Merge pull request #128 from termi-official/do/mtk-update

Update to MTK 9

Project.toml

@@ -8,22 +8,19 @@ EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 MathML = "abcecc63-2b08-419c-80c4-c63dca6fa478"
 Memoize = "c03570c3-d221-55d1-a50c-7939bbd78826"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 Aqua = "0.8"
 EzXML = "1.1"
 MathML = "0.1.14"
 Memoize = "0.4.2"
-ModelingToolkit = "8.71"
+ModelingToolkit = "9"
 OrdinaryDiffEq = "6.56"
-Random = "1.10"
 SafeTestsets = "0.1"
-Setfield = "0.8, 1"
-SymbolicUtils = "1.2"
+Setfield = "1"
+SymbolicUtils = "1.2, 2"
 Test = "1.10"
 julia = "1.10"
 

src/CellMLToolkit.jl

@@ -1,11 +1,14 @@
 module CellMLToolkit
 
-using MathML
-
-using ModelingToolkit
-using SymbolicUtils: FnType, Sym, operation, arguments
-using EzXML
-using Memoize
+using EzXML: EzXML, elements, namespace, nodecontent, parentnode, readxml, root
+using MathML: extract_mathml, parse_node
+using Memoize: @memoize
+using SymbolicUtils: operation
+using ModelingToolkit: ModelingToolkit, @parameters, @variables, Differential,
+                       Equation, ODEProblem, ODESystem,
+                       Symbolics, equations, parameters, structural_simplify,
+                       substitute, unknowns
+using Setfield: @set!
 
 include("structures.jl")
 include("accessors.jl")

src/components.jl

@@ -1,5 +1,3 @@
-using Setfield
-
 const cellml_ns(xml::EzXML.Document) = namespace(root(xml))
 const cellml_ns(node::EzXML.Node) = namespace(node)
 const mathml_ns = "http://www.w3.org/1998/Math/MathML"
@@ -238,7 +236,8 @@ function process_components(doc::Document; simplify = true)
         # Defaults need to be set after simplifying as otherwise parameters and
         # states for which no defaults are available may still be present in
         # the system
-        @set! sys.defaults = Dict(find_list_value(doc, vcat(parameters(sys), states(sys))))
+        @set! sys.defaults = Dict(find_list_value(
+            doc, vcat(parameters(sys), unknowns(sys))))
     end
 
     return sys
@@ -310,7 +309,7 @@ function split_sym(sym)
 end
 
 find_sys_p(doc::Document, sys) = find_list_value(doc, parameters(sys))
-find_sys_u0(doc::Document, sys) = find_list_value(doc, states(sys))
+find_sys_u0(doc::Document, sys) = find_list_value(doc, unknowns(sys))
 
 function find_list_value(doc::Document, names)
     vars, syms = collect_initiated_values(doc)

src/import.jl

@@ -1,5 +1,3 @@
-using Random
-
 sym(x) = Symbol(x)
 
 function populate_dependency!(doc, comp)
@@ -154,7 +152,7 @@ function list_top_cellml_files(dir)
     imported = Set{String}()
     for f in files
         xml = readxml(joinpath(dir, f))
-        for n in CellMLToolkit.list_imports(xml)
+        for n in list_imports(xml)
             push!(imported, n["xlink:href"])
         end
     end

test/noble_1962.jl

@@ -6,7 +6,7 @@ ml = CellModel(path * "/../models/noble_1962/Noble_1962.cellml")
 
 prob = ODEProblem(ml, (0, 10000.0))
 sol1 = solve(prob, Euler(), dt = 0.01, saveat = 1.0)
-sol2 = solve(prob, TRBDF2(), dtmax = 0.5, saveat = 1.0)
+sol2 = solve(prob, TRBDF2(), dtmax = 0.5, saveat = 1.0, reltol = 1e-8, abstol = 1e-8)
 V1 = map(x -> x[2], sol1.u)
 V2 = map(x -> x[2], sol2.u)
 err1 = sum(abs.(V1 .- V2)) / length(V1)