fix failing tests in test/reactionsystem.jl; put variables in testset…

… scope
LCSB-BioCore · Jun 1, 2021 · 44d88f5 · 44d88f5
1 parent dce53c3
commit 44d88f5
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 22 deletions.
diff --git a/test/reactionsystem.jl b/test/reactionsystem.jl
@@ -1,23 +1,19 @@
-using Catalyst, ModelingToolkit, OrdinaryDiffEq
-
-sbmlfile = "reactionsystem_01.xml"
-
-@parameters t, k1, c1
-@variables s1, s2, s1s2
-
-COMP1 = SBML.Compartment("c1", true, 3, 2., "nl") 
-SPECIES1 = SBML.Species("s1", "c1", false, nothing, nothing, (1., "substance"), nothing, true)  # Todo: Maybe not support units in initial_concentration?
-SPECIES2 = SBML.Species("s2", "c1", false, nothing, nothing, nothing, (1., "substance/nl"), false)
-KINETICMATH1 = SBML.MathIdent("k1")
-KINETICMATH2 = SBML.MathApply("*", SBML.Math[
-    SBML.MathIdent("k1"), SBML.MathIdent("s2")])
-REACTION1 = SBML.Reaction(Dict("s1" => 1), nothing, nothing, nothing, nothing, KINETICMATH1, false)
-REACTION2 = SBML.Reaction(Dict("s2" => -1), nothing, nothing, nothing, nothing, KINETICMATH2, false)
-MODEL1 = SBML.Model(Dict("k1" => 1.), Dict(), Dict("c1" => COMP1), Dict("s1" => SPECIES1), Dict("r1" => REACTION1), nothing, nothing)  # PL: For instance in the compartments dict, we may want to enforce that key and compartment.name are identical
-MODEL2 = SBML.Model(Dict("k1" => 1.), Dict(), Dict("c1" => COMP1), Dict("s2" => SPECIES2), Dict("r2" => REACTION2), nothing, nothing)
-
-
 @testset "Model to MTK conversions" begin
+
+    sbmlfile = "reactionsystem_01.xml"
+    @parameters t, k1, c1
+    @variables s1, s2, s1s2
+
+    COMP1 = SBML.Compartment("c1", true, 3, 2., "nl") 
+    SPECIES1 = SBML.Species("s1", "c1", false, nothing, nothing, (1., "substance"), nothing, true)  # Todo: Maybe not support units in initial_concentration?
+    SPECIES2 = SBML.Species("s2", "c1", false, nothing, nothing, nothing, (1., "substance/nl"), false)
+    KINETICMATH1 = SBML.MathIdent("k1")
+    KINETICMATH2 = SBML.MathApply("*", SBML.Math[
+        SBML.MathIdent("k1"), SBML.MathIdent("s2")])
+    REACTION1 = SBML.Reaction(Dict("s1" => 1), nothing, nothing, nothing, nothing, KINETICMATH1, false)
+    REACTION2 = SBML.Reaction(Dict("s2" => -1), nothing, nothing, nothing, nothing, KINETICMATH2, false)
+    MODEL1 = SBML.Model(Dict("k1" => 1.), Dict(), Dict("c1" => COMP1), Dict("s1" => SPECIES1), Dict("r1" => REACTION1), Dict(), Dict())  # PL: For instance in the compartments dict, we may want to enforce that key and compartment.name are identical
+    MODEL2 = SBML.Model(Dict("k1" => 1.), Dict(), Dict("c1" => COMP1), Dict("s2" => SPECIES2), Dict("r2" => REACTION2), Dict(), Dict())
 
     # Test ReactionSystem constructor
     rs = ReactionSystem(MODEL1)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,4 +1,4 @@
-using ModelingToolkit
+using Catalyst, ModelingToolkit, OrdinaryDiffEq
 using Test, SHA, SparseArrays
 using SBML
 using SBML: Model, Reaction, Species
@@ -9,6 +9,6 @@ import Pkg
     # include("ecoli_flux.jl")
     # include("loadmodels.jl")
     # include("sbml2symbolics.jl")
-    # include("reactionsystem.jl")
-    include("loaddynamicmodels.jl")
+    include("reactionsystem.jl")
+    # include("loaddynamicmodels.jl")
 end