Merge branch 'master' into myb/dd

Author: YingboMa

.github/workflows/Tests.yml

@@ -25,6 +25,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        version:
+          - "1"
+          - "lts"
+          - "pre"
         group:
           - InterfaceI
           - InterfaceII
@@ -35,5 +39,6 @@ jobs:
           - RegressionI
     uses: "SciML/.github/.github/workflows/tests.yml@v1"
     with:
+      julia-version: "${{ matrix.version }}"
       group: "${{ matrix.group }}"
     secrets: "inherit"

Project.toml

@@ -1,13 +1,14 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.41.0"
+version = "9.48.0"
 
 [deps]
 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"
@@ -36,6 +37,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 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"
@@ -60,27 +62,30 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
+HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 
 [extensions]
 MTKBifurcationKitExt = "BifurcationKit"
 MTKChainRulesCoreExt = "ChainRulesCore"
 MTKDeepDiffsExt = "DeepDiffs"
+MTKHomotopyContinuationExt = "HomotopyContinuation"
 MTKLabelledArraysExt = "LabelledArrays"
 
 [compat]
 AbstractTrees = "0.3, 0.4"
 ArrayInterface = "6, 7"
-BifurcationKit = "0.3"
+BifurcationKit = "0.4"
 BlockArrays = "1.1"
 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"
+DiffEqBase = "6.157"
 DiffEqCallbacks = "2.16, 3, 4"
 DiffEqNoiseProcess = "5"
 DiffRules = "0.1, 1.0"
@@ -96,6 +101,7 @@ ForwardDiff = "0.10.3"
 FunctionWrappers = "1.1"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
+HomotopyContinuation = "2.11"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
 JumpProcesses = "9.13.1"
@@ -106,23 +112,26 @@ LinearAlgebra = "1"
 MLStyle = "0.4.17"
 NaNMath = "0.3, 1"
 NonlinearSolve = "3.14"
+OffsetArrays = "1"
 OrderedCollections = "1"
 OrdinaryDiffEq = "6.82.0"
+OrdinaryDiffEqCore = "1.7.0"
 PrecompileTools = "1"
+REPL = "1"
 RecursiveArrayTools = "3.26"
 Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.5.9"
-SciMLBase = "2.52.1"
+SciMLBase = "2.57.1"
 SciMLStructures = "1.0"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
 SimpleNonlinearSolve = "0.1.0, 1"
 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"
+SymbolicIndexingInterface = "0.3.31"
 SymbolicUtils = "3.7"
-Symbolics = "6.12"
+Symbolics = "6.15.2"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -145,7 +154,9 @@ 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"
 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"
@@ -158,4 +169,4 @@ 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", "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", "REPL", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]

docs/Project.toml

@@ -1,6 +1,7 @@
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
@@ -22,7 +23,8 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 BenchmarkTools = "1.3"
-BifurcationKit = "0.3"
+BifurcationKit = "0.4"
+DataInterpolations = "6.5"
 DifferentialEquations = "7.6"
 Distributions = "0.25"
 Documenter = "1"

docs/pages.jl

@@ -12,12 +12,12 @@ pages = [
         "tutorials/parameter_identifiability.md",
         "tutorials/bifurcation_diagram_computation.md",
         "tutorials/SampledData.md",
-        "tutorials/domain_connections.md"],
+        "tutorials/domain_connections.md",
+        "tutorials/callable_params.md"],
     "Examples" => Any[
         "Basic Examples" => Any["examples/higher_order.md",
             "examples/spring_mass.md",
             "examples/modelingtoolkitize_index_reduction.md",
-            "examples/parsing.md",
             "examples/remake.md"],
         "Advanced Examples" => Any["examples/tearing_parallelism.md",
             "examples/sparse_jacobians.md",

docs/src/basics/AbstractSystem.md

@@ -63,6 +63,7 @@ Optionally, a system could have:
   - `get_defaults(sys)`: A `Dict` that maps variables into their default values
     for the current-level system.
   - `get_noiseeqs(sys)`: Noise equations of the current-level system.
+  - `get_description(sys)`: A string that describes what a system represents.
   - `get_metadata(sys)`: Any metadata about the system or its origin to be used by downstream packages.
 
 Note that if you know a system is an `AbstractTimeDependentSystem` you could use `get_iv` to get the

docs/src/basics/MTKLanguage.md

@@ -63,16 +63,17 @@ end
     @structural_parameters begin
         f = sin
         N = 2
+        M = 3
     end
     begin
         v_var = 1.0
     end
     @variables begin
         v(t) = v_var
-        v_array(t)[1:2, 1:3]
+        v_array(t)[1:N, 1:M]
         v_for_defaults(t)
     end
-    @extend ModelB(; p1)
+    @extend ModelB(p1 = 1)
     @components begin
         model_a = ModelA(; k_array)
         model_array_a = [ModelA(; k = i) for i in 1:N]
@@ -148,14 +149,18 @@ julia> ModelingToolkit.getdefault(model_c1.v)
 
 #### `@extend` begin block
 
-  - Partial systems can be extended in a higher system as `@extend PartialSystem(; kwargs)`.
-  - Keyword arguments pf partial system in the `@extend` definition are added as the keyword arguments of the base system.
-  - Note that in above example, `p1` is promoted as an argument of `ModelC`. Users can set the value of `p1`. However, as `p2` isn't listed in the model definition, its initial guess can't be specified while creating an instance of `ModelC`.
+Partial systems can be extended in a higher system in two ways:
 
-```julia
-julia> @mtkbuild model_c2 = ModelC(; p1 = 2.0)
+  - `@extend PartialSystem(var1 = value1)`
+    
+      + This is the recommended way of extending a base system.
+      + The default values for the arguments of the base system can be declared in the `@extend` statement.
+      + Note that all keyword arguments of the base system are added as the keyword arguments of the main system.
 
-```
+  - `@extend var_to_unpack1, var_to_unpack2 = partial_sys = PartialSystem(var1 = value1)`
+    
+      + In this method: explicitly list the variables that should be unpacked, provide a name for the partial system and declare the base system.
+      + Note that only the arguments listed out in the declaration of the base system (here: `var1`) are added as the keyword arguments of the higher system.
 
 #### `@components` begin block
 
@@ -301,7 +306,7 @@ end
 
     For more examples of usage, checkout [ModelingToolkitStandardLibrary.jl](https://github.com/SciML/ModelingToolkitStandardLibrary.jl/)
 
-## More on `Model.structure`
+## [More on `Model.structure`](@id model_structure)
 
 `structure` stores metadata that describes composition of a model. It includes:
 
@@ -324,17 +329,57 @@ For example, the structure of `ModelC` is:
 julia> ModelC.structure
 Dict{Symbol, Any} with 10 entries:
   :components            => Any[Union{Expr, Symbol}[:model_a, :ModelA], Union{Expr, Symbol}[:model_array_a, :ModelA, :(1:N)], Union{Expr, Symbol}[:model_array_b, :ModelA, :(1:N)]]
-  :variables             => Dict{Symbol, Dict{Symbol, Any}}(:v=>Dict(:default=>:v_var, :type=>Real), :v_array=>Dict(:type=>Real, :size=>(2, 3)), :v_for_defaults=>Dict(:type=>Real))
+  :variables             => Dict{Symbol, Dict{Symbol, Any}}(:v=>Dict(:default=>:v_var, :type=>Real), :v_array=>Dict(:value=>nothing, :type=>Real, :size=>(:N, :M)), :v_for_defaults=>Dict(:type=>Real))
   :icon                  => URI("https://github.com/SciML/SciMLDocs/blob/main/docs/src/assets/logo.png")
-  :kwargs                => Dict{Symbol, Dict}(:f=>Dict(:value=>:sin), :N=>Dict(:value=>2), :v=>Dict{Symbol, Any}(:value=>:v_var, :type=>Real), :v_array=>Dict{Symbol, Union{Nothing, UnionAll}}(:value=>nothing, :type=>AbstractArray{Real}), :v_for_defaults=>Dict{Symbol, Union{Nothing, DataType}}(:value=>nothing, :type=>Real), :p1=>Dict(:value=>nothing))
-  :structural_parameters => Dict{Symbol, Dict}(:f=>Dict(:value=>:sin), :N=>Dict(:value=>2))
-  :independent_variable  => t
+  :kwargs                => Dict{Symbol, Dict}(:f=>Dict(:value=>:sin), :p2=>Dict(:value=>NoValue()), :N=>Dict(:value=>2), :M=>Dict(:value=>3), :v=>Dict{Symbol, Any}(:value=>:v_var, :type=>Real), :v_array=>Dict{Symbol, Any}(:value=>nothing, :type=>Real, :size=>(:N, :M)), :v_for_defaults=>Dict{Symbol, Union{Nothing, DataType}}(:value=>nothing, :type=>Real), :p1=>Dict(:value=>1))
+  :structural_parameters => Dict{Symbol, Dict}(:f=>Dict(:value=>:sin), :N=>Dict(:value=>2), :M=>Dict(:value=>3))
+  :independent_variable  => :t
   :constants             => Dict{Symbol, Dict}(:c=>Dict{Symbol, Any}(:value=>1, :type=>Int64, :description=>"Example constant."))
   :extend                => Any[[:p2, :p1], Symbol("#mtkmodel__anonymous__ModelB"), :ModelB]
   :defaults              => Dict{Symbol, Any}(:v_for_defaults=>2.0)
   :equations             => Any["model_a.k ~ f(v)"]
 ```
 
+### Different ways to define symbolics arrays:
+
+`@mtkmodel` supports symbolics arrays in both `@parameters` and `@variables`.
+Using a structural parameters, symbolic arrays of arbitrary lengths can be defined.
+Refer the following example for different ways to define symbolic arrays.
+
+```@example mtkmodel-example
+@mtkmodel ModelWithArrays begin
+    @structural_parameters begin
+        N = 2
+        M = 3
+    end
+    @parameters begin
+        p1[1:4]
+        p2[1:N]
+        p3[1:N, 1:M] = 10,
+        [description = "A multi-dimensional array of arbitrary length with description"]
+        (p4[1:N, 1:M] = 10),
+        [description = "An alternate syntax for p3 to match the syntax of vanilla parameters macro"]
+    end
+    @variables begin
+        v1(t)[1:2] = 10, [description = "An array of variable `v1`"]
+        v2(t)[1:3] = [1, 2, 3]
+    end
+end
+```
+
+The size of symbolic array can be accessed via `:size` key, along with other metadata (refer [More on `Model.structure`](@ref model_structure))
+of the symbolic variable.
+
+```julia
+julia> ModelWithArrays.structure
+Dict{Symbol, Any} with 5 entries:
+    :variables => Dict{Symbol, Dict{Symbol, Any}}(:v2 => Dict(:value => :([1, 2, 3]), :type => Real, :size => (3,)), :v1 => Dict(:value => :v1, :type => Real, :description => "An array of variable `v1`", :size => (2,)))
+    :kwargs => Dict{Symbol, Dict}(:p2 => Dict{Symbol, Any}(:value => nothing, :type => Real, :size => (:N,)), :v1 => Dict{Symbol, Any}(:value => :v1, :type => Real, :description => "An array of variable `v1`", :size => (2,)), :N => Dict(:value => 2), :M => Dict(:value => 3), :p4 => Dict{Symbol, Any}(:value => 10, :type => Real, :description => "An alternate syntax for p3 to match the syntax of vanilla parameters macro", :size => (:N, :M)), :v2 => Dict{Symbol, Any}(:value => :([1, 2, 3]), :type => Real, :size => (3,)), :p1 => Dict{Symbol, Any}(:value => nothing, :type => Real, :size => (4,)), :p3 => Dict{Symbol, Any}(:value => :p3, :type => Real, :description => "A multi-dimensional array of arbitrary length with description", :size => (:N, :M)))
+    :structural_parameters => Dict{Symbol, Dict}(:N => Dict(:value => 2), :M => Dict(:value => 3))
+    :independent_variable => :t
+    :parameters => Dict{Symbol, Dict{Symbol, Any}}(:p2 => Dict(:value => nothing, :type => Real, :size => (:N,)), :p4 => Dict(:value => 10, :type => Real, :description => "An alternate syntax for p3 to match the syntax of vanilla parameters macro", :size => (:N, :M)), :p1 => Dict(:value => nothing, :type => Real, :size => (4,)), :p3 => Dict(:value => :p3, :type => Real, :description => "A multi-dimensional array of arbitrary length with description", :size => (:N, :M)))), false)
+```
+
 ### Using conditional statements
 
 #### Conditional elements of the system