Merge pull request #325 from SciML/myb/up

Update to SymbolicUtils v0.10

Author: ChrisRackauckas

src/Catalyst.jl

@@ -6,6 +6,7 @@ module Catalyst
 using DocStringExtensions
 using Reexport, ModelingToolkit
 using ModelingToolkit: Symbolic, value, istree, get_states, get_ps, get_iv, get_systems, get_eqs
+const DEFAULT_IV = (@parameters t)[1]
 @reexport using ModelingToolkit
 import MacroTools
 import Base: (==), merge!, merge

src/networkapi.jl

@@ -236,13 +236,12 @@ end
 ######################## functions to extend a network ####################
 
 """
-    make_empty_network(; iv=Sym{ModelingToolkit.Parameter{Real}}(:t), 
-                         name=gensym(:ReactionSystem))
+    make_empty_network(; iv=DEFAULT_IV, name=gensym(:ReactionSystem))
 
 Construct an empty [`ReactionSystem`](@ref). `iv` is the independent variable,
 usually time, and `name` is the name to give the `ReactionSystem`.
 """
-function make_empty_network(; iv=Sym{ModelingToolkit.Parameter{Real}}(:t), name=gensym(:ReactionSystem))
+function make_empty_network(; iv=DEFAULT_IV, name=gensym(:ReactionSystem))
     ReactionSystem(Reaction[], iv, [], [], Equation[], name, ReactionSystem[])
 end
 

test/api.jl

@@ -1,6 +1,6 @@
 using Catalyst, DiffEqBase, ModelingToolkit, Test
 
-using ModelingToolkit: value, Parameter
+using ModelingToolkit: value
 
 @parameters t k1 k2
 @variables S I R
@@ -62,9 +62,9 @@ addspecies!(rs, Variable(:S))
 @test numspecies(rs) == 3
 addspecies!(rs, Variable(:S), disablechecks=true)
 @test numspecies(rs) == 4
-addparam!(rs, Sym{Parameter{Real}}(:k1))
+addparam!(rs, k1)
 @test numparams(rs) == 2
-addparam!(rs, Variable{Parameter{Real}}(:k1), disablechecks=true)
+addparam!(rs, k1, disablechecks=true)
 @test numparams(rs) == 3
 
 
@@ -78,4 +78,4 @@ smat = [1 2 0;
 pmat = [0 2 0;
         1 0 2]
 @test all(smat .== substoichmat(rnmat))
-@test all(pmat .== prodstoichmat(rnmat))
+@test all(pmat .== prodstoichmat(rnmat))

test/make_model.jl

@@ -316,7 +316,7 @@ rs_3 = ReactionSystem(rxs_3, t, [X1,X2,X3,X4,X5], [k1,k2,k3])
 push!(identical_networks_4, reaction_networks_weird[7] => rs_3)
 
 for networks in identical_networks_4
-    @test independent_variable(networks[1]) == independent_variable(networks[2])
+    @test isequal(independent_variable(networks[1]), independent_variable(networks[2]))
     @test alleq(get_states(networks[1]), get_states(networks[2]))
     @test alleq(get_ps(networks[1]), get_ps(networks[2]))
     @test ModelingToolkit.get_systems(networks[1]) == ModelingToolkit.get_systems(networks[2])