Merge remote-tracking branch 'origin'

update origin master

Author: vyudu

.github/workflows/Tests.yml

@@ -32,6 +32,7 @@ jobs:
         group:
           - InterfaceI
           - InterfaceII
+          - Initialization
           - SymbolicIndexingInterface
           - Extended
           - Extensions

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.53.0"
+version = "9.60.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -44,6 +44,7 @@ PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
+SCCNonlinearSolve = "9dfe8606-65a1-4bb3-9748-cb89d1561431"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLStructures = "53ae85a6-f571-4167-b2af-e1d143709226"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -64,13 +65,15 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 
 [extensions]
 MTKBifurcationKitExt = "BifurcationKit"
 MTKChainRulesCoreExt = "ChainRulesCore"
 MTKDeepDiffsExt = "DeepDiffs"
 MTKHomotopyContinuationExt = "HomotopyContinuation"
+MTKInfiniteOptExt = "InfiniteOpt"
 MTKLabelledArraysExt = "LabelledArrays"
 
 [compat]
@@ -86,6 +89,7 @@ ConstructionBase = "1"
 DataInterpolations = "6.4"
 DataStructures = "0.17, 0.18"
 DeepDiffs = "1"
+DelayDiffEq = "5.50"
 DiffEqBase = "6.157"
 DiffEqCallbacks = "2.16, 3, 4"
 DiffEqNoiseProcess = "5"
@@ -104,6 +108,7 @@ FunctionWrappers = "1.1"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 HomotopyContinuation = "2.11"
+InfiniteOpt = "0.5"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
 JumpProcesses = "9.13.1"
@@ -112,28 +117,34 @@ Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"
 LinearAlgebra = "1"
 MLStyle = "0.4.17"
+ModelingToolkitStandardLibrary = "2.19"
 NaNMath = "0.3, 1"
-NonlinearSolve = "3.14, 4"
+NonlinearSolve = "4.3"
 OffsetArrays = "1"
 OrderedCollections = "1"
 OrdinaryDiffEq = "6.82.0"
-OrdinaryDiffEqCore = "1.7.0"
+OrdinaryDiffEqCore = "1.13.0"
+OrdinaryDiffEqDefault = "1.2"
+OrdinaryDiffEqNonlinearSolve = "1.3.0"
 PrecompileTools = "1"
 REPL = "1"
 RecursiveArrayTools = "3.26"
 Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.5.9"
-SciMLBase = "2.57.1"
+SCCNonlinearSolve = "1.0.0"
+SciMLBase = "2.68.1"
 SciMLStructures = "1.0"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
 SimpleNonlinearSolve = "0.1.0, 1, 2"
 SparseArrays = "1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
-SymbolicIndexingInterface = "0.3.35"
+StochasticDiffEq = "6.72.1"
+StochasticDelayDiffEq = "1.8.1"
+SymbolicIndexingInterface = "0.3.36"
 SymbolicUtils = "3.7"
-Symbolics = "6.19"
+Symbolics = "6.22.1"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -157,6 +168,8 @@ OptimizationMOI = "fd9f6733-72f4-499f-8506-86b2bdd0dea1"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+OrdinaryDiffEqNonlinearSolve = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -171,4 +184,4 @@ Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DataInterpolations", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "REPL", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]
+test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DataInterpolations", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "REPL", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET", "OrdinaryDiffEqNonlinearSolve"]

README.md

@@ -36,7 +36,7 @@ lower it to a first order system, symbolically generate the Jacobian function
 for the numerical integrator, and solve it.
 
 ```julia
-using DifferentialEquations, ModelingToolkit
+using OrdinaryDiffEqDefault, ModelingToolkit
 using ModelingToolkit: t_nounits as t, D_nounits as D
 
 @parameters σ ρ β

docs/Project.toml

@@ -1,20 +1,22 @@
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+ControlSystemsBase = "aaaaaaaa-a6ca-5380-bf3e-84a91bcd477e"
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+ModelingToolkitStandardLibrary = "16a59e39-deab-5bd0-87e4-056b12336739"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SciMLStructures = "53ae85a6-f571-4167-b2af-e1d143709226"
+Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
@@ -25,18 +27,19 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 BenchmarkTools = "1.3"
 BifurcationKit = "0.4"
 DataInterpolations = "6.5"
-DifferentialEquations = "7.6"
 Distributions = "0.25"
 Documenter = "1"
 DynamicQuantities = "^0.11.2, 0.12, 1"
 ModelingToolkit = "8.33, 9"
+ModelingToolkitStandardLibrary = "2.19"
 NonlinearSolve = "3, 4"
 Optim = "1.7"
 Optimization = "3.9, 4"
 OptimizationOptimJL = "0.1, 0.4"
 OrdinaryDiffEq = "6.31"
 Plots = "1.36"
 SciMLStructures = "1.1"
+Setfield = "1"
 StochasticDiffEq = "6"
 SymbolicIndexingInterface = "0.3.1"
 SymbolicUtils = "3"

docs/make.jl

@@ -25,7 +25,12 @@ makedocs(sitename = "ModelingToolkit.jl",
     modules = [ModelingToolkit],
     clean = true, doctest = false, linkcheck = true,
     warnonly = [:docs_block, :missing_docs, :cross_references],
-    linkcheck_ignore = ["https://epubs.siam.org/doi/10.1137/0903023"],
+    linkcheck_ignore = [
+        "https://epubs.siam.org/doi/10.1137/0903023",
+        # this link tends to fail linkcheck stochastically and often takes much longer to succeed
+        # even in the browser it takes ages
+        "http://www.scholarpedia.org/article/Differential-algebraic_equations"
+    ],
     format = Documenter.HTML(;
         assets = ["assets/favicon.ico"],
         mathengine,

docs/pages.jl

@@ -13,7 +13,8 @@ pages = [
         "tutorials/bifurcation_diagram_computation.md",
         "tutorials/SampledData.md",
         "tutorials/domain_connections.md",
-        "tutorials/callable_params.md"],
+        "tutorials/callable_params.md",
+        "tutorials/linear_analysis.md"],
     "Examples" => Any[
         "Basic Examples" => Any["examples/higher_order.md",
             "examples/spring_mass.md",

docs/src/basics/Composition.md

@@ -56,7 +56,7 @@ x0 = [decay1.x => 1.0
 p = [decay1.a => 0.1
      decay2.a => 0.2]
 
-using DifferentialEquations
+using OrdinaryDiffEq
 prob = ODEProblem(simplified_sys, x0, (0.0, 100.0), p)
 sol = solve(prob, Tsit5())
 sol[decay2.f]