update to default_t and default_time_deriv

Author: paulflang

src/reactions.jl

@@ -168,7 +168,7 @@ function get_massaction(kl::Num, reactants::Union{Vector{Num}, Nothing},
 
     function check_args(::Val{true}, x::SymbolicUtils.BasicSymbolic{Real})
         for arg in SymbolicUtils.arguments(x)
-            if isnan(check_args(arg)) || isequal(arg, Catalyst.DEFAULT_IV)
+            if isnan(check_args(arg)) || isequal(arg, default_t())
                 return NaN
             end
         end

test/events.jl

@@ -2,7 +2,7 @@ using SBMLToolkit
 using Catalyst, SBMLToolkitTestSuite
 using Test
 
-const IV = Catalyst.DEFAULT_IV
+const IV = default_t()
 @parameters compartment
 @species S1(IV) S2(IV)
 

test/reactions.jl

@@ -4,7 +4,7 @@ using Test
 
 cd(@__DIR__)
 sbmlfile = joinpath("data", "reactionsystem_01.xml")
-const IV = Catalyst.DEFAULT_IV
+const IV = default_t()
 @parameters k1, c1
 @species s1(IV), s2(IV), s1s2(IV)
 

test/rules.jl

@@ -3,7 +3,7 @@ using SBML, SBMLToolkitTestSuite
 using Catalyst, ModelingToolkit, OrdinaryDiffEq
 using Test
 
-const IV = Catalyst.DEFAULT_IV
+const IV = default_t()
 @parameters k1, compartment
 @species S1(IV), S2(IV)
 
@@ -24,7 +24,7 @@ o_true = [S1 ~ 7 * compartment]
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00031")  # rateRule
 m = readmodel(sbml)
 a, o, r = SBMLToolkit.get_rules(m)
-r_true = [Differential(IV)(S1) ~ 7 * compartment]
+r_true = [default_time_deriv()(S1) ~ 7 * compartment]
 @test isequal(r, r_true)
 
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00039")  # algebraicRule

test/systems.jl

@@ -4,7 +4,7 @@ using Test
 
 cd(@__DIR__)
 sbmlfile = joinpath("data", "reactionsystem_01.xml")
-const IV = Catalyst.DEFAULT_IV
+const IV = default_t()
 @parameters k1, c1
 @species s1(IV), s2(IV), s1s2(IV)
 
@@ -79,7 +79,7 @@ rs = ReactionSystem(MODEL2)  # Contains reversible reaction
 
 # Test ODESystem constructor
 odesys = ODESystem(MODEL1)
-trueeqs = Equation[Differential(IV)(s1) ~ k1]
+trueeqs = Equation[default_time_deriv()(s1) ~ k1]
 @test isequal(Catalyst.get_eqs(odesys), trueeqs)
 @test isequal(Catalyst.get_iv(odesys), IV)
 @test isequal(Catalyst.get_unknowns(odesys), [s1])
@@ -93,9 +93,9 @@ isequal(nameof(odesys), :odesys)
 
 odesys = ODESystem(readSBML(sbmlfile))
 m = readSBML(sbmlfile)
-trueeqs = Equation[Differential(IV)(s1) ~ -((k1 * s1 * s2) / c1),
-    Differential(IV)(s1s2) ~ (k1 * s1 * s2) / c1,
-    Differential(IV)(s2) ~ -((k1 * s1 * s2) / c1)]
+trueeqs = Equation[default_time_deriv()(s1) ~ -((k1 * s1 * s2) / c1),
+    default_time_deriv()(s1s2) ~ (k1 * s1 * s2) / c1,
+    default_time_deriv()(s2) ~ -((k1 * s1 * s2) / c1)]
 @test isequal(Catalyst.get_eqs(odesys), trueeqs)
 @test isequal(Catalyst.get_iv(odesys), IV)
 @test isequal(Catalyst.get_unknowns(odesys), [s1, s1s2, s2])

test/utils.jl

@@ -25,7 +25,7 @@ MODEL1 = SBML.Model(parameters = Dict("D" => PARAM1, "Dv" => PARAM2),
     species = Dict("B" => SPECIES1, "Bc" => SPECIES2),
     rules = [RULE1])
 
-const IV = Catalyst.DEFAULT_IV
+const IV = default_t()
 @species s1(IV)
 # Test symbolicsRateOf
 rate = SBMLToolkit.symbolicsRateOf(s1)