLStyle", "Pkg", "PrettyTables", "Random", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics", "StructEquality", "Tables"] -git-tree-sha1 = "821d6dcf331981e7c1d6377a6baee112a79a1021" +deps = ["ACSets", "Colors", "CompTime", "Compose", "DataStructures", "GeneralizedGenerated", "JSON", "LightXML", "LinearAlgebra", "Logging", "MLStyle", "PrettyTables", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StructEquality", "Tables"] +git-tree-sha1 = "c610008c7dc9907a0112b3d48f75a6de806e1aeb" uuid = "134e5e36-593f-5add-ad60-77f754baafbe" -version = "0.14.17" +version = "0.15.1" + + [deps.Catlab.extensions] + CatlabConvexExt = "Convex" + CatlabDataFramesExt = "DataFrames" + CatlabGraphsExt = "Graphs" + CatlabGraphvizExt = "Graphviz_jll" + CatlabMetaGraphsExt = "MetaGraphs" + CatlabSCSExt = "SCS" + CatlabTikzPicturesExt = "TikzPictures" + + [deps.Catlab.weakdeps] + Convex = "f65535da-76fb-5f13-bab9-19810c17039a" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" + Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85" + MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5" + SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13" + TikzPictures = "37f6aa50-8035-52d0-81c2-5a1d08754b2d" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "8bae903893aeeb429cf732cf1888490b93ecf265" +git-tree-sha1 = "2afc496e94d15a1af5502625246d172361542133" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.49.0" +version = "1.52.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -331,9 +390,13 @@ version = "1.16.0" [[deps.ChangesOfVariables]] deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "f84967c4497e0e1955f9a582c232b02847c5f589" +git-tree-sha1 = "2fba81a302a7be671aefe194f0525ef231104e7f" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.7" +version = "0.1.8" +weakdeps = ["InverseFunctions"] + + [deps.ChangesOfVariables.extensions] + ChangesOfVariablesInverseFunctionsExt = "InverseFunctions" [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] @@ -395,9 +458,9 @@ 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"] @@ -413,9 +476,9 @@ version = "0.1.2" [[deps.Compat]] deps = ["UUIDs"] -git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" +git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.6.1" +version = "4.7.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -424,7 +487,7 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.0.5+0" [[deps.Compose]] deps = ["Base64", "Colors", "DataStructures", "Dates", "IterTools", "JSON", "LinearAlgebra", "Measures", "Printf", "Random", "Requires", "Statistics", "UUIDs"] @@ -446,6 +509,11 @@ weakdeps = ["InverseFunctions"] [deps.CompositionsBase.extensions] CompositionsBaseInverseFunctionsExt = "InverseFunctions" +[[deps.ConcreteStructs]] +git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" +uuid = "2569d6c7-a4a2-43d3-a901-331e8e4be471" +version = "0.2.3" + [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" @@ -474,6 +542,12 @@ git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.6.2" +[[deps.Copulas]] +deps = ["AlphaStableDistributions", "Cubature", "Distributions", "ForwardDiff", "GSL", "MvNormalCDF", "Random", "Roots", "SpecialFunctions", "StatsBase", "TaylorSeries"] +git-tree-sha1 = "bf5b74cd9b240eea4b713bf3b04211dabf827688" +uuid = "ae264745-0b69-425e-9d9d-cf662c5eec93" +version = "0.1.10" + [[deps.CpuId]] deps = ["Markdown"] git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" @@ -485,6 +559,24 @@ git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" +[[deps.Cubature]] +deps = ["Cubature_jll"] +git-tree-sha1 = "c3f4b3b38abd7b5c3ccf59adab2568212e7530d3" +uuid = "667455a9-e2ce-5579-9412-b964f529a492" +version = "1.5.1" + +[[deps.Cubature_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "0fe9efb84e3eb7b14f885a95aaa0ed50c7e839c8" +uuid = "7bc98958-0e37-5d67-a6ac-a3a19030071a" +version = "1.0.5+0" + +[[deps.DSP]] +deps = ["Compat", "FFTW", "IterTools", "LinearAlgebra", "Polynomials", "Random", "Reexport", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "da8b06f89fce9996443010ef92572b193f8dca1f" +uuid = "717857b8-e6f2-59f4-9121-6e50c889abd2" +version = "0.7.8" + [[deps.DataAPI]] git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" @@ -498,9 +590,9 @@ version = "1.5.0" [[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" @@ -536,9 +628,9 @@ 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", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "1c03e389a28be70cd9049f98ff0b84cf7539d959" +git-tree-sha1 = "62c41421bd0facc43dfe4e9776135fe21fd1e1b9" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.125.0" +version = "6.126.0" [deps.DiffEqBase.extensions] DiffEqBaseDistributionsExt = "Distributions" @@ -569,10 +661,10 @@ 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" @@ -588,15 +680,15 @@ 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"] @@ -610,9 +702,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "5eeb2bd01e5065090ad591a205d8cad432ae6cb6" +git-tree-sha1 = "e76a3281de2719d7c81ed62c6ea7057380c87b1d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.93" +version = "0.25.98" weakdeps = ["ChainRulesCore", "DensityInterface"] [deps.Distributions.extensions] @@ -621,9 +713,9 @@ weakdeps = ["ChainRulesCore", "DensityInterface"] [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "Distributions", "FillArrays", "LinearAlgebra", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "c19c3ee030a0abb9366e6d3c5eafff519471f645" +git-tree-sha1 = "1fb4fedd5a407243d535cc50c8c803c2fce0dc26" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.47" +version = "0.6.49" [deps.DistributionsAD.extensions] DistributionsADForwardDiffExt = "ForwardDiff" @@ -645,9 +737,9 @@ version = "0.9.3" [[deps.DomainSets]] deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "698124109da77b6914f64edd696be8dccf90229e" +git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.6.6" +version = "0.6.7" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -689,29 +781,22 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" -[[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Printf", "Random"] -git-tree-sha1 = "28c09cee567a3b62a8ae2a99035bd477fdbaee3f" -uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.0" - -[[deps.EnzymeCore]] -deps = ["Adapt"] -git-tree-sha1 = "d0840cfff51e34729d20fd7d0a13938dc983878b" -uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.3.0" +[[deps.ErrorfreeArithmetic]] +git-tree-sha1 = "d6863c556f1142a061532e79f611aa46be201686" +uuid = "90fa49ef-747e-5e6f-a989-263ba693cf1a" +version = "0.5.2" -[[deps.Enzyme_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "b83b072e7a5eee2050800658f5676b0ff7b37dc6" -uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.53+0" +[[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"] @@ -744,9 +829,9 @@ version = "4.4.2+2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "f9818144ce7c8c41edf5c4c179c684d92aa4d9fe" +git-tree-sha1 = "b4fbdd20c889804969571cc589900803edda16b7" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.6.0" +version = "1.7.1" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -767,9 +852,15 @@ 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"] +git-tree-sha1 = "6344aa18f654196be82e62816935225b3b9abe44" +uuid = "fa42c844-2597-5d31-933b-ebd51ab2693f" +version = "0.3.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] @@ -788,15 +879,25 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" +git-tree-sha1 = "2250347838b28a108d1967663cba57bfb3c02a58" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.11" +version = "1.3.0" [[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"] @@ -827,10 +928,10 @@ weakdeps = ["StaticArrays"] 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"] @@ -867,33 +968,39 @@ version = "3.3.8+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "9ade6983c3dbbd492cf5729f865fe030d1541463" +git-tree-sha1 = "2e57b4a4f9cc15e85a24d603256fe08e527f48d1" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.6.6" +version = "8.8.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.4" - -[[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "5737dc242dadd392d934ee330c69ceff47f0259c" -uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.19.4" +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 = "d014972cd6f5afb1f8cd7adf000b7a966d62c304" +git-tree-sha1 = "8b8a2fd4536ece6e554168c21860b6820a8a83db" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.72.5" +version = "0.72.7" [[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 = "f670f269909a9114df1380cc0fcaa316fff655fb" +git-tree-sha1 = "19fad9cd9ae44847fe842558a744748084a722d1" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.72.5+0" +version = "0.72.7+0" + +[[deps.GSL]] +deps = ["GSL_jll", "Libdl", "Markdown"] +git-tree-sha1 = "3ebd07d519f5ec318d5bc1b4971e2472e14bd1f0" +uuid = "92c85e6c-cbff-5e0c-80f7-495c94daaecd" +version = "1.0.1" + +[[deps.GSL_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "56f1e2c9e083e0bb7cf9a7055c280beb08a924c0" +uuid = "1b77fbbe-d8ee-58f0-85f9-836ddc23a7a4" +version = "2.7.2+0" [[deps.GeneralizedGenerated]] deps = ["DataStructures", "JuliaVariables", "MLStyle", "Serialization"] @@ -925,10 +1032,10 @@ uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" version = "1.3.1" [[deps.GlobalSensitivity]] -deps = ["Distributions", "FFTW", "ForwardDiff", "KernelDensity", "LinearAlgebra", "Parameters", "QuasiMonteCarlo", "Random", "RecursiveArrayTools", "Statistics", "StatsBase", "Trapz"] -git-tree-sha1 = "e44cdbdc5ee2c4417be3ae244c84de6a6c4eab44" +deps = ["Combinatorics", "Copulas", "Distributions", "FFTW", "ForwardDiff", "KernelDensity", "LinearAlgebra", "Parameters", "QuasiMonteCarlo", "Random", "RecursiveArrayTools", "Statistics", "StatsBase", "ThreadsX", "Trapz"] +git-tree-sha1 = "e5484bc811d0335814e3f7d3815dcea19d261fbc" uuid = "af5da776-676b-467e-8baf-acd8249e4f0f" -version = "2.1.4" +version = "2.2.1" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -949,9 +1056,9 @@ version = "1.0.2" [[deps.Groebner]] deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random", "SnoopPrecompile"] -git-tree-sha1 = "b6c3e9e1eb8dcc6fd9bc68fe08dcc7ab22710de6" +git-tree-sha1 = "c8b55b624a83f60bcd6574cc999ad148d0a47dd6" uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.3.4" +version = "0.3.6" [[deps.GroupsCore]] deps = ["Markdown", "Random"] @@ -966,10 +1073,10 @@ uuid = "19dc6840-f33b-545b-b366-655c7e3ffd49" version = "1.5.1" [[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 = "7f5ef966a02a8fdf3df2ca03108a88447cb3c6f0" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.9.4" +version = "1.9.8" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -985,15 +1092,15 @@ 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 = "0ec02c648befc2f94156eaef13b0f38106212f3f" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.16" +version = "0.3.17" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] @@ -1029,9 +1136,9 @@ uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34" version = "0.3.0" [[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.Integrals]] deps = ["CommonSolve", "HCubature", "LinearAlgebra", "MonteCarloIntegration", "QuadGK", "Reexport", "Requires", "SciMLBase"] @@ -1066,6 +1173,12 @@ git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.14.7" +[[deps.IntervalArithmetic]] +deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"] +git-tree-sha1 = "5ab7744289be503d76a944784bac3f2df7b809af" +uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" +version = "0.20.9" + [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" @@ -1074,9 +1187,9 @@ version = "0.7.4" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" +git-tree-sha1 = "edd1c1ac227767c75e8518defdf6e48dbfa7c3b0" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.9" +version = "0.1.10" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -1095,15 +1208,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" [[deps.IterTools]] -git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.4.0" - -[[deps.IterativeSolvers]] -deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" -uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.2" +version = "1.8.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -1135,10 +1242,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" [[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"] -git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683" +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "5b62d93f2582b09e469b3099d839c2d2ebf5066d" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.12.0" +version = "1.13.1" [[deps.JSONSchema]] deps = ["Downloads", "HTTP", "JSON", "URIs"] @@ -1166,9 +1273,9 @@ version = "2.1.91+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.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1190,9 +1297,9 @@ version = "0.4.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "47be64f040a7ece575c2b5f53ca6da7b548d69f4" +git-tree-sha1 = "b48617c5d764908b5fac493cd907cf33cc11eec1" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.4" +version = "0.9.6" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -1206,12 +1313,6 @@ git-tree-sha1 = "0356a64062656b0cbb43c504ad5de338251f4bda" 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" - [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" @@ -1226,15 +1327,21 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "26a31cdd9f1f4ea74f649a7bf249703c687a953d" +git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "5.1.0" +version = "6.1.0" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "09b7505cc0b1cee87e5d4a26eea61d2e1b0dcd35" +git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.21+0" +version = "0.0.23+0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" [[deps.LRUCache]] git-tree-sha1 = "48c10e3cc27e30de82463c27bef0b8bdbd1dc634" @@ -1265,9 +1372,9 @@ version = "0.4.6" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "099e356f267354f46ba65087981a77da23a279b7" +git-tree-sha1 = "f428ae552340899a935973270b8d98e5a31c49fe" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.0" +version = "0.16.1" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1277,12 +1384,6 @@ version = "0.16.0" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" -[[deps.LatinHypercubeSampling]] -deps = ["Random", "StableRNGs", "StatsBase", "Test"] -git-tree-sha1 = "825289d43c753c7f1bf9bed334c253e9913997f8" -uuid = "a5e1c1ea-c99a-51d3-a14d-a9a37257b02d" -version = "1.9.0" - [[deps.LatticeRules]] deps = ["Random"] git-tree-sha1 = "7f5b02258a3ca0221a6a9710b0a0a2e8fb4957fe" @@ -1410,16 +1511,24 @@ 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 = "93f3a0d88c8f5498bed3ad37ddd844b939fdf899" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.42.0" +version = "2.3.0" [deps.LinearSolve.extensions] - LinearSolveHYPRE = "HYPRE" + 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.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1429,12 +1538,13 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "b726468867eb032ebd7aba0337213eb18ed0566b" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.4.3" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] LogDensityProblemsADEnzymeExt = "Enzyme" + LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] LogDensityProblemsADForwardDiffExt = "ForwardDiff" LogDensityProblemsADReverseDiffExt = "ReverseDiff" @@ -1444,6 +1554,7 @@ version = "1.4.3" [deps.LogDensityProblemsAD.weakdeps] BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -1451,9 +1562,9 @@ version = "1.4.3" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.23" +version = "0.3.24" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1472,9 +1583,9 @@ version = "1.0.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "3bb62b5003bc7d2d49f26663484267dc49fa1bf5" +git-tree-sha1 = "e4eed22d70ac91d7a4bf9e0f6902383061d17105" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.159" +version = "0.12.162" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1483,15 +1594,15 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "5eec3d97404f1df009560e5e17d0d64ea713dc91" +git-tree-sha1 = "8778ea7283a0bf0d7e507a0235adfff38071493b" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "6.0.1" +version = "6.0.3" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "09202be9ac9489905c26f525e7050e014bdb70d5" +git-tree-sha1 = "695e91605361d1932c3e89a812be78480a4a4595" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.2" +version = "0.3.4" [[deps.METIS_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1506,9 +1617,9 @@ version = "0.1.4" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "2ce8695e1e699b68702c03402672a69f54b8aca9" +git-tree-sha1 = "154d7aaa82d24db6d8f7e4ffcfe596f40bff214b" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2022.2.0+0" +version = "2023.1.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] @@ -1555,9 +1666,9 @@ version = "0.1.14" [[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.MathProgBase]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1598,15 +1709,15 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.Mocking]] deps = ["Compat", "ExprTools"] -git-tree-sha1 = "782e258e80d68a73d8c916e55f8ced1de00c2cea" +git-tree-sha1 = "4cc0c5a83933648b615c36c2b956d94fda70641e" uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.7.6" +version = "0.7.7" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "NaNMath", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] -git-tree-sha1 = "e52b0337d18fd6ca8b1e1e3d801636dba203b966" +deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "cad27947bc85b1a3136f395f22a7dd5c382b7209" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.55.1" +version = "8.62.0" [deps.ModelingToolkit.extensions] MTKDeepDiffsExt = "DeepDiffs" @@ -1641,6 +1752,12 @@ git-tree-sha1 = "964cb1a7069723727025ae295408747a0b36a854" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" version = "1.3.0" +[[deps.MvNormalCDF]] +deps = ["Distributions", "FillArrays", "LinearAlgebra", "Primes", "Random", "StatsBase"] +git-tree-sha1 = "e472ed20dfe9f68d9aebc02258dfe31d69deb8eb" +uuid = "37188c8d-bc69-4638-b057-733e744175ec" +version = "0.2.6" + [[deps.MyterialColors]] git-tree-sha1 = "01d8466fb449436348999d7c6ad740f8f853a579" uuid = "1c23619d-4212-4747-83aa-717207fae70f" @@ -1672,15 +1789,19 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "99e6dbb50d8a96702dc60954569e9fe7291cc55d" +git-tree-sha1 = "ec9858db6fcd07f63aeeed105420cc573ce2685a" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.20" +version = "0.9.1" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" + NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] + NNlibCUDAExt = "CUDA" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] deps = ["OpenLibm_jll"] @@ -1715,22 +1836,16 @@ 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" - -[[deps.ObjectFile]] -deps = ["Reexport", "StructIO"] -git-tree-sha1 = "55ce61d43409b1fb0279d1781bf3b0f22c83ab3b" -uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.3.7" +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"] @@ -1740,9 +1855,9 @@ version = "1.3.5+1" [[deps.OpenAPI]] deps = ["Base64", "Dates", "Downloads", "HTTP", "JSON", "LibCURL", "MbedTLS", "TimeZones", "URIs"] -git-tree-sha1 = "d091c5b9feb951f0a674a9792cd5f948507eecaa" +git-tree-sha1 = "6e497e6245770817a7821a2d1d32f8f465166a99" uuid = "d5e62ea6-ddf3-4d43-8e4c-ad5e6c8bfd7d" -version = "0.1.9" +version = "0.1.11" [[deps.OpenBLAS32_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1767,10 +1882,10 @@ 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"] @@ -1780,9 +1895,9 @@ 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.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] @@ -1791,10 +1906,28 @@ uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" version = "0.2.15" [[deps.Optimization]] -deps = ["ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "Enzyme", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "82ffb0d292601b9b64a1a03e043f79536d9d243c" +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "80005bc7d96d4d00e56b8a58c5240a35bd638d4a" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.14.1" +version = "3.15.2" + + [deps.Optimization.extensions] + OptimizationEnzymeExt = "Enzyme" + OptimizationFinitediffExt = "FiniteDiff" + OptimizationForwarddiffExt = "ForwardDiff" + OptimizationMTKExt = "ModelingToolkit" + OptimizationReversediffExt = "ReverseDiff" + OptimizationTrackerExt = "Tracker" + OptimizationZygoteExt = "Zygote" + + [deps.Optimization.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OptimizationBBO]] deps = ["BlackBoxOptim", "Optimization", "Reexport"] @@ -1804,15 +1937,15 @@ version = "0.1.4" [[deps.OptimizationMOI]] deps = ["Ipopt_jll", "MathOptInterface", "ModelingToolkit", "Optimization", "Reexport", "SparseArrays", "Symbolics"] -git-tree-sha1 = "1eb9464b555b98752dbed420583b43cd8fe5f344" +git-tree-sha1 = "32c99127e8caf6b50856d676b56a9382bd5650c6" uuid = "fd9f6733-72f4-499f-8506-86b2bdd0dea1" -version = "0.1.13" +version = "0.1.14" [[deps.OptimizationNLopt]] deps = ["NLopt", "Optimization", "Reexport"] -git-tree-sha1 = "10d58c91cde18c6c576f6559d546d7c94971fa47" +git-tree-sha1 = "105de2db4fad2750921fb59507b8ebf3ccebdd91" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.1.5" +version = "0.1.6" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1826,16 +1959,16 @@ 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.Oxygen]] deps = ["Dates", "HTTP", "JSON3", "MIMEs", "Sockets"] -git-tree-sha1 = "638db9ad1e71ed972e7e4dd2ee4346e6ed66a3b6" +git-tree-sha1 = "dca31e833aafb6277e5aff9fdcb5029be5045255" uuid = "df9a0d86-3283-4920-82dc-4555fc0d1d8b" -version = "1.1.8" +version = "1.1.11" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1856,9 +1989,9 @@ 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.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" @@ -1867,20 +2000,20 @@ version = "1.3.0" [[deps.Pipelines]] deps = ["Dates", "FilePathsBase", "Logging", "OrderedCollections", "Printf", "Reexport", "Test", "UUIDs"] -git-tree-sha1 = "2c9f915f7e815add483c23a88c61eac310f93108" +git-tree-sha1 = "b870d8e0354361e38b0d9fc1997e96c299e948ae" uuid = "ef544631-5c6f-4e9b-994c-12e7a4cd724c" -version = "0.10.1" +version = "0.10.4" [[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", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.0" +version = "1.9.2" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1895,10 +2028,10 @@ 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", "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" @@ -1932,6 +2065,22 @@ git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.1" +[[deps.Polynomials]] +deps = ["LinearAlgebra", "RecipesBase"] +git-tree-sha1 = "3aa2bb4982e575acd7583f01531f241af077b163" +uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" +version = "3.2.13" + + [deps.Polynomials.extensions] + PolynomialsChainRulesCoreExt = "ChainRulesCore" + PolynomialsMakieCoreExt = "MakieCore" + PolynomialsMutableArithmeticsExt = "MutableArithmetics" + + [deps.Polynomials.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" + MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" + [[deps.PooledArrays]] deps = ["DataAPI", "Future"] git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" @@ -1958,9 +2107,9 @@ version = "0.4.12" [[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"] @@ -2018,10 +2167,10 @@ uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" version = "2.8.2" [[deps.QuasiMonteCarlo]] -deps = ["Distributions", "LatinHypercubeSampling", "LatticeRules", "LinearAlgebra", "Primes", "Random", "Sobol", "StatsBase"] -git-tree-sha1 = "b10f1a5345f14f6431712661925ae2d8c02780ee" +deps = ["Accessors", "ConcreteStructs", "Distributions", "LatticeRules", "LinearAlgebra", "Primes", "Random", "Sobol", "StatsBase"] +git-tree-sha1 = "e23bba76fbb0a71991a57b3190126988bc64212a" uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b" -version = "0.2.19" +version = "0.3.1" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -2056,9 +2205,9 @@ version = "0.3.2" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "6d7bb727e76147ba18eed998700998e17b8e4911" +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.4" +version = "0.4.5" weakdeps = ["FixedPointNumbers"] [deps.Ratios.extensions] @@ -2109,6 +2258,12 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" +[[deps.Referenceables]] +deps = ["Adapt"] +git-tree-sha1 = "e681d3bfa49cd46c3c161505caddf20f0e62aaa9" +uuid = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" +version = "0.1.2" + [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" @@ -2141,23 +2296,30 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "e961f57a7d5b1d46059b62a8fb7223d6497a5bc4" +git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.15" +version = "2.0.17" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" + RootsSymPyExt = "SymPy" [deps.Roots.weakdeps] ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" + SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" + +[[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 = "d7d9ebe28062161c1e314ed643097b0c6fe657d9" +git-tree-sha1 = "0b9b18d6236e9ab2b092defaacdffd929d572642" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.7" +version = "0.5.9" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -2170,21 +2332,20 @@ 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.SafeTestsets]] -deps = ["Test"] -git-tree-sha1 = "36ebc5622c82eb9324005cc75e7e2cc51181d181" +git-tree-sha1 = "81ec49d645af090901120a1542e67ecbbe044db3" uuid = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" -version = "0.0.1" +version = "0.1.0" [[deps.SciMLBase]] 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 = "75552338dda481baeb9b9e171f73ecd0171e8f34" +git-tree-sha1 = "a22a12db91f6a921e28a7ae39a9546eed93fd92e" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.92.2" +version = "1.93.0" [[deps.SciMLExpectations]] deps = ["DiffEqBase", "Distributions", "Integrals", "KernelDensity", "LinearAlgebra", "Parameters", "Random", "RecursiveArrayTools", "Reexport", "StaticArrays", "Statistics", "Zygote"] @@ -2194,15 +2355,15 @@ version = "2.0.1" [[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.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -2217,13 +2378,18 @@ 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" +[[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" @@ -2246,14 +2412,10 @@ 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 = ["ArrayInterfaceCore", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase", "SnoopPrecompile", "StaticArraysCore"] +git-tree-sha1 = "3f558105e8ef4aac1e22bf30bd1f1e95698bfc95" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.14" -weakdeps = ["NNlib"] - - [deps.SimpleNonlinearSolve.extensions] - SimpleBatchedNonlinearSolveExt = "NNlib" +version = "0.1.10" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2283,19 +2445,23 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[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 = ["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" +weakdeps = ["Zygote"] + + [deps.SparseDiffTools.extensions] + SparseDiffToolsZygoteExt = "Zygote" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2310,9 +2476,9 @@ version = "0.1.5" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.2.0" +version = "2.3.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2324,12 +2490,6 @@ git-tree-sha1 = "e08a62abc517eb79667d0a29dc08a3b589516bb5" uuid = "171d559e-b47b-412a-8079-5efa626c420e" version = "0.1.15" -[[deps.StableRNGs]] -deps = ["Random", "Test"] -git-tree-sha1 = "3be7d49667040add7ee151fefaf1f8c04c8c8276" -uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" -version = "1.0.0" - [[deps.Static]] deps = ["IfElse"] git-tree-sha1 = "dbde6766fc677423598138a5951269432b0fcc90" @@ -2348,10 +2508,14 @@ weakdeps = ["OffsetArrays", "StaticArrays"] StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "8982b3607a212b070a5e46eea83eb62b4744ae12" +deps = ["LinearAlgebra", "Random", "StaticArraysCore"] +git-tree-sha1 = "0da7e6b70d1bb40b1ace3b576da9ea2992f76318" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.25" +version = "1.6.0" +weakdeps = ["Statistics"] + + [deps.StaticArrays.extensions] + StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -2394,21 +2558,21 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[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 = "26316a9a43d32ecd0c5b342cb36dc86305c73e53" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.4.14" +version = "0.4.16" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -2433,12 +2597,6 @@ git-tree-sha1 = "192a9f1de3cfef80ab1a4ba7b150bb0e11ceedcf" uuid = "6ec83bb0-ed9f-11e9-3b4c-2b04cb4e219c" version = "2.1.0" -[[deps.StructIO]] -deps = ["Test"] -git-tree-sha1 = "010dc73c7146869c042b49adcdb6bf528c12e859" -uuid = "53d494c1-5632-5724-8f4c-31dff12d585f" -version = "0.3.0" - [[deps.StructTypes]] deps = ["Dates", "UUIDs"] git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" @@ -2456,9 +2614,9 @@ version = "5.10.1+6" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "4289695031d663252f38fd114d3e0020d1461cee" +git-tree-sha1 = "4931f9013c53128337ce8df54a2d38c79fe58d4c" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.18.0" +version = "4.19.3" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -2486,9 +2644,9 @@ version = "1.0.5" [[deps.Symbolics]] deps = ["ArrayInterface", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "Markdown", "NaNMath", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "TreeViews"] -git-tree-sha1 = "e23ec62c083ca8f15a4b7174331b3b8d1c511e47" +git-tree-sha1 = "c4e5688a9a5a2f4088cd1a779b0742be31cbe9aa" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.3.1" +version = "5.5.0" [[deps.TOML]] deps = ["Dates"] @@ -2512,6 +2670,12 @@ deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" +[[deps.TaylorSeries]] +deps = ["IntervalArithmetic", "LinearAlgebra", "Markdown", "Requires", "SparseArrays"] +git-tree-sha1 = "b123e0614b0f366e2073c4da7b1367cebda3f579" +uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea" +version = "0.14.0" + [[deps.TensorCore]] deps = ["LinearAlgebra"] git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" @@ -2520,9 +2684,9 @@ version = "0.1.1" [[deps.Term]] deps = ["AbstractTrees", "CodeTracking", "Dates", "Highlights", "InteractiveUtils", "Logging", "Markdown", "MyterialColors", "OrderedCollections", "Parameters", "PrecompileTools", "ProgressLogging", "REPL", "Tables", "UUIDs", "Unicode", "UnicodeFun"] -git-tree-sha1 = "7952fafaecea040260bdc4be2afff92c411c23ce" +git-tree-sha1 = "ffac67f6fbcbb32027d924b93ba91b7633af9220" uuid = "22787eb5-b846-44ae-b979-8e399b8463ab" -version = "2.0.4" +version = "2.0.5" [[deps.TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] @@ -2542,15 +2706,21 @@ 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"] +git-tree-sha1 = "34e6bcf36b9ed5d56489600cf9f3c16843fa2aa2" +uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" +version = "0.1.11" [[deps.TimeZones]] deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "a5404eddfee0cf451cabb8ea8846413323712e25" +git-tree-sha1 = "cdaa0c2a4449724aded839550eca7d7240bb6938" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.9.2" +version = "1.10.0" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] @@ -2558,6 +2728,12 @@ git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.23" +[[deps.ToeplitzMatrices]] +deps = ["AbstractFFTs", "DSP", "LinearAlgebra", "StatsBase"] +git-tree-sha1 = "326388c0c53565fb21eecafb6176b1cc5d225d34" +uuid = "c751599d-da0a-543b-9d20-d0a503d91d24" +version = "0.8.1" + [[deps.Tokenize]] git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" @@ -2565,9 +2741,9 @@ version = "0.5.25" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "8b552cc0a4132c1ce5cee14197bb57d2109d480f" +git-tree-sha1 = "92364c27aa35c0ee36e6e010b704adaade6c409c" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.25" +version = "0.2.26" weakdeps = ["PDMats"] [deps.Tracker.extensions] @@ -2581,9 +2757,23 @@ 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.Trapz]] git-tree-sha1 = "79eb0ed763084a3e7de81fe1838379ac6a23b6a0" @@ -2609,9 +2799,9 @@ 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.Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] @@ -2643,15 +2833,22 @@ 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" -weakdeps = ["InverseFunctions"] +version = "1.15.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] + ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" +[[deps.UnitfulLatexify]] +deps = ["LaTeXStrings", "Latexify", "Unitful"] +git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" +version = "1.6.3" + [[deps.Unityper]] deps = ["ConstructionBase"] git-tree-sha1 = "d5f4ec8c22db63bd3ccb239f640e895cfde145aa" @@ -2665,9 +2862,9 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "ea37e6066bf194ab78f4e747f5245261f17a7175" +git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.2" +version = "0.1.3" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -2728,16 +2925,16 @@ 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"] @@ -2746,10 +2943,10 @@ 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"] @@ -2788,22 +2985,22 @@ 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"] @@ -2836,28 +3033,28 @@ 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.Zlib_jll]] deps = ["Libdl"] @@ -2872,9 +3069,9 @@ version = "1.5.5+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "ebac1ae9f048c669317ad48c9bed815790a468d8" +git-tree-sha1 = "5be3ddb88fc992a7d8ea96c3f10a49a7e98ebc7b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.61" +version = "0.6.62" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] diff --git a/Project.toml b/Project.toml index b065180..9b2bdba 100644 --- a/Project.toml +++ b/Project.toml @@ -10,6 +10,8 @@ Bijections = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" Catlab = "134e5e36-593f-5add-ad60-77f754baafbe" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" +DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" EasyModelAnalysis = "ef4b24a4-a090-4686-a932-e7e56a5a83bd" @@ -19,6 +21,7 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" JSONTables = "b9914132-a727-11e9-1322-f18e41205b0b" JobSchedulers = "eeff360b-c02d-44d3-ab26-4013c616a17e" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" MathML = "abcecc63-2b08-419c-80c4-c63dca6fa478" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" @@ -33,6 +36,7 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Preferences = "21216c6a-2e73-6563-6e65-726566657250" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" SwaggerMarkdown = "1b6eb727-ad4b-44eb-9669-b9596a6e760f" SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" diff --git a/src/operations/Operations.jl b/src/operations/Operations.jl index 37cb4d8..865e840 100644 --- a/src/operations/Operations.jl +++ b/src/operations/Operations.jl @@ -4,34 +4,101 @@ SciML Operation definitions module Operations import AlgebraicPetri: LabelledPetriNet, AbstractPetriNet -import DataFrames: DataFrame -import DifferentialEquations: solve -import ModelingToolkit: remake -import Symbolics: Num +import DataFrames: DataFrame, names +import DifferentialEquations: solve, DiscreteCallback +import ModelingToolkit: remake, ODESystem, ODEProblem +import Symbolics: Num, getname, @variables, substitute import SymbolicIndexingInterface: states, parameters import EasyModelAnalysis +import SciMLBase -include("./Utils.jl"); import .Utils: to_prob, unzip, symbolize_args, select_data +using LinearAlgebra: norm +using Dates: Dates, DateTime, now + +# import MathML # NOTE: Operations exposed to the rest of the Simulation Service export simulate, calibrate, ensemble -""" -Simulate a scenario from a PetriNet -""" -# model::ASKEMModel -function simulate(; model, timespan::Tuple{Float64,Float64}=(0.0, 100.0), context)::DataFrame - sol = solve(to_prob(model, timespan); progress = true, progress_steps = 1) - DataFrame(sol) + +#-----------------------------------------------------------------------------# utils + +# Transform model representation into a SciML ODEProblem +function to_prob(sys, tspan) + ODEProblem(sys, [], tspan, saveat=1) +end + +# Separate keys and values +unzip(d::Dict) = (collect(keys(d)), collect(values(d))) + +# Unzip a collection of pairs +unzip(ps) = first.(ps), last.(ps) + + +# Transform list of args into Symbolics variables +function symbolize_args(incoming_values, sys_vars) + pairs = collect(incoming_values) + ks, values = unzip(pairs) + symbols = Symbol.(ks) + vars_as_symbols = getname.(sys_vars) + symbols_to_vars = Dict(vars_as_symbols .=> sys_vars) + Dict( + [ + symbols_to_vars[vars_as_symbols[findfirst(x -> x == symbol, vars_as_symbols)]] + for symbol in symbols + ] .=> values + ) +end + + +# Generate data and timestep list from a dataframe +function select_data(df::DataFrame) + data = Dict( + key => df[!, key] + for key in names(df) if key != "timestep" + ) + df[!, "timestep"], data +end + +#-----------------------------------------------------------------------------# IntermediateReulsts callback +mutable struct IntermediateResults + last_callback::DateTime # Track the last time the callback was called + every::Dates.TimePeriod # Callback frequency e.g. `Dates.Second(5)` + context # ::Union{Nothing, Context} (context.interactivity_hook sends Dict to frontend via RabbitMQ) +end +IntermediateResults(context; every=Dates.Second(5)) = IntermediateResults(typemin(DateTime), every, context) + +intermediate_results_to_rabbitmq(integrator) = Dict( + :iter => integrator.iter, + :time => integrator.t, + :params => integrator.u, + :abserr => norm(integrator.u - integrator.uprev), + :retcode => Symbol(SciMLBase.check_error(integrator)), +) + +function (o::IntermediateResults)(integrator) + if o.last_callback + o.every ≤ now() + o.last_callback = now() + d = intermediate_results_to_rabbitmq(integrator) + if isnothing(o.context) + @info "IntermediateResults: $(NamedTuple(d))" + else + d[:job_id] = context.job_id + context.interactivity_hook(d) + end + end end -" -for custom loss functions, we probably just allow an enum of functions defined in EMA. (todo) +#-----------------------------------------------------------------------------# simulate +function simulate(; model::ODESystem, timespan::Tuple{Float64,Float64}=(0.0, 100.0), context=nothing) + prob = to_prob(model, timespan) + callback = DiscreteCallback((args...) -> true, IntermediateResults(context)) + sol = solve(prob; progress = true, progress_steps = 1, callback) + DataFrame(sol) +end - datafit is exported in EMA -" -# model::ASKEMModel -function calibrate(; model, dataset::DataFrame, context) +#-----------------------------------------------------------------------------# calibrate +function calibrate(; model, dataset::DataFrame, context=nothing) timesteps, data = select_data(dataset) prob = to_prob(model, extrema(timesteps)) p = Vector{Pair{Num, Float64}}([Num(param) => model.defaults[param] for param in parameters(model)]) @@ -43,13 +110,13 @@ function calibrate(; model, dataset::DataFrame, context) fitp end -""" -NOT IMPLEMENTED -""" -function ensemble(; models::AbstractArray{AbstractPetriNet}, timespan=(0.0, 100.0)::Tuple{Float64, Float64}) +#-----------------------------------------------------------------------------# ensemble +function ensemble(; models::AbstractArray{AbstractPetriNet}, timespan::Tuple{Float64, Float64} = (0.0, 100.0), context=nothing) throw("ENSEMBLE IS NOT YET IMPLEMENTED") end + +# joshday: what is this function? "long running functions like global_datafit and sensitivity wrappers will need to be refactored to share callback info incrementally" function _global_datafit(; model::LabelledPetriNet, parameter_bounds::Dict{String,Tuple{Float64,Float64}}, diff --git a/src/operations/Utils.jl b/src/operations/Utils.jl deleted file mode 100644 index f0e6d35..0000000 --- a/src/operations/Utils.jl +++ /dev/null @@ -1,63 +0,0 @@ -""" -Unexposed helper functions for operations -""" -module Utils - -import DataFrames: DataFrame, names -import ModelingToolkit: ODESystem, ODEProblem -import Symbolics: getname, @variables, substitute -import SymbolicIndexingInterface: states, parameters -import MathML - -export to_prob, unzip, symbolize_args, select_data - -""" -Transform model representation into a SciML ODEProblem -""" -function to_prob(sys, tspan) - ODEProblem(sys, [], tspan, saveat=1) -end - -""" -Separate keys and values -""" -unzip(d::Dict) = (collect(keys(d)), collect(values(d))) - -""" -Unzip a collection of pairs -""" -unzip(ps) = first.(ps), last.(ps) - - -""" -Transform list of args into Symbolics variables -""" -function symbolize_args(incoming_values, sys_vars) - pairs = collect(incoming_values) - ks, values = unzip(pairs) - symbols = Symbol.(ks) - vars_as_symbols = getname.(sys_vars) - symbols_to_vars = Dict(vars_as_symbols .=> sys_vars) - Dict( - [ - symbols_to_vars[vars_as_symbols[findfirst(x -> x == symbol, vars_as_symbols)]] - for symbol in symbols - ] .=> values - ) -end - - -""" -Generate data and timestep list from a dataframe -""" -function select_data(dataframe::DataFrame) - data = Dict( - key => dataframe[!, key] - for key in names(dataframe) if key != "timestep" - ) - - dataframe[!, "timestep"], data -end - - -end # module Utils.jl diff --git a/src/service/ArgIO.jl b/src/service/ArgIO.jl index df45f7f..fc3feb0 100644 --- a/src/service/ArgIO.jl +++ b/src/service/ArgIO.jl @@ -15,11 +15,11 @@ include("./AssetManager.jl"); import .AssetManager: fetch_dataset, fetch_model, export prepare_input, prepare_output -""" -Transform requests into arguments to be used by operation +# """ +# Transform requests into arguments to be used by operation -Optionally, IDs are hydrated with the corresponding entity from TDS. -""" +# Optionally, IDs are hydrated with the corresponding entity from TDS. +# """ function prepare_input(args; context...) if settings["ENABLE_TDS"] update_simulation(context[:job_id], Dict([:status=>"running", :start_time => time()])) @@ -40,27 +40,27 @@ function prepare_input(args; context...) args[:timespan] = nothing end if in(:extra, keys(args)) - for (key, value) in Dict(args[:extra]) + for (key, value) in Dict(args[:extra]) args[Symbol(key)] = value end end args end -""" -Generate a `prepare_input` function that is already contextualized -""" +# """ +# Generate a `prepare_input` function that is already contextualized +# """ function prepare_input(context) function contextualized_prepare_input(args) prepare_input(args; context...) end end -""" -Normalize the header of the resulting dataframe and return a CSV +# """ +# Normalize the header of the resulting dataframe and return a CSV -Optionally, the CSV is saved to TDS instead an the coreresponding ID is returned. -""" +# Optionally, the CSV is saved to TDS instead an the coreresponding ID is returned. +# """ function prepare_output(dataframe::DataFrame; name="0", context...) stripped_names = names(dataframe) .=> (r -> replace(r, "(t)"=>"")).(names(dataframe)) rename!(dataframe, stripped_names) @@ -74,9 +74,9 @@ function prepare_output(dataframe::DataFrame; name="0", context...) end end -""" -Coerces NaN values to nothing for each parameter -""" +# """ +# Coerces NaN values to nothing for each parameter +# """ function prepare_output(params::Vector{Pair{Symbolics.Num, Float64}}; name="0", context...) nan_to_nothing(value) = isnan(value) ? nothing : value fixed_params = Dict(key => nan_to_nothing(value) for (key, value) in params) @@ -86,9 +86,9 @@ function prepare_output(params::Vector{Pair{Symbolics.Num, Float64}}; name="0", end -""" -Coerces NaN values to nothing for each parameter -""" +# """ +# Coerces NaN values to nothing for each parameter +# """ function prepare_output(results::Dict{String}; context...) if settings["ENABLE_TDS"] urls = [] @@ -99,9 +99,9 @@ function prepare_output(results::Dict{String}; context...) end end -""" -Generate a `prepare_output` function that is already contextualized -""" +# """ +# Generate a `prepare_output` function that is already contextualized +# """ function prepare_output(context) function contextualized_prepare_output(arg) prepare_output(arg; context...) @@ -109,4 +109,4 @@ function prepare_output(context) end -end \ No newline at end of file +end diff --git a/test/runtests.jl b/test/runtests.jl index bed1d6c..9afcca1 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -8,22 +8,18 @@ using SimulationService #-----------------------------------------------------------------------------# Operations @testset "Operations" begin - - for (url, op) in [ - ("https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/petrinet/examples/sir.json", :simulate), - ("https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/regnet/examples/lotka_volterra.json", :calibrate), - ] - @testset "Operations.$op" begin - @info "Testing $op" - - json_string = read(download(url), String) - - f = SimulationService.Service.Execution.Interface.Available.get_operation(op) - - model = SimulationService.Service.Execution.Interface.Available.ProblemInputs.coerce_model(json_string) - - f(; model, context=nothing) - end + @testset "simulate" begin + url = "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/petrinet/examples/sir.json" + json_string = read(download(url), String) + model = SimulationService.Service.Execution.Interface.Available.ProblemInputs.coerce_model(json_string) + f = SimulationService.Service.Execution.Interface.Available.get_operation(:simulate) + f(; model, context=nothing) + end + @testset "calibrate" begin + # TODO + end + @testset "ensemble" begin + # TODO end end