Merge pull request #49 from SciML/YingboMa-patch-1

Actually return parameters

Author: YingboMa

Project.toml

@@ -1,14 +1,15 @@
 name = "CellMLToolkit"
 uuid = "03cb29e0-1ef4-4721-aa24-cf58a006576f"
 authors = ["Shahriar Iravanian <siravan@svtsim.com>"]
-version = "2.4.1"
+version = "2.4.2"
 
 [deps]
 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"
 
@@ -17,14 +18,15 @@ EzXML = "1.1"
 MathML = "0.1"
 Memoize = "0.4"
 ModelingToolkit = "5.14.1"
-SymbolicUtils = "0.10.2"
+Setfield = "0.7"
+SymbolicUtils = "0.10.2, 0.11"
 julia = "1.5"
 
 [extras]
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-  
+
 [targets]
 test = ["Test", "ModelingToolkit", "OrdinaryDiffEq", "JSON3"]

src/analysis.jl

@@ -5,10 +5,10 @@
 function simplify_systems(systems)
     for x in systems
         sys = last(x)
-        print("simplifying $(sys.name)")
+        print("simplifying $(nameof(sys))")
         try
             sys = structural_simplify(sys)
-            k = max(1, 50-length(string(sys.name)))
+            k = max(1, 50-length(string(nameof(sys))))
             printstyled(repeat(" ", k) * "OK!"; color=:green)
             println()
         catch e

src/components.jl

@@ -1,3 +1,5 @@
+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"
@@ -8,7 +10,6 @@ create_var(x, iv) = Num(Variable{Symbolics.FnType{Tuple{Any},Real}}(Symbol(x)))(
 function create_param(x)
   p = Sym{Real}(Symbol(x))
   ModelingToolkit.toparam(p)
-  p
 end
 
 to_symbol(x::Symbol) = x
@@ -234,7 +235,7 @@ function process_components(doc::Document; simplify=true)
 
     if simplify
         sys = structural_simplify(sys)
-        sys = ODESystem(substitute_eqs(sys.eqs, post_sub), sys.iv, sys.states, sys.ps)
+        @set! sys.eqs = substitute_eqs(equations(sys), post_sub)
     end
 
     return sys