diff --git a/.gitignore b/.gitignore index e32cd21..13d1290 100644 --- a/.gitignore +++ b/.gitignore @@ -16,3 +16,6 @@ deps/src/ # Build artifacts for creating documentation generated by the Documenter package docs/build/ docs/site/ +LotkaVolterra/.DS_Store +*.DS_Store +Project.toml diff --git a/LotkaVolterra/Manifest.toml b/LotkaVolterra/Manifest.toml index 502527d..b2f5419 100644 --- a/LotkaVolterra/Manifest.toml +++ b/LotkaVolterra/Manifest.toml @@ -1,21 +1,38 @@ # This file is machine-generated - editing it directly is not advised +[[AbstractAlgebra]] +deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] +git-tree-sha1 = "e1205b8ce43e3bf8102aa7416a3c1f0862c479a0" +uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" +version = "0.27.0" + [[AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.0.1" +version = "1.2.1" [[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" +git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +version = "0.4.2" + +[[Accessors]] +deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"] +git-tree-sha1 = "c877a35749324754d3c8fffb09fc1f9db144ff8f" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.18" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" + +[[ArgCheck]] +git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" +version = "2.3.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -27,74 +44,185 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.1.0" [[ArrayInterface]] -deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "045ff5e1bc8c6fb1ecb28694abba0a0d55b5f4f5" +deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "Static"] +git-tree-sha1 = "621913bff3923ff489e4268ba2b425bfacbb1759" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.17" +version = "6.0.21" + +[[ArrayInterfaceCore]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "8d9e48436c5589fbd51ae8c8165a299a219188c0" +uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" +version = "0.1.15" + +[[ArrayInterfaceGPUArrays]] +deps = ["Adapt", "ArrayInterfaceCore", "GPUArraysCore", "LinearAlgebra"] +git-tree-sha1 = "febba7add2873aecc0b6620b55969e73ec875bce" +uuid = "6ba088a2-8465-4c0a-af30-387133b534db" +version = "0.2.1" + +[[ArrayInterfaceOffsetArrays]] +deps = ["ArrayInterface", "OffsetArrays", "Static"] +git-tree-sha1 = "c49f6bad95a30defff7c637731f00934c7289c50" +uuid = "015c0d05-e682-4f19-8f0a-679ce4c54826" +version = "0.1.6" + +[[ArrayInterfaceStaticArrays]] +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"] +git-tree-sha1 = "efb000a9f643f018d5154e56814e338b5746c560" +uuid = "b0d46f97-bff5-4637-a19a-dd75974142cd" +version = "0.1.4" + +[[ArrayInterfaceStaticArraysCore]] +deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] +git-tree-sha1 = "a1e2cf6ced6505cbad2490532388683f1e88c3ed" +uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9" +version = "0.1.0" + +[[ArrayInterfaceTracker]] +deps = ["ArrayInterfaceCore", "Tracker"] +git-tree-sha1 = "9600e1ef98f7067dc91c22c0759c60580a0320dd" +uuid = "a2b0951a-f94f-4742-8780-617792921f9b" +version = "0.1.1" + +[[ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "ebe4bbfc4de38ef88323f67d60a4e848fb550f0e" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "0.8.9" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +[[AutoHashEquals]] +git-tree-sha1 = "45bb6705d93be619b81451bb2006b7ee5d4e4453" +uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" +version = "0.2.0" + [[AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] -git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" +git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" -version = "1.0.0" +version = "1.0.1" [[BFloat16s]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "4af69e205efc343068dc8722b8dfec1ade89254a" +deps = ["LinearAlgebra", "Printf", "Random", "Test"] +git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.1.0" +version = "0.2.0" + +[[BandedMatrices]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "0227886a3141dfbb9fab5bfbf2133ac57677c1f9" +uuid = "aae01518-5342-5314-be14-df237901396f" +version = "0.17.3" + +[[BangBang]] +deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] +git-tree-sha1 = "b15a6bc52594f5e4a3b825858d1089618871bf9d" +uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" +version = "0.3.36" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +[[Baselet]] +git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" +uuid = "9718e550-a3fa-408a-8086-8db961cd8217" +version = "0.1.1" + +[[Bijections]] +git-tree-sha1 = "fe4f8c5ee7f76f2198d5c2a06d3961c249cce7bd" +uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" +version = "0.1.4" + +[[BitTwiddlingConvenienceFunctions]] +deps = ["Static"] +git-tree-sha1 = "eaee37f76339077f86679787a71990c4e465477f" +uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" +version = "0.1.4" + +[[BlockArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] +git-tree-sha1 = "43b09ac794ed8347592dd90539756d1c3416e5f2" +uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" +version = "0.16.19" + +[[BlockBandedMatrices]] +deps = ["ArrayLayouts", "BandedMatrices", "BlockArrays", "FillArrays", "LinearAlgebra", "MatrixFactorizations", "SparseArrays", "Statistics"] +git-tree-sha1 = "85c30bf983cb20748f126c235f0696dff8a83612" +uuid = "ffab5731-97b5-5995-9138-79e8c1846df0" +version = "0.11.7" + [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.6+5" +version = "1.0.8+0" [[CEnum]] -git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9" +git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.1" +version = "0.4.2" + +[[CPUSummary]] +deps = ["CpuId", "IfElse", "Static"] +git-tree-sha1 = "8a43595f7b3f7d6dd1e07ad9b94081e1975df4af" +uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" +version = "0.1.25" [[CSTParser]] deps = ["Tokenize"] -git-tree-sha1 = "9723e1c07c1727082e169ca50789644a552fb023" +git-tree-sha1 = "3ddd48d200eb8ddf9cb3e0189fc059fd49b97c1f" uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f" -version = "3.2.3" +version = "3.3.6" [[CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "DataStructures", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] -git-tree-sha1 = "3e5a6cf59289a60202a0f63fdded29473544d553" +deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] +git-tree-sha1 = "49549e2c28ffb9cc77b3689dc10e46e6271e9452" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.3.2" +version = "3.12.0" [[Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "e2f47f6d8337369411569fd45ae5753ca10394c6" +git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.0+6" +version = "1.16.1+1" + +[[Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" [[Cassette]] -git-tree-sha1 = "087e76b8d48c014112ba890892c33be42ad10504" +git-tree-sha1 = "063b2e77c5537a548c5bf2f44161f1d3e1ab3227" uuid = "7057c7e9-c182-5462-911a-8362d720325c" -version = "0.3.7" +version = "0.3.10" [[ChainRules]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "4d6ed39877332d0e2157f703cb84f2619056292f" +deps = ["ChainRulesCore", "Compat", "Distributed", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"] +git-tree-sha1 = "e762b70af7c1d914f677d9588a1d3b32e5f832af" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "0.8.20" +version = "1.39.1" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "be770c08881f7bb928dfd86d1ba83798f76cf62a" +git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.10.9" +version = "1.15.3" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.4" + +[[CloseOpenIntervals]] +deps = ["ArrayInterface", "Static"] +git-tree-sha1 = "5522c338564580adf5d58d91e43a55db0fa5fb39" +uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" +version = "0.1.10" [[CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -103,16 +231,22 @@ uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.0" [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] -git-tree-sha1 = "c8fd01e4b736013bc61b704871d20503b33ea402" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] +git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.12.1" +version = "3.19.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" +git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.0" +version = "0.11.4" + +[[ColorVectorSpace]] +deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] +git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" +version = "0.9.9" [[Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] @@ -127,14 +261,14 @@ version = "1.0.2" [[CommonMark]] deps = ["Crayons", "JSON", "URIs"] -git-tree-sha1 = "7632afc57f92720a01d9aedf23f413f4e5e21015" +git-tree-sha1 = "4cd7063c9bdebdbd55ede1af70f3c2f48fab4215" uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6" -version = "0.8.1" +version = "0.8.6" [[CommonSolve]] -git-tree-sha1 = "68a0743f578349ada8bc911a5cbd5a2ef6ed6d1f" +git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.0" +version = "0.2.1" [[CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -144,19 +278,30 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "dc7dedc2c2aa9faf59a55c622760a25cbefbe941" +git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.31.0" +version = "3.45.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +[[ComponentArrays]] +deps = ["ArrayInterface", "ChainRulesCore", "LinearAlgebra", "Requires"] +git-tree-sha1 = "bdbd8f6d825682ba991b69842a4053ac0f588226" +uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" +version = "0.12.4" + [[CompositeTypes]] git-tree-sha1 = "d5b014b216dc891e81fea299638e4c10c657b582" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" version = "0.1.2" +[[CompositionsBase]] +git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.1" + [[ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] git-tree-sha1 = "3ab7b2136722890b9af903859afcf457fa3059e8" @@ -165,43 +310,54 @@ version = "0.1.2" [[ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" +git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.3.0" +version = "1.4.0" + +[[ContextVariablesX]] +deps = ["Compat", "Logging", "UUIDs"] +git-tree-sha1 = "8ccaa8c655bc1b83d2da4d569c9b28254ababd6e" +uuid = "6add18c4-b38d-439d-96f6-d6bc489c04c5" +version = "0.1.2" [[Contour]] -deps = ["StaticArrays"] -git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" +git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.5.7" +version = "0.6.2" + +[[CpuId]] +deps = ["Markdown"] +git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" +uuid = "adafc99b-e345-5852-983c-f28acb93d879" +version = "0.3.1" [[Crayons]] -git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d" +git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.0.4" +version = "4.1.1" [[DataAPI]] -git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385" +git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.7.0" +version = "1.10.0" [[DataDrivenDiffEq]] -deps = ["Compat", "DataInterpolations", "DiffEqBase", "DocStringExtensions", "LinearAlgebra", "ModelingToolkit", "ProgressMeter", "QuadGK", "Reexport", "Statistics", "StatsBase", "Symbolics", "Test"] -git-tree-sha1 = "b0c8c835a78b4d906da052a8ad07a2157e9a13f9" +deps = ["CommonSolve", "DataInterpolations", "DiffEqBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "Literate", "Measurements", "ModelingToolkit", "Parameters", "ProgressMeter", "QuadGK", "Random", "RecipesBase", "Reexport", "Requires", "Statistics", "StatsBase", "SymbolicUtils", "Symbolics", "Test"] +git-tree-sha1 = "f65c39707b06b2bb71344e10e9635d94ce5a5828" uuid = "2445eb08-9709-466a-b3fc-47e12bd697a2" -version = "0.6.2" +version = "0.8.5" [[DataInterpolations]] -deps = ["ChainRulesCore", "LinearAlgebra", "Optim", "RecipesBase", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "2f20fd64fa6e5af06de832f42b2ce07beb4ade57" +deps = ["ChainRulesCore", "LinearAlgebra", "Optim", "RecipesBase", "RecursiveArrayTools", "Reexport", "RegularizationTools", "Symbolics"] +git-tree-sha1 = "e660731df2175355e573b55796ffb4d6d4f60093" uuid = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" -version = "3.4.1" +version = "3.10.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.9" +version = "0.18.13" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -212,45 +368,56 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[DefineSingletons]] +git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" +uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" +version = "0.1.2" + [[DelimitedFiles]] deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +[[DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" + [[DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "FastBroadcast", "FunctionWrappers", "IterativeSolvers", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "RecursiveFactorization", 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-git-tree-sha1 = "3cc57ad0a213808473eafef4845a74766242e05f" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.3.1+4" +version = "4.4.2+0" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "f985af3b9f4e278b1d24434cbb546d6092fca661" +git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.4.3" +version = "1.5.0" [[FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3676abafff7e4ff07bbd2c42b3d8201f31653dcc" +git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = 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+deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "e3af8444c9916abed11f4357c2f59b6801e5b376" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.8.0" +version = "2.13.1" [[FixedPointNumbers]] deps = ["Statistics"] @@ -409,16 +603,22 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[Flux]] -deps = ["AbstractTrees", "Adapt", "CUDA", "CodecZlib", "Colors", "DelimitedFiles", "Functors", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NNlibCUDA", "Pkg", "Printf", "Random", "Reexport", "SHA", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"] -git-tree-sha1 = "0b3c6d0ce57d3b793eabd346ccc8f605035ef079" +deps = ["Adapt", "ArrayInterface", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Test", "Zygote"] +git-tree-sha1 = "96dc065bf4a998e8adeebc0ff1302902b6e59362" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.12.4" +version = "0.13.4" + +[[FoldsThreads]] +deps = ["Accessors", "FunctionWrappers", "InitialValues", "SplittablesBase", "Transducers"] +git-tree-sha1 = "eb8e1989b9028f7e0985b4268dabe94682249025" +uuid = "9c68100b-dfe1-47cf-94c8-95104e173443" +version = "0.1.1" [[Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "35895cf184ceaab11fd778b4590144034a167a2f" +git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.1+14" +version = "2.13.93+0" [[Formatting]] deps = ["Printf"] @@ -427,16 +627,16 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "e2af66012e08966366a43251e1fd421522908be6" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.18" +version = "0.10.30" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "cbd58c9deb1d304f5a245a0b7eb841a2560cfec6" +git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.1+5" +version = "2.10.4+0" [[FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -450,10 +650,9 @@ uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" version = "1.1.2" [[Functors]] -deps = ["MacroTools"] -git-tree-sha1 = "a7bb2af991c43dcf5c3455d276dd83976799634f" +git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.1" +version = "0.2.8" [[Future]] deps = ["Random"] @@ -461,45 +660,57 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157" +git-tree-sha1 = "51d2dfe8e590fbd74e7a842cf6d13d8a2f45dc01" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.5+0" +version = "3.3.6+0" [[GPUArrays]] -deps = ["AbstractFFTs", "Adapt", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"] -git-tree-sha1 = "ececbf05f8904c92814bdbd0aafd5540b0bf2e9a" +deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] +git-tree-sha1 = "73145f1d724b5ee0e90098aec39a65e9697429a6" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "7.0.1" +version = "8.4.2" + +[[GPUArraysCore]] +deps = ["Adapt"] +git-tree-sha1 = "d88b17a38322e153c519f5a9ed8d91e9baa03d8f" +uuid = "46192b85-c4d5-4398-a991-12ede77f4527" +version = "0.1.1" [[GPUCompiler]] -deps = ["DataStructures", "ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "03c3fb77362c08c3722bcef8dec488b708a95d52" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "1067cd05184719ba86f19cf1d49d57f0bcbabbf6" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.12.4" +version = "0.16.2" [[GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "b83e3125048a9c3158cbb7ca423790c7b1b57bea" +deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] +git-tree-sha1 = "037a1ca47e8a5989cc07d19729567bb71bfabd0c" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.57.5" +version = "0.66.0" [[GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "e14907859a1d3aee73a019e7b3c98e9e7b8b5b3e" +git-tree-sha1 = "c8ab731c9127cd931c93221f65d6a1008dad7256" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.57.3+0" +version = "0.66.0+0" [[GalacticOptim]] -deps = ["ArrayInterface", "ConsoleProgressMonitor", "DiffResults", "DocStringExtensions", "Logging", "LoggingExtras", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "TerminalLoggers"] -git-tree-sha1 = "fd355a5e3657d4159fb8dbf9d04138b115ac1442" +deps = ["ArrayInterfaceCore", "ConsoleProgressMonitor", "DiffResults", "DocStringExtensions", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "TerminalLoggers"] +git-tree-sha1 = "6725ceb3d9afbbae9ad08aa7ef206a6ab9559600" uuid = "a75be94c-b780-496d-a8a9-0878b188d577" -version = "2.0.3" +version = "3.4.0" + +[[GenericSchur]] +deps = ["LinearAlgebra", "Printf"] +git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" +version = "0.5.3" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "15ff9a14b9e1218958d3530cc288cf31465d9ae2" +git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.13" +version = "0.4.2" [[Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -509,26 +720,62 @@ version = "0.21.0+0" [[Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "47ce50b742921377301e15005c96e979574e130b" +git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.1+0" +version = "2.68.3+2" [[GlobalSensitivity]] deps = ["Distributions", "FFTW", "ForwardDiff", "KernelDensity", "LinearAlgebra", "Parameters", "QuasiMonteCarlo", "Random", "RecursiveArrayTools", "Statistics", "StatsBase", "Trapz"] -git-tree-sha1 = "01ad95275c8578acd7cf6cdf987501e23f0a9830" +git-tree-sha1 = "a083eb2d419b80e0c9edbf39ad8fad00eead152d" uuid = "af5da776-676b-467e-8baf-acd8249e4f0f" -version = "1.1.0" +version = "2.0.0" + +[[Graphite2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" +version = "1.3.14+0" + +[[Graphs]] +deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "db5c7e27c0d46fd824d470a3c32a4fc6c935fa96" +uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" +version = "1.7.1" [[Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" +[[Groebner]] +deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random"] +git-tree-sha1 = "5531337afa01d679c8ce97ff751291fd4760e962" +uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" +version = "0.2.8" + +[[GroupsCore]] +deps = ["Markdown", "Random"] +git-tree-sha1 = "9e1a5e9f3b81ad6a5c613d181664a0efc6fe6dd7" +uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" +version = "0.4.0" + [[HTTP]] -deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "c6a1fff2fd4b1da29d3dccaffb1e1001244d844e" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "ed47af35905b7cc8f1a522ca684b35a212269bd8" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.12" +version = "1.2.0" + +[[HarfBuzz_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] +git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" +version = "2.8.1+1" + +[[HostCPUFeatures]] +deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] +git-tree-sha1 = "b7b88a4716ac33fe31d6556c02fc60017594343c" +uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" +version = "0.1.8" [[Hwloc]] deps = ["Hwloc_jll"] @@ -538,20 +785,32 @@ version = "2.0.0" [[Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3395d4d4aeb3c9d31f5929d32760d8baeee88aaf" +git-tree-sha1 = "303d70c961317c4c20fafaf5dbe0e6d610c38542" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.5.0+0" +version = "2.7.1+0" + +[[HypergeometricFunctions]] +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] +git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" +version = "0.3.11" + +[[IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "95215cd0076a150ef46ff7928892bc341864c73c" +git-tree-sha1 = "af14a478780ca78d5eb9908b263023096c2b9d64" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.3" +version = "0.4.6" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[Inflate]] git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" @@ -559,10 +818,19 @@ uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.2" [[IniFile]] -deps = ["Test"] -git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8" +git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.0" +version = "0.5.1" + +[[InitialValues]] +git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" +uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" +version = "0.3.1" + +[[IntegerMathUtils]] +git-tree-sha1 = "f366daebdfb079fd1fe4e3d560f99a0c892e15bc" +uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" +version = "0.1.0" [[IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -576,26 +844,37 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "1470c80592cf1f0a35566ee5e93c5f8221ebc33a" +git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.3" +version = "0.13.6" [[IntervalSets]] -deps = ["Dates", "EllipsisNotation", "Statistics"] -git-tree-sha1 = "3cc368af3f110a767ac786560045dceddfc16758" +deps = ["Dates", "Random", "Statistics"] +git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.5.3" +version = "0.7.1" + +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.7" + +[[IrrationalConstants]] +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" +version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IterativeSolvers]] deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1a8c6237e78b714e901e406c096fc8a65528af7d" +git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.1" +version = "0.9.2" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -603,34 +882,46 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[JLD2]] -deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "4813826871754cf52607e76ad37acb36ccf52719" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "81b9477b49402b47fbe7f7ae0b252077f53e4a08" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.11" +version = "0.4.22" [[JLLWrappers]] deps = ["Preferences"] -git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" +git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.3.0" +version = "1.4.1" [[JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4" +git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.1" +version = "0.21.3" [[JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d735490ac75c5cb9f1b00d8b5509c11984dc6943" +git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.0+0" +version = "2.1.2+0" [[JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Pkg", "Tokenize"] -git-tree-sha1 = "9e7476b5e1dc749e525497eef53809893cb6c898" +git-tree-sha1 = "6f13ba89febc5c12f882902e1f5dcd11a8913fa5" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "0.14.8" +version = "1.0.7" + +[[JuliaVariables]] +deps = ["MLStyle", "NameResolution"] +git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" +uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" +version = "0.2.4" + +[[JumpProcesses]] +deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] +git-tree-sha1 = "4aa139750616fee7216ddcb30652357c60c3683e" +uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" +version = "9.0.1" [[Juno]] deps = ["Base64", "Logging", "Media", "Profile"] @@ -638,11 +929,29 @@ git-tree-sha1 = "07cb43290a840908a771552911a6274bc6c072c7" uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" version = "0.8.4" +[[KLU]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] +git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0" +uuid = "ef3ab10e-7fda-4108-b977-705223b18434" +version = "0.3.0" + [[KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" +git-tree-sha1 = "0a7ca818440ce8c70ebb5d42ac4ebf3205675f04" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.3" +version = "0.6.4" + +[[Krylov]] +deps = ["LinearAlgebra", "Printf", "SparseArrays"] +git-tree-sha1 = "a2327039e1c84615e22d662adb3df113caf44b70" +uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" +version = "0.8.3" + +[[KrylovKit]] +deps = ["LinearAlgebra", "Printf"] +git-tree-sha1 = "49b0c1dd5c292870577b8f58c51072bd558febb9" +uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" +version = "0.5.4" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -650,11 +959,23 @@ git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.1+0" +[[LERC_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "3.0.0+1" + [[LLVM]] -deps = ["CEnum", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "f57ac3fd2045b50d3db081663837ac5b4096947e" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] +git-tree-sha1 = "e7e9184b0bf0158ac4e4aa9daf00041b5909bf1a" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "3.9.0" +version = "4.14.0" + +[[LLVMExtra_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] +git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" +version = "0.0.16+0" [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -663,21 +984,21 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[LabelledArrays]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "StaticArrays"] -git-tree-sha1 = "248a199fa42ec62922225334131c9330e1dd72f6" +deps = ["ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "ChainRulesCore", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] +git-tree-sha1 = "b86aeff13358dfef82efd9f66a9d44705c9a4746" uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.6.1" +version = "1.11.1" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a4b12a1bd2ebade87891ab7e36fdbce582301a92" +git-tree-sha1 = "1a43be956d433b5d0321197150c2f94e16c0aaa0" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.6" +version = "0.15.16" [[LatinHypercubeSampling]] deps = ["Random", "StableRNGs", "StatsBase", "Test"] @@ -691,15 +1012,51 @@ git-tree-sha1 = "7f5b02258a3ca0221a6a9710b0a0a2e8fb4957fe" uuid = "73f95e8e-ec14-4e6a-8b18-0d2e271c4e55" version = "0.0.1" +[[LayoutPointers]] +deps = ["ArrayInterface", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] +git-tree-sha1 = "b67e749fb35530979839e7b4b606a97105fe4f1c" +uuid = "10f19ff3-798f-405d-979b-55457f8fc047" +version = "0.1.10" + +[[Lazy]] +deps = ["MacroTools"] +git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" +uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" +version = "0.15.1" + +[[LazyArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "d9a962fac652cc6b0224622b18199f0ed46d316a" +uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" +version = "0.22.11" + [[LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +[[LazyBandedMatrices]] +deps = ["ArrayLayouts", "BandedMatrices", "BlockArrays", "BlockBandedMatrices", "FillArrays", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "034d371419140f14a986ab7325d11f90f30b0c6d" +uuid = "d7e5e226-e90b-4449-9968-0f923699bf6f" +version = "0.7.17" + +[[LeastSquaresOptim]] +deps = ["FiniteDiff", "ForwardDiff", "LinearAlgebra", "Optim", "Printf", "SparseArrays", "Statistics", "SuiteSparse"] +git-tree-sha1 = "06ea4a7c438f434dc0dc8d03c72e61ee0bf3629d" +uuid = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" +version = "0.8.3" + [[LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] -git-tree-sha1 = "71be1eb5ad19cb4f61fa8c73395c0338fd092ae0" +git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" -version = "0.1.2" +version = "0.2.0" + +[[LevyArea]] +deps = ["LinearAlgebra", "Random", "SpecialFunctions"] +git-tree-sha1 = "56513a09b8e0ae6485f34401ea9e2f31357958ec" +uuid = "2d8b4e74-eb68-11e8-0fb9-d5eb67b50637" +version = "1.0.0" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -728,9 +1085,9 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [[Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "761a393aeccd6aa92ec3515e428c26bf99575b3b" +git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+0" +version = "3.2.2+1" [[Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] @@ -763,10 +1120,10 @@ uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" version = "2.35.0+0" [[Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "340e257aada13f95f98ee352d316c3bed37c8ab9" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.3.0+0" +version = "4.4.0+0" [[Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -787,56 +1144,102 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.1.1" [[LinearAlgebra]] -deps = ["Libdl"] +deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[LinearSolve]] +deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"] +git-tree-sha1 = "92cc95b66f1459d230af9e67089eeeea6c6b2ee9" +uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" +version = "1.23.0" + +[[Literate]] +deps = ["Base64", "IOCapture", "JSON", "REPL"] +git-tree-sha1 = "5b5ec7696d40868945c407f28a6672a230448b70" +uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +version = "2.13.4" + [[LogExpFunctions]] -deps = ["DocStringExtensions", "LinearAlgebra"] -git-tree-sha1 = "7bd5f6565d80b6bf753738d2bc40a5dfea072070" +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "7c88f63f9f0eb5929f15695af9a4d7d3ed278a91" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.2.5" +version = "0.3.16" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "dfeda1c1130990428720de0024d4516b1902ce98" +git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.7" +version = "0.4.9" [[LoopVectorization]] -deps = ["ArrayInterface", "DocStringExtensions", "IfElse", "LinearAlgebra", "OffsetArrays", "Polyester", "Requires", "SLEEFPirates", "Static", "StrideArraysCore", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "20316f08f70fae085ed90c7169ae318c036ee83b" +deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "adc9421494fd93e31a18a66e49d79615ad6b2efa" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.49" +version = "0.12.120" + +[[Lux]] +deps = ["Adapt", "CUDA", "ChainRulesCore", "ComponentArrays", "FillArrays", "Functors", "LinearAlgebra", "Markdown", "NNlib", "NNlibCUDA", "Optimisers", "Random", "Requires", "Setfield", "SparseArrays", "Statistics", "Zygote"] +git-tree-sha1 = "94dc5071b0a99368ec4588b90046016db86f702d" +uuid = "b2108857-7c20-44ae-9111-449ecde12c47" +version = "0.4.11" [[MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "c253236b0ed414624b083e6b72bfe891fbd2c7af" +git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2021.1.1+1" +version = "2022.0.0+0" + +[[MLStyle]] +git-tree-sha1 = "c4f433356372cc8838da59e3608be4b0c4c2c280" +uuid = "d8e11817-5142-5d16-987a-aa16d5891078" +version = "0.4.13" + +[[MLUtils]] +deps = ["ChainRulesCore", "DelimitedFiles", "FLoops", "FoldsThreads", "Random", "ShowCases", "Statistics", "StatsBase", "Transducers"] +git-tree-sha1 = "79cc42c45972b176339988fffdcb5360ef841bbc" +uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" +version = "0.2.9" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.6" +version = "0.5.9" + +[[ManualMemory]] +git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" +uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" +version = "0.1.8" [[Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[MatrixFactorizations]] +deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] +git-tree-sha1 = "2212d36f97e01347adb1460a6914e20f2feee853" +uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" +version = "0.9.1" + [[MbedTLS]] -deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"] -git-tree-sha1 = "1c38e51c3d08ef2278062ebceade0e46cefc96fe" +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] +git-tree-sha1 = "9f4f5a42de3300439cb8300236925670f844a555" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.0.3" +version = "1.1.1" [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" +[[Measurements]] +deps = ["Calculus", "LinearAlgebra", "Printf", "RecipesBase", "Requires"] +git-tree-sha1 = "dd8b9e6d7be9731fdaecc813acc5c3083496a251" +uuid = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" +version = "2.7.2" + [[Measures]] git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" @@ -848,20 +1251,38 @@ git-tree-sha1 = "75a54abd10709c01f1b86b84ec225d26e840ed58" uuid = "e89f7d12-3494-54d1-8411-f7d8b9ae1f27" version = "0.5.0" +[[Memoize]] +deps = ["MacroTools"] +git-tree-sha1 = "2b1dfcba103de714d31c033b5dacc2e4a12c7caa" +uuid = "c03570c3-d221-55d1-a50c-7939bbd78826" +version = "0.4.4" + +[[Metatheory]] +deps = ["AutoHashEquals", "DataStructures", "Dates", "DocStringExtensions", "Parameters", "Reexport", "TermInterface", "ThreadsX", "TimerOutputs"] +git-tree-sha1 = "a160e323d3684889e6026914576f1f4288de131d" +uuid = "e9d8d322-4543-424a-9be4-0cc815abe26c" +version = "1.3.4" + +[[MicroCollections]] +deps = ["BangBang", "InitialValues", "Setfield"] +git-tree-sha1 = "6bb7786e4f24d44b4e29df03c69add1b63d88f01" +uuid = "128add7d-3638-4c79-886c-908ea0c25c34" +version = "0.1.2" + [[Missings]] deps = ["DataAPI"] -git-tree-sha1 = "4ea90bd5d3985ae1f9a908bd4500ae88921c5ce7" +git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.0" +version = "1.0.2" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqJump", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "IfElse", "JuliaFormatter", "LabelledArrays", "Latexify", "Libdl", "LightGraphs", "LinearAlgebra", "MacroTools", "NaNMath", "NonlinearSolve", "RecursiveArrayTools", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SafeTestsets", "SciMLBase", "Serialization", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] -git-tree-sha1 = "7344cc0ba1e2c4933f9b2545b8860483a9acf0d4" +deps = ["AbstractTrees", "ArrayInterfaceCore", "Combinatorics", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MacroTools", "NaNMath", "NonlinearSolve", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] +git-tree-sha1 = "98919c7f37fee67d7f625f8c453a85673706ea89" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "5.21.0" +version = "8.18.1" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" @@ -872,22 +1293,22 @@ uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.2" [[MultivariatePolynomials]] -deps = ["DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "db4718c1b40e0b0ff739159c7230d5266bbfc7db" +deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] +git-tree-sha1 = "393fc4d82a73c6fe0e2963dd7c882b09257be537" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.3.17" +version = "0.4.6" [[MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "3927848ccebcc165952dc0d9ac9aa274a87bfe01" +git-tree-sha1 = "4e675d6e9ec02061800d6cfb695812becbd03cdf" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "0.2.20" +version = "1.0.4" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50608f411a1e178e0129eab4110bd56efd08816f" +git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.0" +version = "7.8.2" [[NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -896,30 +1317,36 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" [[NNlib]] -deps = ["Adapt", "ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "7e6f31cfa39b1ff1c541cc8580b14b0ff4ba22d0" +deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] +git-tree-sha1 = "415108fd88d6f55cedf7ee940c7d4b01fad85421" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.23" +version = "0.8.9" [[NNlibCUDA]] -deps = ["CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "5c970b9fd6098e5f04349b4d1a43fdd3e69c9e97" +deps = ["Adapt", "CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] +git-tree-sha1 = "4429261364c5ea5b7308aecaa10e803ace101631" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.1.6" +version = "0.2.4" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = 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"e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.10+0" +version = "1.1.17+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -952,10 +1387,34 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[Optim]] -deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d34366a3abc25c41f88820762ef7dfdfe9306711" +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "7351d1daa3dad1bcf67c79d1ba34dd3f6136c9aa" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.3.0" +version = "1.7.1" + +[[Optimisers]] +deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "62844c5525c3f13b3107aa2c25a06208ecadde88" +uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" +version = "0.2.8" + +[[Optimization]] +deps = ["ArrayInterfaceCore", "ConsoleProgressMonitor", "DiffResults", "DocStringExtensions", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "34e947f0cdb8172f25533279d6abc28d03b29584" +uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +version = "3.8.0" + +[[OptimizationOptimJL]] +deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] +git-tree-sha1 = "76ac41f9e82ba98a600d8a380532adef76b27e15" +uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" +version = "0.1.2" + +[[OptimizationOptimisers]] +deps = ["Optimisers", "Optimization", "Printf", "ProgressLogging", "Reexport"] +git-tree-sha1 = "e2f152fc4adc9a634ca6ec00de2f2500d8642789" +uuid = "42dfb2eb-d2b4-4451-abcd-913932933ac1" +version = "0.1.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -969,10 +1428,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" [[OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "Polyester", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "f865c198eb4041535c9d27e0835c5b59cdb759d4" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "c3b30b0c3ec02849cd30001e3de3f63e5842bbfd" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.59.2" +version = "6.19.2" [[PCRE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -982,21 +1441,21 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.1" +version = "0.11.16" [[Parameters]] deps = ["OrderedCollections", "UnPack"] -git-tree-sha1 = "2276ac65f1e236e0a6ea70baff3f62ad4c625345" +git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" -version = "0.12.2" +version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc" +git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" uuid = 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"GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "67db176835858a8e51be8a027e97665f95b4a38b" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "0a0da27969e8b6b2ee67c112dcf7001a659049a0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.16.8" +version = "1.31.4" [[PoissonRandom]] -deps = ["Random", "Statistics", "Test"] -git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850" +deps = ["Random"] +git-tree-sha1 = "9ac1bb7c15c39620685a3a7babc0651f5c64c35b" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.0" +version = "0.4.1" [[Polyester]] -deps = ["ArrayInterface", "IfElse", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities", "VectorizationBase"] -git-tree-sha1 = "04a03d3f8ae906f4196b9085ed51506c4b466340" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "94e20822bd7427b1b1b843a3980003f5d5e8696b" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.3.1" +version = "0.6.14" + +[[PolyesterWeave]] +deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] +git-tree-sha1 = "cf82af4e114b0da31c4896aef6c5b8be3fe0916d" +uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" +version = "0.1.7" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1044,11 +1509,28 @@ 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+version = "0.5.0" + +[[ThreadsX]] +deps = ["ArgCheck", "BangBang", "ConstructionBase", "InitialValues", "MicroCollections", "Referenceables", "Setfield", "SplittablesBase", "Transducers"] +git-tree-sha1 = "d223de97c948636a4f34d1f84d92fd7602dc555b" +uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" +version = "0.1.10" [[TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "209a8326c4f955e2442c07b56029e88bb48299c7" +git-tree-sha1 = "464d64b2510a25e6efe410e7edab14fffdc333df" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.12" +version = "0.5.20" [[Tokenize]] -git-tree-sha1 = "37018506dc445ad7db288442fbb846105f26c43f" +git-tree-sha1 = "2b3af135d85d7e70b863540160208fa612e736b9" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.17" +version = "0.5.24" [[Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "bf4adf36062afc921f251af4db58f06235504eff" +deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "0874c1b5de1b5529b776cfeca3ec0acfada97b1b" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.16" +version = "0.2.20" [[TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" +git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.5" +version = "0.9.6" + +[[Transducers]] +deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] +git-tree-sha1 = "c76399a3bbe6f5a88faa33c8f8a65aa631d95013" +uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" +version = "0.4.73" [[Trapz]] -git-tree-sha1 = "aff96deaaa38e3b52a5af1dd3da376d49bf6ec9a" +git-tree-sha1 = "79eb0ed763084a3e7de81fe1838379ac6a23b6a0" uuid = "592b5752-818d-11e9-1e9a-2b8ca4a44cd1" -version = "2.0.2" +version = "2.0.3" [[TreeViews]] deps = ["Test"] @@ -1409,10 +1982,16 @@ git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" version = "0.3.0" +[[TriangularSolve]] +deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] +git-tree-sha1 = "caf797b6fccbc0d080c44b4cb2319faf78c9d058" +uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" +version = "0.1.12" + [[URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.0" [[UUIDs]] deps = ["Random", "SHA"] @@ -1423,26 +2002,42 @@ git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" version = "1.0.2" +[[Underscores]] +git-tree-sha1 = "6e6de5a5e7116dcff8effc99f6f55230c61f6862" +uuid = "d9a01c3f-67ce-4d8c-9b55-35f6e4050bb1" +version = "3.0.0" + [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +[[UnicodeFun]] +deps = ["REPL"] +git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" +uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +version = "0.4.1" + [[Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "b3682a0559219355f1e3c8024e9f97adce2d4623" +git-tree-sha1 = "b649200e887a487468b71821e2644382699f1b0f" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.8.0" +version = "1.11.0" + +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" [[VectorizationBase]] -deps = ["ArrayInterface", "Hwloc", "IfElse", "Libdl", "LinearAlgebra", "Static"] -git-tree-sha1 = "0ba060e248edfacacafd764926cdd6de51af1343" +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] +git-tree-sha1 = "81d19dae338dd4cf3ecd6331fb4763a1002f9580" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.20.19" +version = "0.21.43" [[VertexSafeGraphs]] -deps = ["LightGraphs"] -git-tree-sha1 = "b9b450c99a3ca1cc1c6836f560d8d887bcbe356e" +deps = ["Graphs"] +git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" -version = "0.1.2" +version = "0.2.0" [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] @@ -1451,22 +2046,22 @@ uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" version = "1.19.0+0" [[Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"] -git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.18.0+4" +version = "1.25.0+0" [[WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "59e2ad8fd1591ea019a5259bd012d7aee15f995c" +git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.3" +version = "0.5.5" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" +git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.12+0" +version = "2.9.14+0" [[XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1602,9 +2197,9 @@ version = "1.4.0+3" [[ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] -git-tree-sha1 = "c3a5637e27e914a7a445b8d0ad063d701931e9f7" +git-tree-sha1 = "ef4f23ffde3ee95114b461dc667ea4e6906874b2" uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" -version = "0.9.3" +version = "0.10.0" [[Zlib_jll]] deps = ["Libdl"] @@ -1612,33 +2207,43 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" [[Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" +git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.0+0" +version = "1.5.2+0" [[Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "531474afbc343c3c7cb9b71c2771813c6defd550" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "3cfdb31b517eec4173584fba2b1aa65daad46e09" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.14" +version = "0.6.41" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" + +[[libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.4.0+0" [[libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.14.0+4" +version = "0.15.1+0" + +[[libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "0.1.6+4" +version = "2.0.2+0" [[libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1648,9 +2253,9 @@ version = "1.6.38+0" [[libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" +git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+0" +version = "1.3.7+1" [[nghttp2_jll]] deps = ["Artifacts", "Libdl"] @@ -1662,15 +2267,15 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" [[x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" [[xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] diff --git a/LotkaVolterra/plots/Scenario_1__losses.pdf 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+6,8 @@ using Pkg; Pkg.activate("."); Pkg.instantiate() using OrdinaryDiffEq using ModelingToolkit using DataDrivenDiffEq -using LinearAlgebra, Optim -using Optimization, OptimizationFlux, OptimizationOptimJL #OptimizationFlux for ADAM and OptimizationOptimJL for BFGS +using LinearAlgebra, ComponentArrays +using Optimization, OptimizationOptimisers, OptimizationOptimJL #OptimizationFlux for ADAM and OptimizationOptimJL for BFGS using DiffEqSensitivity using Lux using Plots @@ -34,19 +34,22 @@ function lotka!(du, u, p, t) end # Define the experimental parameter -tspan = (0.0f0,3.0f0) -u0 = Float32[0.44249296,4.6280594] -p_ = Float32[1.3, 0.9, 0.8, 1.8] +tspan = (0.0,3.0) +u0 = [0.44249296,4.6280594] +p_ = [1.3, 0.9, 0.8, 1.8] prob = ODEProblem(lotka!, u0,tspan, p_) solution = solve(prob, Vern7(), abstol=1e-12, reltol=1e-12, saveat = 0.1) # Ideal data X = Array(solution) t = solution.t +DX = Array(solution(solution.t, Val{1})) + +full_problem = DataDrivenProblem(X, t = t, DX = DX) # Add noise in terms of the mean x̄ = mean(X, dims = 2) -noise_magnitude = Float32(5e-3) +noise_magnitude = 5e-3 Xₙ = X .+ (noise_magnitude*x̄) .* randn(eltype(X), size(X)) plot(solution, alpha = 0.75, color = :black, label = ["True Data" nothing]) @@ -77,8 +80,8 @@ prob_nn = ODEProblem(nn_dynamics!,Xₙ[:, 1], tspan, p) ## Function to train the network # Define a predictor function predict(θ, X = Xₙ[:,1], T = t) - Array(solve(prob_nn, Vern7(), u0 = X, p=θ, - saveat = T, + _prob = remake(prob_nn, u0 = X, tspan = (T[1], T[end]), p = θ) + Array(solve(_prob, Vern7(), saveat = T, abstol=1e-6, reltol=1e-6, sensealg = ForwardDiffSensitivity() )) @@ -91,7 +94,7 @@ function loss(θ) end # Container to track the losses -losses = Float32[] +losses = Float64[] callback = function (p, l) push!(losses, l) @@ -107,7 +110,7 @@ end # favourable starting positing for BFGS adtype = Optimization.AutoZygote() optf = Optimization.OptimizationFunction((x,p)->loss(x), adtype) -optprob = Optimization.OptimizationProblem(optf, Lux.ComponentArray(p)) +optprob = Optimization.OptimizationProblem(optf, ComponentVector{Float64}(p)) res1 = Optimization.solve(optprob, ADAM(0.1), callback=callback, maxiters = 200) println("Training loss after $(length(losses)) iterations: $(losses[end])") # Train with BFGS @@ -156,18 +159,17 @@ b = [polynomial_basis(u, 5); sin.(u)] basis = Basis(b,u); # Create the thresholds which should be used in the search process -λ = Float32.(exp10.(-7:0.1:0)) +λ = exp10.(-3:0.01:5) # Create an optimizer for the SINDy problem opt = STLSQ(λ) # Define different problems for the recovery -full_problem = ContinuousDataDrivenProblem(X, t) -ideal_problem = ContinuousDataDrivenProblem(X̂, ts, DX = Ȳ) -nn_problem = ContinuousDataDrivenProblem(X̂, ts, DX = Ŷ) +ideal_problem = DirectDataDrivenProblem(X̂, Ȳ) +nn_problem = DirectDataDrivenProblem(X̂, Ŷ) # Test on ideal derivative data for unknown function ( not available ) println("Sparse regression") full_res = solve(full_problem, basis, opt, maxiter = 10000, progress = true) ideal_res = solve(ideal_problem, basis, opt, maxiter = 10000, progress = true) -nn_res = solve(nn_problem, basis, opt, maxiter = 10000, progress = true) +nn_res = solve(nn_problem, basis, opt, maxiter = 10000, progress = true, sampler = DataSampler(Batcher(n = 4, shuffle = true))) # Store the results results = [full_res; ideal_res; nn_res] # Show the results @@ -195,7 +197,7 @@ plot!(estimate) ## Simulation # Look at long term prediction -t_long = (0.0f0, 50.0f0) +t_long = (0.0, 50.0) estimation_prob = ODEProblem(recovered_dynamics!, u0, t_long, parameters(nn_res)) estimate_long = solve(estimation_prob, Tsit5(), saveat = 0.1) # Using higher tolerances here results in exit of julia plot(estimate_long) diff --git a/LotkaVolterra/scenario_2.jl b/LotkaVolterra/scenario_2.jl index 4780d2e..eb764d7 100644 --- a/LotkaVolterra/scenario_2.jl +++ b/LotkaVolterra/scenario_2.jl @@ -1,3 +1,4 @@ + ## Environment and packages cd(@__DIR__) using Pkg; Pkg.activate("."); Pkg.instantiate() @@ -5,14 +6,18 @@ using Pkg; Pkg.activate("."); Pkg.instantiate() using OrdinaryDiffEq using ModelingToolkit using DataDrivenDiffEq -using LinearAlgebra, Optim -using DiffEqFlux, Flux +using LinearAlgebra +using Optimization, OptimizationOptimisers, OptimizationOptimJL #OptimizationFlux for ADAM and OptimizationOptimJL for BFGS +using DiffEqSensitivity +using Lux +using ComponentArrays using Plots gr() using JLD2, FileIO using Statistics # Set a random seed for reproduceable behaviour using Random +rng = Random.default_rng() Random.seed!(2345) #### NOTE @@ -31,30 +36,31 @@ function lotka!(du, u, p, t) end # Define the experimental parameter -tspan = (0.0f0,6.0f0) -u0 = Float32[0.44249296,4.6280594] -p_ = Float32[1.3, 0.9, 0.8, 1.8] +tspan = (0.0,6.0) +u0 = [0.44249296,4.6280594] +p_ = [1.3, 0.9, 0.8, 1.8] prob = ODEProblem(lotka!, u0,tspan, p_) solution = solve(prob, Vern7(), abstol=1e-6, reltol=1e-6, saveat = 0.1) -scatter(solution, alpha = 0.25) -plot!(solution, alpha = 0.5) - # Ideal data X = Array(solution) t = solution.t +DX = Array(solution(solution.t, Val{1})) + +full_problem = DataDrivenProblem(X, t = t, DX = DX) + # Add noise in terms of the mean x̄ = mean(X, dims = 2) -noise_magnitude = Float32(1e-2) +noise_magnitude = 5e-3 Xₙ = X .+ (noise_magnitude*x̄) .* randn(eltype(X), size(X)) # Subsample the data in y # We assume we have only 5 measurements in y, evenly distributed -ty = collect(t[1]:Float32(6/5):t[end]) +ty = collect(t[1]:Float64(6/5):t[end]) # Create datasets for the different measurements round(Int64, mean(diff(ty))/mean(diff(t))) -XS = zeros(eltype(X), length(ty)-1, floor(Int64, mean(diff(ty))/mean(diff(t)))+1) # All x data -TS = zeros(eltype(t), length(ty)-1, floor(Int64, mean(diff(ty))/mean(diff(t)))+1) # Time data +XS = zeros(eltype(X), length(ty)-1, ceil(Int64, mean(diff(ty))/mean(diff(t)))+1) # All x data +TS = zeros(eltype(t), length(ty)-1, ceil(Int64, mean(diff(ty))/mean(diff(t)))+1) # Time data YS = zeros(eltype(X), length(ty)-1, 2) # Just two measurements in y for i in 1:length(ty)-1 @@ -64,26 +70,28 @@ for i in 1:length(ty)-1 YS[i, :] = [Xₙ[2, t .== ty[i]]'; Xₙ[2, t .== ty[i+1]]] end -XS - scatter!(t, transpose(Xₙ)) ## Define the network # Gaussian RBF as activation rbf(x) = exp.(-(x.^2)) -# Define the network 2->5->5->5->2 -U = FastChain( - FastDense(2,5,rbf), FastDense(5,5, rbf), FastDense(5,5, rbf), FastDense(5,2) +# Multilayer FeedForward +U = Lux.Chain( + Lux.Dense(2,5,rbf), Lux.Dense(5,5, rbf), Lux.Dense(5,5, rbf), Lux.Dense(5,2) ) -# Get the initial parameters, first is linear decay -p = [rand(Float32); initial_params(U)] +# Get the initial parameters and state variables of the model +p_nn, st_nn = Lux.setup(rng, U) + +# Merge the parameters +p = (;δ = rand(rng), ude = p_nn) +p = ComponentVector{Float64}(p) # Define the hybrid model function ude_dynamics!(du,u, p, t, p_true) - û = U(u, p[2:end]) # Network prediction + û = U(u, p.ude, st_nn)[1] # Network prediction du[1] = p_true[1]*u[1] + û[1] # We assume a linear decay rate for the predator - du[2] = -p[1]*u[2] + û[2] + du[2] = -p.δ*u[2] + û[2] end # Closure with the known parameter @@ -94,8 +102,8 @@ prob_nn = ODEProblem(nn_dynamics!,Xₙ[:, 1], tspan, p) ## Function to train the network # Define a predictor function predict(θ, X = Xₙ[:,1], T = t) - Array(solve(prob_nn, Vern7(), u0 = X, p=θ, - tspan = (T[1], T[end]), saveat = T, + _prob = remake(prob_nn, u0 = X, tspan = (T[1], T[end]), p = θ) + Array(solve(_prob, Vern7(), saveat = T, abstol=1e-6, reltol=1e-6, sensealg = ForwardDiffSensitivity() )) @@ -116,32 +124,34 @@ function loss(θ) end # Container to track the losses -losses = Float32[] - -# Callback to show the loss during training -callback(θ,l) = begin - push!(losses, l) - if length(losses)%50==0 - println("Current loss after $(length(losses)) iterations: $(losses[end])") - end - false +losses = Float64[] + +callback = function (p, l) + push!(losses, l) + if length(losses)%50==0 + println("Current loss after $(length(losses)) iterations: $(losses[end])") + end + return false end ## Training # First train with ADAM for better convergence -> move the parameters into a # favourable starting positing for BFGS -res1 = DiffEqFlux.sciml_train(loss, p, ADAM(0.1f0), cb=callback, maxiters = 300) +adtype = Optimization.AutoZygote() +optf = Optimization.OptimizationFunction((x,p)->loss(x), adtype) +optprob = Optimization.OptimizationProblem(optf, p) +res1 = Optimization.solve(optprob, ADAM(0.1), callback=callback, maxiters = 200) println("Training loss after $(length(losses)) iterations: $(losses[end])") # Train with BFGS -res2 = DiffEqFlux.sciml_train(loss, res1.minimizer, BFGS(initial_stepnorm=0.01f0), cb=callback, maxiters = 10000, g_tol = 1e-10) +optprob2 = Optimization.OptimizationProblem(optf, res1.minimizer) +res2 = Optimization.solve(optprob2, Optim.BFGS(initial_stepnorm=0.01), callback=callback, maxiters = 10000) println("Final training loss after $(length(losses)) iterations: $(losses[end])") # Plot the losses -pl_losses = plot(1:300, losses[1:300], yaxis = :log10, xaxis = :log10, xlabel = "Iterations", ylabel = "Loss", label = "ADAM", color = :blue) -plot!(301:length(losses), losses[301:end], yaxis = :log10, xaxis = :log10, xlabel = "Iterations", ylabel = "Loss", label = "BFGS", color = :red) +pl_losses = plot(1:200, losses[1:200], yaxis = :log10, xaxis = :log10, xlabel = "Iterations", ylabel = "Loss", label = "ADAM", color = :blue) +plot!(201:length(losses), losses[201:end], yaxis = :log10, xaxis = :log10, xlabel = "Iterations", ylabel = "Loss", label = "BFGS", color = :red) savefig(pl_losses, joinpath(pwd(), "plots", "$(svname)_losses.pdf")) - # Rename the best candidate p_trained = res2.minimizer @@ -160,7 +170,7 @@ savefig(pl_trajectory, joinpath(pwd(), "plots", "$(svname)_trajectory_reconstruc # Ideal unknown interactions of the predictor Ȳ = [-p_[2]*(X̂[1,:].*X̂[2,:])';p_[3]*(X̂[1,:].*X̂[2,:])'] # Neural network guess -Ŷ = U(X̂,p_trained[2:end]) +Ŷ = U(X̂,p_trained.ude, st_nn)[1] pl_reconstruction = plot(ts, transpose(Ŷ), xlabel = "t", ylabel ="U(x,y)", color = :red, label = ["UDE Approximation" nothing]) plot!(ts, transpose(Ȳ), color = :black, label = ["True Interaction" nothing], legend = :topleft) @@ -182,21 +192,22 @@ b = [polynomial_basis(u, 5); sin.(u)] basis = Basis(b, u) # Create the thresholds which should be used in the search process -λ = Float32.(exp10.(-3:0.01:5)) +λ = exp10.(-3:0.01:5) # Create an optimizer for the SINDy problem opt = STLSQ(λ) # Target function to choose the results from; x = L0 of coefficients and L2-Error of the model g(x) = x[1] <= 1 ? Inf : 2*x[1]-2*log(x[2]) # Define different problems for the recovery -full_problem = ContinuousDataDrivenProblem(solution) -ideal_problem = ContinuousDataDrivenProblem(X̂, ts, DX = Ȳ) -nn_problem = ContinuousDataDrivenProblem(X̂, ts, DX = Ŷ) +ideal_problem = DirectDataDrivenProblem(X̂, Ȳ) +nn_problem = DirectDataDrivenProblem(X̂,Ŷ) + # Test on ideal derivative data for unknown function ( not available ) println("Sparse regression") full_res = solve(full_problem, basis, opt, maxiter = 10000, progress = true) ideal_res = solve(ideal_problem, basis, opt, maxiter = 10000, progress = true) nn_res = solve(nn_problem, basis, opt, maxiter = 10000, progress = true) + # Store the results results = [full_res; ideal_res; nn_res] # Show the results @@ -226,7 +237,7 @@ plot!(estimate) ## Simulation # Look at long term prediction -t_long = (0.0f0, 50.0f0) +t_long = (0.0, 50.0) estimation_prob = ODEProblem(estimated_dynamics!, u0, t_long, parameters(nn_res)) estimate_long = solve(estimation_prob, Tsit5(), saveat = 0.1) # Using higher tolerances here results in exit of julia plot(estimate_long) diff --git a/LotkaVolterra/scenario_3.jl b/LotkaVolterra/scenario_3.jl index 8945db7..9290888 100644 --- a/LotkaVolterra/scenario_3.jl +++ b/LotkaVolterra/scenario_3.jl @@ -5,14 +5,17 @@ using Pkg; Pkg.activate("."); Pkg.instantiate() using OrdinaryDiffEq using ModelingToolkit using DataDrivenDiffEq -using LinearAlgebra, Optim -using DiffEqFlux, Flux +using LinearAlgebra, ComponentArrays +using Optimization, OptimizationOptimisers, OptimizationOptimJL #OptimizationFlux for ADAM and OptimizationOptimJL for BFGS +using DiffEqSensitivity +using Lux using Plots gr() using JLD2, FileIO using Statistics # Set a random seed for reproduceable behaviour using Random +rng = Random.default_rng() Random.seed!(1235) # Create a name for saving ( basically a prefix ) @@ -59,7 +62,7 @@ t = solution.t # Add noise in terms of the mean x̄ = mean(X, dims = 2) -noise_magnitude = Float32(2.5e-2) +noise_magnitude = Float32(5e-3) Xₙ = X .+ (noise_magnitude*x̄) .* randn(eltype(X), size(X)) @@ -77,41 +80,53 @@ savefig(pl_initial_data, joinpath(pwd(), "plots","$(svname)full_data_$(noise_mag rbf(x) = exp.(-(x.^2)) # Create the network to recover the reaction -rx_nn = FastChain( - FastDense(1, 5, rbf), - FastDense(5, 5, rbf), - FastDense(5, 5, rbf), - FastDense(5, 1) +rx_nn = Lux.Chain( + Lux.Dense(1, 5, rbf), + Lux.Dense(5, 5, rbf), + Lux.Dense(5, 5, rbf), + Lux.Dense(5, 1) ) #initialize D0 close to D/dx^2 D0 = Float32[6.5] -p1s = initial_params(rx_nn) + +# Get the initial parameters and state variables of the model +p_nn, st_nn = Lux.setup(rng, rx_nn) p2s = zeros(Float32, 4) -p = [p1s;p2s;D0] +p = ComponentVector(; + ude = p_nn, + p2s = p2s, + D0 = D0 +) + function nn_ode(u,p,t) # This is the dircetional derivative - u_cnn_1 = [p[end-4] * u[end] + p[end-3] * u[1] + p[end-2] * u[2]] - u_cnn = [p[end-4] * u[i-1] + p[end-3] * u[i] + p[end-2] * u[i+1] for i in 2:size(u, 1)-1] - u_cnn_end = [p[end-4] * u[end-1] + p[end-3] * u[end] + p[end-2] * u[1]] - [rx_nn([ui], p[1:length(p1s)])[1] for ui in u] + p[end] * vcat(u_cnn_1, u_cnn, u_cnn_end) + ps_ = p.p2s + u_cnn_1 = [ps_[end-3] * u[end] + ps_[end-2] * u[1] + ps_[end-1] * u[2]] + u_cnn = [ps_[end-3] * u[i-1] + ps_[end-2] * u[i] + ps_[end-1] * u[i+1] for i in 2:size(u, 1)-1] + u_cnn_end = [ps_[end-3] * u[end-1] + ps_[end-2] * u[end] + ps_[end-1] * u[1]] + + reduce(vcat, map(u) do ui + rx_nn([ui], p.ude, st_nn)[1] + end) + p.D0 .* vcat(u_cnn_1, u_cnn, u_cnn_end) end prob_nn = ODEProblem(nn_ode, Xₙ[:, 1], (t[1], t[end]), p) - +nn_ode(rho_ic(Delta), p, 0.0) ## Necessary functions function predict_pde(θ, X = Xₙ[:, 1], T = t) - # No ReverseDiff if using Flux - Array(solve(prob_nn, Vern7(), - u0 = X, p = θ, tspan = (T[1], T[end]), saveat=T, - sensealg=ForwardDiffSensitivity(convert_tspan = false)#, reltol = 1e-4, abstol = 1e-4 - )) + _prob = remake(prob_nn, u0 = X, tspan = (T[1], T[end]), p = θ) + Array(solve(_prob, Vern7(), saveat = T, + sensealg = ForwardDiffSensitivity(convert_tspan = false) + )) end +predict_pde(p) + #match data and force the weights of the CNN to add up to zero function objective_pde(p) pred = predict_pde(p) @@ -130,18 +145,24 @@ callback(θ,l) = begin false end -## Train the model -# First train with ADAM -res1 = DiffEqFlux.sciml_train(objective_pde, p, ADAM(0.1f0), cb=callback, maxiters = 40) +# First train with ADAM for better convergence -> move the parameters into a +# favourable starting positing for BFGS +adtype = Optimization.AutoZygote() +optf = Optimization.OptimizationFunction((x,p)->objective_pde(x), adtype) +optprob = Optimization.OptimizationProblem(optf, p) +res1 = Optimization.solve(optprob, ADAM(0.1), callback=callback, maxiters = 10) +println("Training loss after $(length(losses)) iterations: $(losses[end])") # Train with BFGS -res2 = DiffEqFlux.sciml_train(objective_pde, res1.minimizer, BFGS(initial_stepnorm=0.1f0), cb=callback, maxiters = 10000) +optprob2 = Optimization.OptimizationProblem(optf, res1.minimizer) +res2 = Optimization.solve(optprob2, Optim.BFGS(initial_stepnorm=0.001), callback=callback, maxiters = 100) +println("Final training loss after $(length(losses)) iterations: $(losses[end])") + p_trained = res2.minimizer ## Data evaluation -> we subsample here! -tsample = t[1]:1.0*mean(diff(t)):t[end] -X̂ = predict_pde(p_trained, Xₙ[:,1], tsample) +X̂ = predict_pde(p_trained) # Trained on noisy data vs real solution -pl_trajectory = plot(tsample, transpose(X̂), xlabel = "t", ylabel ="rho(x,t)", color = :red, +pl_trajectory = plot(t, transpose(X̂), xlabel = "t", ylabel ="rho(x,t)", color = :red, label = ["UDE Approximation" [nothing for i in 1:25]...]) scatter!(t, transpose(Xₙ), color = :black, label = ["Measurements" [nothing for i in 1:25]...], legend = :bottomright) savefig(pl_trajectory, joinpath(pwd(), "plots", "$(svname)_trajectory_reconstruction.pdf")) @@ -151,7 +172,7 @@ savefig(pl_trajectory, joinpath(pwd(), "plots", "$(svname)_trajectory_reconstruc R̂ = similar(X̂) R̄ = similar(X̂) for i in 1:size(X̂, 1), j in 1:size(X̂, 2) - R̂[i,j] = rx_nn(X̂[i,j], p_trained[1:length(p1s)])[1] + R̂[i,j] = rx_nn([X̂[i,j]], p_trained.ude, st_nn)[1][1] R̄[i,j] = reaction(X̂[i,j]) end @@ -175,7 +196,7 @@ Rs = Matrix(vcat(eachrow(R̂[1:end, :])...)') # Technically this is cheating until a general DataDrivenProblem is defined properly. # we work with the continuous form -nn_prob = ContinuousDataDrivenProblem(Xs, zeros(Float32, size(Xs, 2)), DX = Rs) +nn_prob = DirectDataDrivenProblem(Xs, Rs) λs = Float32.(exp10.(-3:0.01:5)) opt = STLSQ(λs) diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 0000000..6d5c0ad --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,6 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.7.3" +manifest_format = "2.0" + +[deps]