.github/workflows/Documentation.yml

@@ -20,7 +20,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1'
+          version: 'lts'
       - run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
       - name: Install dependencies
         run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
@@ -31,8 +31,8 @@ jobs:
           JULIA_DEBUG: "Documenter"
         run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ --code-coverage=user docs/make.jl
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

.github/workflows/Downstream.yml

@@ -27,17 +27,17 @@ jobs:
         package:
           - {user: SciML, repo: SciMLBase.jl, group: Downstream}
           - {user: SciML, repo: Catalyst.jl, group: All}
-          - {user: SciML, repo: CellMLToolkit.jl, group: All}
+          - {user: SciML, repo: CellMLToolkit.jl, group: Core}
           - {user: SciML, repo: SBMLToolkit.jl, group: All}
           - {user: SciML, repo: NeuralPDE.jl, group: NNPDE}
           - {user: SciML, repo: DataDrivenDiffEq.jl, group: Downstream}
-          - {user: SciML, repo: StructuralIdentifiability.jl, group: All}
+          - {user: SciML, repo: StructuralIdentifiability.jl, group: Core}
           - {user: SciML, repo: ModelingToolkitStandardLibrary.jl, group: Core}
           - {user: SciML, repo: ModelOrderReduction.jl, group: All}
           - {user: SciML, repo: MethodOfLines.jl, group: Interface}
           - {user: SciML, repo: MethodOfLines.jl, group: 2D_Diffusion}
           - {user: SciML, repo: MethodOfLines.jl, group: DAE}
-          - {user: ai4energy, repo: Ai4EComponentLib.jl, group: Downstream}
+          - {user: SciML, repo: ModelingToolkitNeuralNets.jl, group: All}
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
@@ -68,8 +68,8 @@ jobs:
             exit(0)  # Exit immediately, as a success
           end
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          fail_ci_if_error: false

.github/workflows/Tests.yml

@@ -25,15 +25,22 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        version:
+          - "1"
+          - "lts"
+          - "pre"
         group:
           - InterfaceI
           - InterfaceII
+          - Initialization
           - SymbolicIndexingInterface
           - Extended
           - Extensions
           - Downstream
           - RegressionI
+          - FMI
     uses: "SciML/.github/.github/workflows/tests.yml@v1"
     with:
+      julia-version: "${{ matrix.version }}"
       group: "${{ matrix.group }}"
     secrets: "inherit"

.typos.toml

@@ -4,4 +4,6 @@ nd = "nd"
 Strat = "Strat"
 eles = "eles"
 ser = "ser"
-isconnection = "isconnection"
+isconnection = "isconnection"
+Ue = "Ue"
+Derivate = "Derivate"

Project.toml

@@ -1,29 +1,33 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <mayingbo5@gmail.com>", "Chris Rackauckas <accounts@chrisrackauckas.com> and contributors"]
-version = "9.39.1"
+version = "9.72.0"
 
 [deps]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
+CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b"
+DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
+EnumX = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 ExprTools = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
-Expronicon = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636"
 FindFirstFunctions = "64ca27bc-2ba2-4a57-88aa-44e436879224"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
@@ -33,13 +37,16 @@ Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+Moshi = "2e0e35c7-a2e4-4343-998d-7ef72827ed2d"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
+OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 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"
@@ -59,67 +66,92 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
+FMI = "14a09403-18e3-468f-ad8a-74f8dda2d9ac"
+InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 
 [extensions]
 MTKBifurcationKitExt = "BifurcationKit"
 MTKChainRulesCoreExt = "ChainRulesCore"
 MTKDeepDiffsExt = "DeepDiffs"
+MTKFMIExt = "FMI"
+MTKInfiniteOptExt = "InfiniteOpt"
 MTKLabelledArraysExt = "LabelledArrays"
 
 [compat]
+ADTypes = "1.14.0"
 AbstractTrees = "0.3, 0.4"
 ArrayInterface = "6, 7"
-BifurcationKit = "0.3"
+BifurcationKit = "0.4"
 BlockArrays = "1.1"
+BoundaryValueDiffEqAscher = "1.1.0"
+BoundaryValueDiffEqMIRK = "1.4.0"
 ChainRulesCore = "1"
 Combinatorics = "1"
+CommonSolve = "0.2.4"
 Compat = "3.42, 4"
 ConstructionBase = "1"
+DataInterpolations = "6.4"
 DataStructures = "0.17, 0.18"
 DeepDiffs = "1"
-DiffEqBase = "6.103.0"
-DiffEqCallbacks = "2.16, 3"
+DelayDiffEq = "5.50"
+DiffEqBase = "6.165.1"
+DiffEqCallbacks = "2.16, 3, 4"
 DiffEqNoiseProcess = "5"
 DiffRules = "0.1, 1.0"
+DifferentiationInterface = "0.6.47"
 Distributed = "1"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.7, 0.8, 0.9"
 DomainSets = "0.6, 0.7"
 DynamicQuantities = "^0.11.2, 0.12, 0.13, 1"
+EnumX = "1.0.4"
 ExprTools = "0.1.10"
-Expronicon = "0.8"
+FMI = "0.14"
 FindFirstFunctions = "1"
 ForwardDiff = "0.10.3"
+FunctionWrappers = "1.1"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
+InfiniteOpt = "0.5"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
 JumpProcesses = "9.13.1"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"
 LinearAlgebra = "1"
+Logging = "1"
 MLStyle = "0.4.17"
+ModelingToolkitStandardLibrary = "2.19"
+Moshi = "0.3"
 NaNMath = "0.3, 1"
-NonlinearSolve = "3.14"
+NonlinearSolve = "4.3"
+OffsetArrays = "1"
 OrderedCollections = "1"
 OrdinaryDiffEq = "6.82.0"
+OrdinaryDiffEqCore = "1.15.0"
+OrdinaryDiffEqDefault = "1.2"
+OrdinaryDiffEqNonlinearSolve = "1.5.0"
 PrecompileTools = "1"
+REPL = "1"
 RecursiveArrayTools = "3.26"
 Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.5.9"
-SciMLBase = "2.52.1"
-SciMLStructures = "1.0"
+SCCNonlinearSolve = "1.0.0"
+SciMLBase = "2.75"
+SciMLStructures = "1.7"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
-SimpleNonlinearSolve = "0.1.0, 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 = "0.3.29"
-SymbolicUtils = "3.2"
-Symbolics = "6.3"
+StochasticDelayDiffEq = "1.8.1"
+StochasticDiffEq = "6.72.1"
+SymbolicIndexingInterface = "0.3.37"
+SymbolicUtils = "3.25.1"
+Symbolics = "6.37"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -128,20 +160,28 @@ julia = "1.9"
 [extras]
 AmplNLWriter = "7c4d4715-977e-5154-bfe0-e096adeac482"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+BoundaryValueDiffEqAscher = "7227322d-7511-4e07-9247-ad6ff830280e"
+BoundaryValueDiffEqMIRK = "1a22d4ce-7765-49ea-b6f2-13c8438986a6"
 ControlSystemsBase = "aaaaaaaa-a6ca-5380-bf3e-84a91bcd477e"
+DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
 Ipopt_jll = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ModelingToolkitStandardLibrary = "16a59e39-deab-5bd0-87e4-056b12336739"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 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"
 ReferenceTests = "324d217c-45ce-50fc-942e-d289b448e8cf"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
@@ -154,4 +194,4 @@ Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "OrdinaryDiffEq", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]
+test = ["AmplNLWriter", "BenchmarkTools", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqAscher", "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", "Logging"]

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

@@ -1,40 +1,55 @@
 [deps]
+Attractors = "f3fd9213-ca85-4dba-9dfd-7fc91308fec7"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ControlSystemsBase = "aaaaaaaa-a6ca-5380-bf3e-84a91bcd477e"
+DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
+FMI = "14a09403-18e3-468f-ad8a-74f8dda2d9ac"
+FMIZoo = "724179cf-c260-40a9-bd27-cccc6fe2f195"
 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"
+PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 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"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
+Attractors = "1.24"
 BenchmarkTools = "1.3"
-BifurcationKit = "0.3"
-DifferentialEquations = "7.6"
+BifurcationKit = "0.4"
+CairoMakie = "0.13"
+DataInterpolations = "6.5, 8"
 Distributions = "0.25"
 Documenter = "1"
 DynamicQuantities = "^0.11.2, 0.12, 1"
+FMI = "0.14"
+FMIZoo = "1"
 ModelingToolkit = "8.33, 9"
-NonlinearSolve = "3"
+ModelingToolkitStandardLibrary = "2.19"
+NonlinearSolve = "3, 4"
 Optim = "1.7"
-Optimization = "3.9"
-OptimizationOptimJL = "0.1"
+Optimization = "3.9, 4"
+OptimizationOptimJL = "0.1, 0.4"
 OrdinaryDiffEq = "6.31"
 Plots = "1.36"
+PreallocationTools = "0.4"
 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,