Restore current SBML test-suite compatibility

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

Author: ChrisRackauckas

Project.toml

@@ -19,10 +19,10 @@ ModelingToolkit = "9.84, 10, 11"
 OrdinaryDiffEq = "6.107, 7"
 Plots = "1.41.6"
 SBML = "1.6"
-SBMLToolkitTestSuite = "0.0.5"
+SBMLToolkitTestSuite = "0.0.5, 1"
 SafeTestsets = "0.1, 1"
 SciMLTesting = "2.1"
-Sundials = "4.28, 5"
+Sundials = "4.28, 5, 6.1"
 SymbolicUtils = "3.32, 4"
 Symbolics = "6.58, 7"
 Test = "1"

src/events.jl

@@ -7,10 +7,9 @@ function get_events(model)  # Todo: implement up or downpass and parameters
     mtk_evs = Pair{Vector{Equation}, Vector{Equation}}[]
     for (_, e) in evs
         trigger = SBML.extensive_kinetic_math(model, e.trigger.math)
-        trigger = Symbolics.unwrap(interpret_as_num(trigger, model))
         lhs, rhs = map(
-            x -> substitute(x, subsdict),
-            SymbolicUtils.arguments(trigger),
+            x -> substitute(Symbolics.unwrap(interpret_as_num(x, model)), subsdict),
+            trigger.args,
         )
         trig = [lhs ~ rhs]
         mtk_evas = Equation[]

src/systems.jl

@@ -41,9 +41,9 @@ function SBML.readSBML(
         sbmlfile::String, ::ODESystemImporter;
         include_zero_odes::Bool = true, kwargs...
     )  # Returns an MTK.ODESystem
-    odesys = convert(
-        ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
-        include_zero_odes = include_zero_odes
+    odesys = _rs_to_odesys(
+        readSBML(sbmlfile, ReactionSystemImporter(); kwargs...);
+        include_zero_odes
     )
     return complete(odesys)
 end

src/utils.jl

@@ -154,7 +154,10 @@ function create_symbol(k::String, model::SBML.Model)
         v = model.parameters[k]
         if v.constant == false &&
                 (SBML.seemsdefined(k, model) || is_event_assignment(k, model))
-            sym = create_var(k, IV; isbcspecies = true)
+            sym = create_var(
+                k, IV; isbcspecies = true,
+                irreducible = is_event_assignment(k, model)
+            )
         else
             sym = create_param(k)
         end

test/systems.jl

@@ -1,5 +1,6 @@
 using SBMLToolkit
-using Catalyst, SBML
+using Catalyst, ModelingToolkit, SBML
+import Symbolics
 using Test
 
 cd(@__DIR__)
@@ -110,8 +111,15 @@ rs = ReactionSystem(MODEL2)  # Contains reversible reaction
 @test isequal(Catalyst.get_species(rs), [s1])
 @test issetequal(Catalyst.get_ps(rs), [k1, c1])
 
-@test convert(ModelingToolkit.ODESystem, rs) isa ODESystem
-@test structural_simplify(convert(ModelingToolkit.ODESystem, rs)) isa ODESystem
+if pkgversion(Catalyst) >= v"16"
+    odesys_from_rs = Catalyst.ode_model(rs)
+    @test odesys_from_rs isa ODESystem
+    @test mtkcompile(odesys_from_rs) isa ODESystem
+else
+    odesys_from_rs = convert(ModelingToolkit.ODESystem, rs)
+    @test odesys_from_rs isa ODESystem
+    @test structural_simplify(odesys_from_rs) isa ODESystem
+end
 
 # Test ODESystem constructor
 odesys = ODESystem(MODEL1)
@@ -123,7 +131,19 @@ trueeqs = Equation[default_time_deriv()(s1) ~ k1]
 u0 = [s1 => 1.0]
 par = [k1 => 1.0, c1 => 2.0]
 testdef = merge(Dict(u0), Dict(par))
-@test issubset(testdef, defaults(odesys))
+if pkgversion(ModelingToolkit) >= v"11"
+    initial_conditions = ModelingToolkit.initial_conditions(odesys)
+    bindings = ModelingToolkit.bindings(odesys)
+    @test all(
+        isequal(Symbolics.wrap(initial_conditions[Symbolics.unwrap(k)]), v)
+            for (k, v) in u0
+    )
+    @test all(
+        isequal(Symbolics.wrap(bindings[Symbolics.unwrap(k)]), v) for (k, v) in par
+    )
+else
+    @test issubset(testdef, ModelingToolkit.defaults(odesys))
+end
 @named odesys = ODESystem(MODEL1)
 isequal(nameof(odesys), :odesys)
 @test structural_simplify(odesys) isa ODESystem
@@ -142,7 +162,19 @@ trueeqs = Equation[
 u0 = [s1 => 2 * 1.0, s2 => 2 * 1.0, s1s2 => 2 * 1.0]
 par = [k1 => 1.0, c1 => 2.0]
 testdef = merge(Dict(u0), Dict(par))
-@test issubset(testdef, ModelingToolkit.defaults(odesys))
+if pkgversion(ModelingToolkit) >= v"11"
+    initial_conditions = ModelingToolkit.initial_conditions(odesys)
+    bindings = ModelingToolkit.bindings(odesys)
+    @test all(
+        isequal(Symbolics.wrap(initial_conditions[Symbolics.unwrap(k)]), v)
+            for (k, v) in u0
+    )
+    @test all(
+        isequal(Symbolics.wrap(bindings[Symbolics.unwrap(k)]), v) for (k, v) in par
+    )
+else
+    @test issubset(testdef, ModelingToolkit.defaults(odesys))
+end
 @named odesys = ODESystem(MODEL1)
 isequal(nameof(odesys), :odesys)