Merge pull request #502 from SciML/v9

Update for MTK v9

Author: ChrisRackauckas

.github/workflows/CI.yml

@@ -24,7 +24,6 @@ jobs:
           - DataDrivenLux
         version:
           - '1'
-          - '1.6'
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1

Project.toml

@@ -29,7 +29,7 @@ DataInterpolations = "4"
 DiffEqBase = "6"
 DocStringExtensions = "0.7, 0.8, 0.9"
 MLUtils = "0.3, 0.4"
-ModelingToolkit = "7, 8"
+ModelingToolkit = "9"
 Parameters = "0.12"
 ProgressMeter = "1.6"
 QuadGK = "2.4"
@@ -40,7 +40,7 @@ Statistics = "1"
 StatsBase = "0.32.0, 0.33, 0.34"
 SymbolicUtils = "1"
 Symbolics = "5"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

docs/Project.toml

@@ -13,7 +13,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 DataDrivenDiffEq = "1"
 Documenter = "1"
 Literate = "2.14"
-ModelingToolkit = "8"
+ModelingToolkit = "9"
 OrdinaryDiffEq = "6"
 Plots = "1"
 StableRNGs = "1"

src/DataDrivenDiffEq.jl

@@ -17,7 +17,7 @@ using ModelingToolkit: AbstractSystem
 using SymbolicUtils: operation, arguments, istree, issym
 using Symbolics
 using Symbolics: scalarize, variable, value
-@reexport using ModelingToolkit: states, parameters, independent_variable, observed,
+@reexport using ModelingToolkit: unknowns, parameters, independent_variable, observed,
                                  controls, get_iv, get_observed
 
 using Random
@@ -97,7 +97,7 @@ include("./basis/utils.jl")
 include("./basis/type.jl")
 export Basis
 export jacobian, dynamics
-export implicit_variables
+export implicit_variables, states
 export get_parameter_values, get_parameter_map
 
 include("./utils/basis_generators.jl")

src/basis/type.jl

@@ -53,7 +53,7 @@ struct Basis{IMPL, CTRLS} <: AbstractBasis
     """The equations of the basis"""
     eqs::Vector{Equation}
     """Dependent (state) variables"""
-    states::Vector
+    unknowns::Vector
     """Control variables"""
     ctrls::Vector
     """Parameters"""
@@ -168,7 +168,7 @@ end
 ## Printing
 
 @inline function Base.print(io::IO, x::AbstractBasis)
-    state = states(x)
+    state = unknowns(x)
     ps = parameters(x)
     Base.printstyled(io, "Model $(nameof(x)) with $(length(x)) equations\n"; bold = true)
     print(io, "States :")
@@ -207,7 +207,7 @@ end
 @inline function Base.print(io::IO, x::AbstractBasis, fullview::Bool)
     !fullview && return print(io, x)
 
-    state = states(x)
+    state = unknowns(x)
     ps = parameters(x)
     Base.printstyled(io, "Model $(nameof(x)) with $(length(x)) equations\n"; bold = true)
     print(io, "States :")
@@ -259,6 +259,10 @@ function implicit_variables(b::AbstractBasis)
     return getfield(b, :implicit)
 end
 
+function states(b::AbstractBasis)
+    return getfield(b, :unknowns)
+end
+
 # For internal use
 is_implicit(b::Basis{X, <:Any}) where {X} = X
 is_controlled(b::Basis{<:Any, X}) where {X} = X
@@ -380,7 +384,7 @@ Base.iterate(x::B, id) where {B <: AbstractBasis} = iterate(equations(x), id)
 ## Internal update
 function __update!(b::AbstractBasis, eval_expression = false)
     ff = DataDrivenFunction([bi.rhs for bi in collect(equations(b))],
-        implicit_variables(b), states(b), parameters(b), [get_iv(b)],
+        implicit_variables(b), unknowns(b), parameters(b), [get_iv(b)],
         controls(b), eval_expression)
     @set! b.f = ff
     return
@@ -403,13 +407,14 @@ If control variables are defined, the function can also be called by `f(u,p,t,co
 
 If the Jacobian with respect to other variables is needed, it can be passed via a second argument.
 """
-jacobian(x::Basis, eval_expression::Bool = false) = jacobian(x, states(x), eval_expression)
+jacobian(x::Basis, eval_expression::Bool = false) = jacobian(
+    x, unknowns(x), eval_expression)
 
 function jacobian(x::Basis, s, eval_expression::Bool = false)
     j = Symbolics.jacobian([xi.rhs for xi in equations(x)], s)
 
     return DataDrivenFunction(j,
-        implicit_variables(x), states(x), parameters(x), [get_iv(x)],
+        implicit_variables(x), unknowns(x), parameters(x), [get_iv(x)],
         controls(x), eval_expression)
 end
 
@@ -481,7 +486,7 @@ end
 
 function Base.merge!(x::Basis, y::Basis; eval_expression = false)
     push!(x, equations(y))
-    @set! x.states = unique(vcat(states(x), states(y)))
+    @set! x.unknowns = unique(vcat(unknowns(x), unknowns(y)))
     @set! x.ps = unique(vcat(parameters(x), parameters(y)))
     @set! x.ctrls = unique(vcat(controls(x), controls(y)))
     @set! x.observed = unique(vcat(get_observed(x), get_observed(y)))

src/problem/type.jl

@@ -287,7 +287,7 @@ get_name(p::AbstractDataDrivenProblem) = getfield(p, :name)
 
 ## Utils
 
-function ModelingToolkit.states(p::AbstractDataDrivenProblem, i = :, j = :)
+function states(p::AbstractDataDrivenProblem, i = :, j = :)
     x = getfield(p, :X)
     isempty(x) ? x : getindex(x, i, j)
 end

test/basis/basis.jl

@@ -114,7 +114,7 @@ end
 
     @test size(basis) == (6,)
     @test size(basis_2) == (5,)
-    @test basis_2([1.0; 2.0; π], [0.0; 1.0]) ≈ [1.0; -1.0; π; 2.0; 1.0]
+    @test basis_2([1.0; 2.0; π], [0.0; 1.0]) ≈ [1.0; -1.0; 2.0; π; 1.0]
     @test basis([1.0; 2.0; π], [0.0; 1.0]) ≈ [1.0; 2.0; π; -1.0; 5 * π + 2.0; 1.0]
 
     @test size(basis) == size(basis_2) .+ (1,)

test/runtests.jl

@@ -1,4 +1,4 @@
-using SafeTestsets, Pkg
+using SafeTestsets, Test, Pkg
 
 @info "Finished loading packages"
 
@@ -18,26 +18,28 @@ end
 
 @time begin
     if GROUP == "All" || GROUP == "Core" || GROUP == "Downstream"
-        @safetestset "Basis" begin
-            include("./basis/basis.jl")
-        end
-        @safetestset "Implicit Basis" begin
-            include("./basis/implicit_basis.jl")
-        end
-        @safetestset "Basis generators" begin
-            include("./basis/generators.jl")
-        end
-        @safetestset "DataDrivenProblem" begin
-            include("./problem/problem.jl")
-        end
-        @safetestset "DataDrivenSolution" begin
-            include("./solution/solution.jl")
-        end
-        @safetestset "Utilities" begin
-            include("./utils.jl")
-        end
-        @safetestset "CommonSolve" begin
-            include("./commonsolve/commonsolve.jl")
+        @testset "All" begin
+            @safetestset "Basis" begin
+                include("./basis/basis.jl")
+            end
+            @safetestset "Implicit Basis" begin
+                include("./basis/implicit_basis.jl")
+            end
+            @safetestset "Basis generators" begin
+                include("./basis/generators.jl")
+            end
+            @safetestset "DataDrivenProblem" begin
+                include("./problem/problem.jl")
+            end
+            @safetestset "DataDrivenSolution" begin
+                include("./solution/solution.jl")
+            end
+            @safetestset "Utilities" begin
+                include("./utils.jl")
+            end
+            @safetestset "CommonSolve" begin
+                include("./commonsolve/commonsolve.jl")
+            end
         end
     else
         dev_subpkg(GROUP)