Julia Dependency Update (#340)

Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action

Manifest.toml

@@ -196,16 +196,20 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 version = "0.5.1"
 
 [[deps.Catalyst]]
-deps = ["DataStructures", "DiffEqBase", "DocStringExtensions", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"]
-git-tree-sha1 = "8e7e57c2ed4ecfb798f5a8cb230a9dd84765e7b1"
+deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "Setfield", "SparseArrays", "Symbolics", "Unitful"]
+git-tree-sha1 = "6964e1126cf683c0a429d377db305c06d51d28f7"
 uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
-version = "13.5.1"
+version = "14.0.0"
 
     [deps.Catalyst.extensions]
+    CatalystBifurcationKitExtension = "BifurcationKit"
     CatalystHomotopyContinuationExtension = "HomotopyContinuation"
+    CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
     [deps.Catalyst.weakdeps]
+    BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
     HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+    StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
@@ -422,10 +426,10 @@ version = "6.151.5"
     Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [[deps.DiffEqCallbacks]]
-deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "ee954c8b9d348b7a8a6aec5f28288bf5adecd4ee"
+deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
+git-tree-sha1 = "c959cfd2657d16beada157a74d52269e8556500e"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-version = "2.37.0"
+version = "3.6.2"
 weakdeps = ["OrdinaryDiffEq", "Sundials"]
 
 [[deps.DiffEqNoiseProcess]]
@@ -460,9 +464,9 @@ version = "7.13.0"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"]
-git-tree-sha1 = "695217e97ee1ce0248f4a56c14af88ba33c585fd"
+git-tree-sha1 = "b04acb57861ae60ce548e6041795cac9e4ad96fa"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.5.7"
+version = "0.5.8"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -532,10 +536,16 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
 [[deps.DomainSets]]
-deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"]
-git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9"
+deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"]
+git-tree-sha1 = "490392af2c7d63183bfa2c8aaa6ab981c5ba7561"
 uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-version = "0.6.7"
+version = "0.7.14"
+
+    [deps.DomainSets.extensions]
+    DomainSetsMakieExt = "Makie"
+
+    [deps.DomainSets.weakdeps]
+    Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
@@ -554,15 +564,33 @@ git-tree-sha1 = "30a1848c4f4fc35d1d4bbbd125650f6a11b5bc6c"
 uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07"
 version = "0.5.7"
 
+[[deps.DynamicQuantities]]
+deps = ["Compat", "PackageExtensionCompat", "Tricks"]
+git-tree-sha1 = "412b25c7d99ec6b06967d315c7b29bb8e484f092"
+uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
+version = "0.13.2"
+
+    [deps.DynamicQuantities.extensions]
+    DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra"
+    DynamicQuantitiesMeasurementsExt = "Measurements"
+    DynamicQuantitiesScientificTypesExt = "ScientificTypes"
+    DynamicQuantitiesUnitfulExt = "Unitful"
+
+    [deps.DynamicQuantities.weakdeps]
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+    ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
 [[deps.EnumX]]
 git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237"
 uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 version = "1.0.4"
 
 [[deps.EnzymeCore]]
-git-tree-sha1 = "3a3177ba05b4763234819060fb6c2e1613379ca6"
+git-tree-sha1 = "d445df66dd8761a4c27df950db89c6a3a0629fe7"
 uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
-version = "0.7.6"
+version = "0.7.7"
 weakdeps = ["Adapt"]
 
     [deps.EnzymeCore.extensions]
@@ -653,6 +681,11 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
     FillArraysSparseArraysExt = "SparseArrays"
     FillArraysStatisticsExt = "Statistics"
 
+[[deps.FindFirstFunctions]]
+git-tree-sha1 = "e90fef90f7d75e6a5b435b0fd65609759f99717a"
+uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224"
+version = "1.2.0"
+
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"]
 git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3"
@@ -828,16 +861,17 @@ uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9"
 version = "0.1.5"
 
 [[deps.InlineStrings]]
-deps = ["Parsers"]
-git-tree-sha1 = "86356004f30f8e737eff143d57d41bd580e437aa"
+git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.4.1"
+version = "1.4.2"
 
     [deps.InlineStrings.extensions]
     ArrowTypesExt = "ArrowTypes"
+    ParsersExt = "Parsers"
 
     [deps.InlineStrings.weakdeps]
     ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
+    Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -921,9 +955,9 @@ version = "3.0.3+0"
 
 [[deps.JuliaFormatter]]
 deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "1c4880cb70a5c6c87ea36deccc3d7f9e7969c18c"
+git-tree-sha1 = "b101a476705594c2a8ba106d731497058874bcf4"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.56"
+version = "1.0.57"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
@@ -1009,9 +1043,9 @@ version = "0.1.17"
 
 [[deps.LazyArrays]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"]
-git-tree-sha1 = "35d73607f9e74c18db8a434b4886a479faa8e6fa"
+git-tree-sha1 = "46dd13736e33cc3bfc610f62b6c7f84b9c95539a"
 uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-version = "2.1.4"
+version = "2.1.8"
 
     [deps.LazyArrays.extensions]
     LazyArraysBandedMatricesExt = "BandedMatrices"
@@ -1261,10 +1295,10 @@ version = "1.2.0"
 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", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"]
-git-tree-sha1 = "082c90f19d8d5be0f441e61e4cc7d616bef4de24"
+deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"]
+git-tree-sha1 = "ca53d85a54e5d54e0c7458d784af8fe5078064ce"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
-version = "8.76.0"
+version = "9.24.0"
 
     [deps.ModelingToolkit.extensions]
     MTKBifurcationKitExt = "BifurcationKit"
@@ -1867,9 +1901,9 @@ weakdeps = ["ChainRulesCore"]
 
 [[deps.Static]]
 deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"]
-git-tree-sha1 = "0bbff21027dd8a107551847528127b62a35f7594"
+git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "1.1.0"
+version = "1.1.1"
 
 [[deps.StaticArrayInterface]]
 deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"]
@@ -1928,9 +1962,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
 [[deps.SteadyStateDiffEq]]
 deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"]
-git-tree-sha1 = "a735fd5053724cf4de31c81b4e2cc429db844be5"
+git-tree-sha1 = "1158cfdf0da5b0eacdfcfba7c16b174a37bdf6c7"
 uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
-version = "2.0.1"
+version = "2.2.0"
 
 [[deps.StochasticDiffEq]]
 deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
@@ -1984,16 +2018,16 @@ uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3"
 version = "0.2.1"
 
 [[deps.SymbolicUtils]]
-deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TimerOutputs", "Unityper"]
-git-tree-sha1 = "669e43e90df46fcee4aa859b587da7a7948272ac"
+deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"]
+git-tree-sha1 = "cc049913a449be8c7ac00979831f26891e01add2"
 uuid = "d1185830-fcd6-423d-90d6-eec64667417b"
-version = "1.5.1"
+version = "2.1.0"
 
 [[deps.Symbolics]]
-deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "ForwardDiff", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils"]
-git-tree-sha1 = "4104548fff14d7370b278ee767651d6ec61eb195"
+deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "ForwardDiff", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"]
+git-tree-sha1 = "8539a734b448ca27707709c62420b1bf115ed7d9"
 uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7"
-version = "5.28.0"
+version = "5.33.0"
 
     [deps.Symbolics.extensions]
     SymbolicsGroebnerExt = "Groebner"
@@ -2035,6 +2069,11 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
 uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
 version = "0.1.1"
 
+[[deps.TermInterface]]
+git-tree-sha1 = "6f0cee95e74d1f6891ba6b35b8b219fd3d11b567"
+uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c"
+version = "0.4.1"
+
 [[deps.Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

docs/figs/ch1-07.jl

@@ -36,12 +36,12 @@ function build_collins(;name)
     D = Differential(t)
 
     eqs = [
-        D(s1) ~ a1 * hil(1 + i2, s2, β) - s1
-        D(s2) ~ a2 * hil(1 + i1, s1, γ) - s2
-        i2 ~ 10 * (10 < t) * (t < 20)
-        i1 ~ 10 * (30 < t) * (t < 40)
+        D(s1) ~ a1 * hil(1 + i2, s2, β) - s1,
+        D(s2) ~ a2 * hil(1 + i1, s1, γ) - s2,
+        i2 ~ 10 * (10 < t) * (t < 20),
+        i1 ~ 10 * (30 < t) * (t < 40),
     ]
-    sys = ODESystem(eqs; name)
+    sys = ODESystem(eqs, t; name)
     return structural_simplify(sys)
 end
 

docs/figs/ch1-09.jl

@@ -64,7 +64,7 @@ function build_hh(;name)
         D(n) ~ -(nα + nβ) * n + nα,
     ]
 
-    sys = ODESystem(eqs; name)
+    sys = ODESystem(eqs, t; name)
     return structural_simplify(sys)
 end
 

docs/figs/ch2-04.jl

@@ -2,7 +2,6 @@
 # Fig 2.04
 Exponential decay
 ===#
-
 using Plots
 Plots.default(linewidth=2)
 

docs/figs/ch2-09.jl

@@ -5,7 +5,6 @@ Metabolic network simulation
 
 Using `Catalyst.jl` to simulate a metabolic network.
 ===#
-
 using DifferentialEquations
 using Catalyst
 using ModelingToolkit

docs/figs/ch2-11.jl

@@ -3,7 +3,6 @@
 
 Model reduction of ODE metabolic networks.
 ===#
-
 using DifferentialEquations
 using Catalyst
 using ModelingToolkit
@@ -45,15 +44,15 @@ function make_212(;name)
         B ~ C * k1 / (km1 + k1)
         D(C) ~ k0 - k2 * B
     ]
-    sys = ODESystem(eqs; name)
+    sys = ODESystem(eqs, t; name)
     structural_simplify(sys)
 end
 
 #---
 @named model212 = make_212()
 
 #---
-states(model212)
+unknowns(model212)
 
 #---
 observed(model212)
@@ -121,7 +120,7 @@ function make_214(;name)
         A ~ (k0 + km1 * B)/k1
         D(B) ~ k1 * A - (km1 + k2) * B
     ]
-    sys = ODESystem(eqs; name)
+    sys = ODESystem(eqs, t; name)
     structural_simplify(sys)
 end
 

docs/figs/ch2-p246.jl

@@ -1,5 +1,4 @@
 # # Prob 2.4.6
-
 using DifferentialEquations
 using Plots
 Plots.default(linewidth=2)

docs/figs/ch3-03.jl

@@ -3,7 +3,6 @@
 
 Michaelis-Menten kinetics
 ===#
-
 using DifferentialEquations
 using Catalyst
 using Plots
@@ -26,10 +25,11 @@ setdefaults!(rn, [
     :k2 => 10.,
 ])
 
-osys = convert(ODESystem, rn; remove_conserved = true)
+osys = convert(ODESystem, rn; remove_conserved = true) |> structural_simplify
 
 #---
 observed(osys)
+
 #---
 tend = 1.0
 
@@ -56,7 +56,7 @@ setdefaults!(rn303mm, [
     :k2 => 10.,
 ])
 
-osysmm = convert(ODESystem, rn303mm; remove_conserved = true)
+osysmm = convert(ODESystem, rn303mm; remove_conserved = true) |> structural_simplify
 
 #---
 tend = 1.0

docs/figs/ch3-13.jl

@@ -3,10 +3,9 @@
 
 Generalized mass action (GMA) vs. Michaelis-Menten rate laws
 ===#
-
 using Plots
 Plots.default(linewidth=2)
-#---
+
 mm = t -> 2t / (1+t)
 gma = t -> t^0.4
 

docs/figs/ch4-01.jl

@@ -3,7 +3,6 @@
 
 Steady states and phase plots in an asymmetric network.
 ===#
-
 using DifferentialEquations
 using SimpleUnPack
 using Plots