diff --git a/calcium_homeo.jl b/calcium_homeo.jl index 89a7019..08c3ca0 100644 --- a/calcium_homeo.jl +++ b/calcium_homeo.jl @@ -4,18 +4,8 @@ using Markdown using InteractiveUtils -# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). -macro bind(def, element) - quote - local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end - local el = $(esc(element)) - global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) - el - end -end - # ╔═╡ bf5d2811-82db-4068-859d-0b2e6c6366e5 -using PlutoUI, MinimallyDisruptiveCurves, Statistics, ModelingToolkit, Ipopt, Plots, LinearAlgebra, OrdinaryDiffEq, PlutoUI, JLD2, JuMP, ForwardDiff +using NeuronBuilder, PlutoUI, MinimallyDisruptiveCurves, Statistics, ModelingToolkit, Ipopt, Plots, LinearAlgebra, OrdinaryDiffEq, JLD2, JuMP, ForwardDiff # ╔═╡ e58a9316-ab83-11ec-277d-493810607706 md""" @@ -78,6 +68,8 @@ fast sodium, Na ; delayed rectifier potassium, Kd ; fast transient and slow calc begin tspan = (0.0, 5000.0) p0 = [700.0, 4.0, 2.0, 50.0, 40.0, 70.0, 0.03] + const Cm = 10 #specific capacitance in nF/mm^2 + const Area = 0.0628 #mm^2 end # ╔═╡ a933890e-ca6d-4d00-9f30-cd5e56d0e531 @@ -110,7 +102,7 @@ function neuron(g_params) neur = b() #no synapses - prob = ODEProblem(neur.sys, [], (0.0, 5000.0), []) + prob = ODEProblem(neur, [], (0.0, 5000.0), []) sol = solve(prob, AutoTsit5(Rosenbrock23()), save_idxs=[1, 2], abstol=1e-9, reltol=1e-9) @@ -120,7 +112,7 @@ end # ╔═╡ b8ae9d21-1c1f-48fd-8ec2-a976c7064532 begin _, sol = neuron(p0) - plot(sol) + plot(sol, xlims=(3000,5000)) end # ╔═╡ e3edc18b-7771-41a7-a4cd-b255be08e3e2 @@ -310,23 +302,23 @@ You could also disable/enable that cell. Run a single curve by selecting a particular direction. """ -# ╔═╡ d7233d7e-2cd1-4119-813a-c8814c947f11 -@bind i html""" """ +# ╔═╡ 75d2bff9-e7b2-464d-bec4-37a34a5dc442 +i = 1 # ╔═╡ c0292c71-7410-4ede-93f1-174a75fcd25d -#begin -# mdc = curve(dirs[i], dist, C, θnew) -# save_object("mdc_$i.jld2", mdc) -#end +begin + mycurve = curve(dirs[i], dist, C, θnew) + save_object("mdc_$i.jld2", mycurve) +end # ╔═╡ 4dce4235-9971-43c9-ae89-54258d0c65dd md""" -#### You can save a curve as an abstract object using JLD2 and easily recover it later! -If after closing this notebook you want to opening a new session and load a curve, there's no need to generate it all over again, simply do : +You can save a curve as an abstract object using JLD2 and easily recover it later! +Simply do : """ # ╔═╡ c4b40826-8fc4-4a49-841c-08cae0a05d57 -mdc = load_object("calcium_homeo/mdc_1.jld2"); +#mdc = load_object("/mdc_1.jld2"); # ╔═╡ 4be2a848-5b18-49de-9e7f-38b661df159d @@ -436,18 +428,31 @@ function animate_it(mdc, name) end # ╔═╡ 1fb2caa4-bfc9-41ab-a183-34a5b1fca899 -#animate_it(mdc, "curve1") +animate_it(mycurve, "curve1") -# ╔═╡ cdc273c4-faee-41b0-bd88-404dbbfd6f35 +# ╔═╡ 56f3d76d-d8dd-4a3f-b3f1-63dfabe6eebf md""" -$(PlutoUI.LocalResource("calcium_homeo/curve1.gif")) +Note that the cost function stays well below 1 most of the time, wich means that the deviation from target calcium is << 10% (since $Ca_{tgt}$ is 10 $\mu M$). """ +# ╔═╡ e5dc02e9-005f-4736-8983-1db70c204c93 +function threeplts(mdc) + ps = ["gNa", "gCaS", "gCaT", "gKa", "gKCa", "gKd", "gH"] + cc = [C(el) for el in eachcol(trajectory(mdc))] + plt1 = plot(mdc; pnames=ps, what=:trajectory, title="log change in parameters", legendfontsize=6, fg_legend=:transparent, background_color_legend=nothing) + plt2 = plot(distances(mdc), cc, ylabel="cost", xlabel="distance", title="cost over curve", legend=false, ylims=(0, 2)) + plt3 = plot(mdc; pnames=ps, what=:final_changes) + plt = plot(plt1, plt2, plt3, layout=(3, 1), legendfontsize=6, fg_legend=:transparent) +end + +# ╔═╡ 20226001-560d-4131-bf8c-896f1a840534 +threeplts(mycurve) + # ╔═╡ 2b7d38bb-2264-43c0-89a3-cf3bc0757603 md""" ### 6. Scientific analysis -We analyse the first curve. Its initial direction involves only T-type and slow calcium conductances. +We analyse the precomputed curve shown in the gif below. Its initial direction involves only T-type and slow calcium conductances. - Slow calcium and T-type calcium, as well as calcium-activated potassium channels, are a source of ultraslow negative feedback to the membrane potential and therefore crucial for bursting. @@ -474,19 +479,6 @@ Around the starting point of the curve, see the interval (-0.3, 0.5), only CaS a """ -# ╔═╡ e5dc02e9-005f-4736-8983-1db70c204c93 -function threeplts(mdc) - ps = ["gNa", "gCaS", "gCaT", "gKa", "gKCa", "gKd", "gH"] - cc = [C(el) for el in eachcol(trajectory(mdc))] - plt1 = plot(mdc; pnames=ps, what=:trajectory, title="log change in parameters", legendfontsize=6, fg_legend=:transparent, background_color_legend=nothing) - plt2 = plot(distances(mdc), cc, ylabel="cost", xlabel="distance", title="cost over curve", legend=false, ylims=(0, 2)) - plt3 = plot(mdc; pnames=ps, what=:final_changes) - plt = plot(plt1, plt2, plt3, layout=(3, 1), legendfontsize=6, fg_legend=:transparent) -end - -# ╔═╡ 20226001-560d-4131-bf8c-896f1a840534 -threeplts(mdc) - # ╔═╡ 0b3c43cd-1099-47e9-aede-00a128f4904f md""" When the initial direction is no longer a good one, more conductances start to move. @@ -495,9 +487,12 @@ When the initial direction is no longer a good one, more conductances start to m - In the last portion of this curve, changes in conductances roughly preserve behavior and therefore average calcium too. +""" - -- Note that the cost function stays well below 1 most of the time, wich means that the deviation from target calcium is << 10% (since $Ca_{tgt}$ is 10 $\mu M$). +# ╔═╡ cdc273c4-faee-41b0-bd88-404dbbfd6f35 +#one of the pre-computed curves as an example +md""" +$(PlutoUI.LocalResource("calcium_homeo/curve1.gif")) """ # ╔═╡ 00000000-0000-0000-0000-000000000001 @@ -510,6 +505,7 @@ JuMP = "4076af6c-e467-56ae-b986-b466b2749572" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MinimallyDisruptiveCurves = "c6328df5-4af8-4637-a9e9-78ed74a2ae2b" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" +NeuronBuilder = "bdec0aff-bc35-4528-862d-7dacab2b11a0" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" @@ -517,13 +513,14 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] ForwardDiff = "~0.10.35" -Ipopt = "~1.3.0" +Ipopt = "~1.4.1" JLD2 = "~0.4.31" JuMP = "~1.11.1" MinimallyDisruptiveCurves = "~0.3.2" -ModelingToolkit = "~8.57.0" -OrdinaryDiffEq = "~6.52.0" -Plots = "~1.38.14" +ModelingToolkit = "~8.59.0" +NeuronBuilder = "~0.2.5" +OrdinaryDiffEq = "~6.53.0" +Plots = "~1.38.15" PlutoUI = "~0.7.51" """ @@ -531,9 +528,9 @@ PlutoUI = "~0.7.51" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.0" +julia_version = "1.8.2" manifest_format = "2.0" -project_hash = "94e21ea9adad46efa7173753f9cfd8863380bec2" +project_hash = "4380ef94604f5768e3182b321c2cece9278efe93" [[deps.ADTypes]] git-tree-sha1 = "dcfdf328328f2645531c4ddebf841228aef74130" @@ -548,9 +545,9 @@ version = "0.1.3+0" [[deps.AbstractAlgebra]] deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "602749d9c19dda762e58a29ea548b720b78c8530" +git-tree-sha1 = "1bd8a536c949eb3de9b58042d57790ded6b70fa6" uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.30.8" +version = "0.30.9" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -568,10 +565,6 @@ deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.6.2" -weakdeps = ["StaticArrays"] - - [deps.Adapt.extensions] - AdaptStaticArraysExt = "StaticArrays" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -594,22 +587,6 @@ git-tree-sha1 = "d3f758863a47ceef2248d136657cb9c033603641" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" version = "7.4.8" - [deps.ArrayInterface.extensions] - ArrayInterfaceBandedMatricesExt = "BandedMatrices" - ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" - ArrayInterfaceCUDAExt = "CUDA" - ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" - ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" - ArrayInterfaceTrackerExt = "Tracker" - - [deps.ArrayInterface.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" - BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" @@ -621,23 +598,9 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[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" - - [deps.BangBang.extensions] - BangBangChainRulesCoreExt = "ChainRulesCore" - BangBangDataFramesExt = "DataFrames" - BangBangStaticArraysExt = "StaticArrays" - BangBangStructArraysExt = "StructArrays" - BangBangTypedTablesExt = "TypedTables" - - [deps.BangBang.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" - StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" - TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" +version = "0.3.39" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -705,6 +668,12 @@ git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" version = "1.16.0" +[[deps.ChangesOfVariables]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "f84967c4497e0e1955f9a582c232b02847c5f589" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.7" + [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" @@ -759,9 +728,9 @@ 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"] @@ -770,19 +739,15 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["UUIDs"] +deps = ["Dates", "LinearAlgebra", "UUIDs"] git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" version = "4.6.1" -weakdeps = ["Dates", "LinearAlgebra"] - - [deps.Compat.extensions] - CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "0.5.2+0" [[deps.CompositeTypes]] git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" @@ -794,12 +759,6 @@ git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.2" - [deps.CompositionsBase.extensions] - CompositionsBaseInverseFunctionsExt = "InverseFunctions" - - [deps.CompositionsBase.weakdeps] - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] git-tree-sha1 = "96d823b94ba8d187a6d8f0826e731195a74b90e9" @@ -811,11 +770,6 @@ deps = ["LinearAlgebra"] git-tree-sha1 = "738fec4d684a9a6ee9598a8bfee305b26831f28c" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" version = "1.5.2" -weakdeps = ["IntervalSets", "StaticArrays"] - - [deps.ConstructionBase.extensions] - ConstructionBaseIntervalSetsExt = "IntervalSets" - ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -860,37 +814,19 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] -git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -version = "1.9.1" + +[[deps.DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "1c03e389a28be70cd9049f98ff0b84cf7539d959" +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "0a7dd11dd243a1f8c71f72f2e5fd54c0bfdeaaab" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.125.0" - - [deps.DiffEqBase.extensions] - DiffEqBaseDistributionsExt = "Distributions" - DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" - DiffEqBaseMPIExt = "MPI" - DiffEqBaseMeasurementsExt = "Measurements" - DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" - DiffEqBaseReverseDiffExt = "ReverseDiff" - DiffEqBaseTrackerExt = "Tracker" - DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" - - [deps.DiffEqBase.weakdeps] - Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" - GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" - MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" - Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" - MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "6.125.1" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] @@ -906,9 +842,9 @@ 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.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -921,19 +857,11 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"] git-tree-sha1 = "c72970914c8a21b36bbc244e9df0ed1834a0360b" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" version = "0.25.95" - [deps.Distributions.extensions] - DistributionsChainRulesCoreExt = "ChainRulesCore" - DistributionsDensityInterfaceExt = "DensityInterface" - - [deps.Distributions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" - [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -1025,26 +953,16 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "ed569cb9e7e3590d5ba884da7edc50216aac5811" +git-tree-sha1 = "589d3d3bff204bdd80ecc53293896b4f39175723" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.1.0" +version = "1.1.1" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" 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"] git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" @@ -1064,14 +982,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" version = "0.10.35" -weakdeps = ["StaticArrays"] - - [deps.ForwardDiff.extensions] - ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1166,9 +1080,9 @@ version = "1.0.2" [[deps.Groebner]] deps = ["AbstractAlgebra", "Combinatorics", "Logging", "MultivariatePolynomials", "Primes", "Random", "SnoopPrecompile"] -git-tree-sha1 = "06022d793870e05b9cb34046125539f43d289f51" +git-tree-sha1 = "c8b55b624a83f60bcd6574cc999ad148d0a47dd6" uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.3.5" +version = "0.3.6" [[deps.GroupsCore]] deps = ["Markdown", "Random"] @@ -1234,9 +1148,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.IntegerMathUtils]] -git-tree-sha1 = "f366daebdfb079fd1fe4e3d560f99a0c892e15bc" +git-tree-sha1 = "70f65ced5129d36dbf200b07c51ea8a955294660" uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" -version = "0.1.0" +version = "0.1.1" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1248,29 +1162,29 @@ git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" version = "0.7.4" +[[deps.InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "6667aadd1cdee2c6cd068128b3d226ebc4fb0c67" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.9" + [[deps.Ipopt]] deps = ["Ipopt_jll", "LinearAlgebra", "MathOptInterface", "OpenBLAS32_jll", "PrecompileTools"] -git-tree-sha1 = "349e4c61bd7eb867e8fb1e8bd1ace76c7764e572" +git-tree-sha1 = "fdb3430a3b7b909bcb5abf9439d61450f49e3e2c" uuid = "b6b21f68-93f8-5de0-b562-5493be1d77c9" -version = "1.3.0" +version = "1.4.1" [[deps.Ipopt_jll]] -deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "libblastrampoline_jll"] -git-tree-sha1 = "0d3939fb672b84082f3ee930b51de03df935be31" +deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "Pkg"] +git-tree-sha1 = "e3e202237d93f18856b6ff1016166b0f172a49a8" uuid = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7" -version = "300.1400.1200+0" +version = "300.1400.400+0" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" -[[deps.IterativeSolvers]] -deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" -uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.2" - [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" @@ -1314,9 +1228,9 @@ version = "1.11.1" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "832629821a3c64bbabb8ad7f31fd62a37aad27be" +git-tree-sha1 = "60567b51bd9e1e19ae2fd8a54dcd6bc5994727f0" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.31" +version = "1.0.34" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] @@ -1336,12 +1250,6 @@ 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" @@ -1382,14 +1290,6 @@ git-tree-sha1 = "099e356f267354f46ba65087981a77da23a279b7" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" version = "0.16.0" - [deps.Latexify.extensions] - DataFramesExt = "DataFrames" - SymEngineExt = "SymEngine" - - [deps.Latexify.weakdeps] - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" - [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" @@ -1479,36 +1379,20 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] +deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -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 = "d829e01d7557f0c755dbb34ade286b9742734b4d" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.42.0" - - [deps.LinearSolve.extensions] - LinearSolveHYPRE = "HYPRE" - - [deps.LinearSolve.weakdeps] - HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" +version = "2.1.12" [[deps.LogExpFunctions]] -deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.23" - - [deps.LogExpFunctions.extensions] - LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" - LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" - LogExpFunctionsInverseFunctionsExt = "InverseFunctions" - - [deps.LogExpFunctions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.3.24" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1520,15 +1404,10 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] git-tree-sha1 = "3bb62b5003bc7d2d49f26663484267dc49fa1bf5" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" version = "0.12.159" -weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] - - [deps.LoopVectorization.extensions] - ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] - SpecialFunctionsExt = "SpecialFunctions" [[deps.METIS_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1547,10 +1426,10 @@ uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" [[deps.MUMPS_seq_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "OpenBLAS32_jll", "Pkg", "libblastrampoline_jll"] -git-tree-sha1 = "f429d6bbe9ad015a2477077c9e89b978b8c26558" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "OpenBLAS32_jll", "Pkg"] +git-tree-sha1 = "29de2841fa5aefe615dea179fcde48bb87b58f57" uuid = "d7ed1dd3-d0ae-5e8e-bfb4-87a502085b8d" -version = "500.500.101+0" +version = "5.4.1+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1569,9 +1448,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "6ba094e471106981b278f60179170d8b10985052" +git-tree-sha1 = "19a3636968e802918f8891d729c74bd64dff6d00" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.16.0" +version = "1.17.1" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] @@ -1582,7 +1461,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.0+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1612,19 +1491,13 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "UnPack", "Unitful"] -git-tree-sha1 = "3228b51eccf83e111e1e0b7f5e19d203f52d1fbe" +git-tree-sha1 = "bf01b8d119aae2bf3779149173da22a51a277aef" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.57.0" - - [deps.ModelingToolkit.extensions] - MTKDeepDiffsExt = "DeepDiffs" - - [deps.ModelingToolkit.weakdeps] - DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" +version = "8.59.0" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2022.2.1" [[deps.MuladdMacro]] git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" @@ -1665,11 +1538,17 @@ version = "1.0.2" uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" +[[deps.NeuronBuilder]] +deps = ["ModelingToolkit"] +git-tree-sha1 = "99cab00184e03cec50fc26ec6c277564c27c2d31" +uuid = "bdec0aff-bc35-4528-862d-7dacab2b11a0" +version = "0.2.5" + [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "a6000c813371cd3cd9cbbdf8a356fc3a97138d92" +deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "2a7f28c62eb2c16b9c375c38f664cdcf22313cf5" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.6.0" +version = "1.8.0" [[deps.OffsetArrays]] deps = ["Adapt"] @@ -1685,14 +1564,14 @@ version = "1.3.5+1" [[deps.OpenBLAS32_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "2fb9ee2dc14d555a6df2a714b86b7125178344c2" +git-tree-sha1 = "9c6c2ed4b7acd2137b878eb96c68e63b76199d0f" uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2" -version = "0.3.21+0" +version = "0.3.17+0" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.20+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1729,15 +1608,15 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.0" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "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", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "7f758238ce4202ced5e08aa2903d19d3a4f0dd7c" +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 = "2205eff89c992bb6d21bc44feb4b26e6d20f54d4" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.52.0" +version = "6.53.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+0" +version = "10.40.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1769,9 +1648,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.40.1+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.0" +version = "1.8.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1787,23 +1666,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "ad59edfb711a4751e0b8271454df47f84a47a29e" +git-tree-sha1 = "ceb1ec8d4fbeb02f8817004837d924583707951b" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.14" - - [deps.Plots.extensions] - FileIOExt = "FileIO" - GeometryBasicsExt = "GeometryBasics" - IJuliaExt = "IJulia" - ImageInTerminalExt = "ImageInTerminal" - UnitfulExt = "Unitful" - - [deps.Plots.weakdeps] - FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" - GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" - IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" - ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.38.15" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] @@ -1835,17 +1700,11 @@ git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" version = "0.4.12" - [deps.PreallocationTools.extensions] - PreallocationToolsReverseDiffExt = "ReverseDiff" - - [deps.PreallocationTools.weakdeps] - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "259e206946c293698122f63e2b513a7c99a244e8" +git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.1" +version = "1.1.2" [[deps.Preferences]] deps = ["TOML"] @@ -1917,16 +1776,6 @@ git-tree-sha1 = "02ef02926f30d53b94be443bfaea010c47f6b556" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" version = "2.38.5" - [deps.RecursiveArrayTools.extensions] - RecursiveArrayToolsMeasurementsExt = "Measurements" - RecursiveArrayToolsTrackerExt = "Tracker" - RecursiveArrayToolsZygoteExt = "Zygote" - - [deps.RecursiveArrayTools.weakdeps] - Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" - [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] git-tree-sha1 = "9088515ad915c99026beb5436d0a09cd8c18163e" @@ -1970,9 +1819,9 @@ version = "0.4.0+0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "1c608ae9509aea592e278961828d42ba8559c1f6" +git-tree-sha1 = "0b9b18d6236e9ab2b092defaacdffd929d572642" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.10" +version = "0.5.9" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1991,15 +1840,15 @@ version = "0.6.39" [[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 = "ddf57a23d610d30d0c4bd01132f4646a2a77d171" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.92.2" +version = "1.92.5" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "a8eb97c56cac50c21096582afb2a0110784dc36e" +git-tree-sha1 = "2d00015fa0a190220dc5605406b85073f6634391" uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.6" +version = "0.1.7" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -2043,12 +1892,6 @@ git-tree-sha1 = "7c55a3e65aad4ce6e610409cdd564b8d590b9726" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" version = "0.1.15" - [deps.SimpleNonlinearSolve.extensions] - SimpleBatchedNonlinearSolveExt = "NNlib" - - [deps.SimpleNonlinearSolve.weakdeps] - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" - [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" @@ -2076,20 +1919,14 @@ uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.1.0" [[deps.SparseArrays]] -deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] +deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Reexport", "Requires", "SciMLOperators", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "VertexSafeGraphs"] -git-tree-sha1 = "04f060e66a61a909ed59efd79f64943688d7568d" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Reexport", "Requires", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "VertexSafeGraphs"] +git-tree-sha1 = "c5144590905924f1d1c6c3e82f9e5a5007459109" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.3.0" - - [deps.SparseDiffTools.extensions] - SparseDiffToolsZygote = "Zygote" - - [deps.SparseDiffTools.weakdeps] - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "2.4.0" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2098,14 +1935,10 @@ uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" version = "0.3.9" [[deps.SpecialFunctions]] -deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" version = "2.2.0" -weakdeps = ["ChainRulesCore"] - - [deps.SpecialFunctions.extensions] - SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -2124,11 +1957,6 @@ deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "Snoo git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" version = "1.4.0" -weakdeps = ["OffsetArrays", "StaticArrays"] - - [deps.StaticArrayInterface.extensions] - StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" - StaticArrayInterfaceStaticArraysExt = "StaticArrays" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] @@ -2144,7 +1972,6 @@ version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2159,19 +1986,11 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" version = "0.34.0" [[deps.StatsFuns]] -deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" - [deps.StatsFuns.extensions] - StatsFunsChainRulesCoreExt = "ChainRulesCore" - StatsFunsInverseFunctionsExt = "InverseFunctions" - - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] git-tree-sha1 = "564451a262696334a3bab19108a99dd90d5a22c8" @@ -2191,7 +2010,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "5.10.1+0" [[deps.SymbolicIndexingInterface]] deps = ["DocStringExtensions"] @@ -2207,14 +2026,14 @@ 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"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.3" +version = "1.0.0" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -2231,7 +2050,7 @@ version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.0" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -2330,12 +2149,6 @@ git-tree-sha1 = "ba4aa36b2d5c98d6ed1f149da916b3ba46527b2b" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" version = "1.14.0" - [deps.Unitful.extensions] - InverseFunctionsUnitfulExt = "InverseFunctions" - - [deps.Unitful.weakdeps] - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" @@ -2518,7 +2331,7 @@ version = "1.4.0+3" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.12+3" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2551,9 +2364,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.7.0+0" +version = "5.1.1+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2632,7 +2445,7 @@ version = "1.4.1+0" # ╠═d70bdeab-7956-45d9-9343-c7cf32d59569 # ╠═7280f393-474e-401f-aa91-4cb2091c5f93 # ╟─e5a239b0-4f2f-4165-bdea-c684a8aac64a -# ╟─d7233d7e-2cd1-4119-813a-c8814c947f11 +# ╠═75d2bff9-e7b2-464d-bec4-37a34a5dc442 # ╠═c0292c71-7410-4ede-93f1-174a75fcd25d # ╟─4dce4235-9971-43c9-ae89-54258d0c65dd # ╠═c4b40826-8fc4-4a49-841c-08cae0a05d57 @@ -2643,10 +2456,12 @@ version = "1.4.1+0" # ╠═1fde1b55-cf75-4d26-9305-7b864d5f65bb # ╠═101cf791-e10e-4f7e-a879-2dcfc150ada4 # ╠═1fb2caa4-bfc9-41ab-a183-34a5b1fca899 -# ╠═cdc273c4-faee-41b0-bd88-404dbbfd6f35 -# ╟─2b7d38bb-2264-43c0-89a3-cf3bc0757603 -# ╟─e5dc02e9-005f-4736-8983-1db70c204c93 +# ╟─56f3d76d-d8dd-4a3f-b3f1-63dfabe6eebf +# ╠═e5dc02e9-005f-4736-8983-1db70c204c93 # ╠═20226001-560d-4131-bf8c-896f1a840534 +# ╟─2b7d38bb-2264-43c0-89a3-cf3bc0757603 # ╟─0b3c43cd-1099-47e9-aede-00a128f4904f +# ╠═cdc273c4-faee-41b0-bd88-404dbbfd6f35 # ╟─00000000-0000-0000-0000-000000000001 # ╟─00000000-0000-0000-0000-000000000002 +