save changes (init)

Author: TorkelE

.github/workflows/CI.yml

@@ -14,7 +14,16 @@ jobs:
     strategy:
       matrix:
         group:
-          - Core
+          - ReactionSystem
+          - DSL
+          - CompositionalModelling
+          - Miscellaneous
+          - NetworkAnalysis
+          - Simulation
+          - Upstream
+          - Spatial
+          - Visualisation
+          - Extensions
         version:
           - '1.10.2'
     steps:

test/programmatic_model_creation/component_based_model_creation.jl renamed to test/compositional_modelling/component_based_model_creation.jl

@@ -10,7 +10,16 @@ t = default_t()
 
 ### Naming Tests ###
 
-# Test that the correct name is generated.
+# Basic name test.
+let
+    rn = @reaction_network SIR1 begin
+        k1, S + I --> 2I
+        k2, I --> R
+    end
+    @test nameof(rn) == :SIR1
+end
+
+# Advanced name tests.
 let
     @parameters k
     @species A(t)
@@ -323,58 +332,6 @@ let
     @test length(equations(osys2)) == 2
 end
 
-# Test @variables in DSL.
-let
-    rn = @reaction_network tester begin
-        @parameters k1
-        @variables V1(t) V2(t) V3(t)
-        @species B1(t) B2(t)
-        (k1*k2 + V3), V1*A + 2*B1 --> V2*C + B2
-    end
-
-    @parameters k1 k2
-    @variables V1(t) V2(t) V3(t)
-    @species A(t) B1(t) B2(t) C(t)
-    rx = Reaction(k1*k2 + V3, [A, B1], [C, B2], [V1, 2], [V2, 1])
-    @named tester = ReactionSystem([rx], t)
-    @test tester == rn
-
-    sts = (A, B1, B2, C, V1, V2, V3)
-    spcs = (A, B1, B2, C)
-    @test issetequal(unknowns(rn), sts)
-    @test issetequal(species(rn), spcs)
-
-    @test_throws ArgumentError begin
-        rn = @reaction_network begin
-            @variables K
-            k, K*A --> B
-        end
-    end
-end
-
-# Test ivs in DSL.
-let
-    rn = @reaction_network ivstest begin
-        @ivs s x
-        @parameters k2
-        @variables D(x) E(s) F(s,x)
-        @species A(s,x) B(s) C(x)
-        k*k2*D, E*A +B --> F*C + C2
-    end
-
-    @parameters k k2
-    @variables s x D(x) E(s) F(s,x)
-    @species A(s,x) B(s) C(x) C2(s,x)
-    rx = Reaction(k*k2*D, [A, B], [C, C2], [E, 1], [F, 1])
-    @named ivstest = ReactionSystem([rx], s; spatial_ivs = [x])
-
-    @test ivstest == rn
-    @test issetequal(unknowns(rn), [D, E, F, A, B, C, C2])
-    @test issetequal(species(rn), [A, B, C, C2])
-    @test isequal(ModelingToolkit.get_iv(rn), s)
-    @test issetequal(Catalyst.get_sivs(rn), [x])
-end
-
 # Array variables test.
 let
     rn = @reaction_network arrtest begin

test/dsl/dsl_basics.jl renamed to test/dsl/dsl_advanced_model_construction.jl

@@ -435,15 +435,3 @@ let
     @test_throws LoadError @eval @reaction k, 0 --> im
     @test_throws LoadError @eval @reaction k, 0 --> nothing
 end
-
-
-### Other Tests ###
-
-# Test names work.
-let
-    rn = @reaction_network SIR1 begin
-        k1, S + I --> 2I
-        k2, I --> R
-    end
-    @test nameof(rn) == :SIR1
-end

test/dsl/dsl_model_construction.jl renamed to test/dsl/dsl_basic_model_construction.jl

@@ -14,7 +14,7 @@ seed = rand(rng, 1:100)
 # Sets the default `t` to use.
 t = default_t()
 
-### Tests `@parameters` and `@species` Options ###
+### Tests `@parameters`, `@species`, and `@variables` Options ###
 
 # Test creating networks with/without options.
 let
@@ -394,6 +394,61 @@ let
     @test !ModelingToolkit.hasdescription(unwrap(rn.k5))
 end
 
+# Test @variables in DSL.
+let
+    rn = @reaction_network tester begin
+        @parameters k1
+        @variables V1(t) V2(t) V3(t)
+        @species B1(t) B2(t)
+        (k1*k2 + V3), V1*A + 2*B1 --> V2*C + B2
+    end
+
+    @parameters k1 k2
+    @variables V1(t) V2(t) V3(t)
+    @species A(t) B1(t) B2(t) C(t)
+    rx = Reaction(k1*k2 + V3, [A, B1], [C, B2], [V1, 2], [V2, 1])
+    @named tester = ReactionSystem([rx], t)
+    @test tester == rn
+
+    sts = (A, B1, B2, C, V1, V2, V3)
+    spcs = (A, B1, B2, C)
+    @test issetequal(unknowns(rn), sts)
+    @test issetequal(species(rn), spcs)
+
+    @test_throws ArgumentError begin
+        rn = @reaction_network begin
+            @variables K
+            k, K*A --> B
+        end
+    end
+end
+
+### Test independent variable designation ###
+
+# Test ivs in DSL.
+let
+    rn = @reaction_network ivstest begin
+        @ivs s x
+        @parameters k2
+        @variables D(x) E(s) F(s,x)
+        @species A(s,x) B(s) C(x)
+        k*k2*D, E*A +B --> F*C + C2
+    end
+
+    @parameters k k2
+    @variables s x D(x) E(s) F(s,x)
+    @species A(s,x) B(s) C(x) C2(s,x)
+    rx = Reaction(k*k2*D, [A, B], [C, C2], [E, 1], [F, 1])
+    @named ivstest = ReactionSystem([rx], s; spatial_ivs = [x])
+
+    @test ivstest == rn
+    @test issetequal(unknowns(rn), [D, E, F, A, B, C, C2])
+    @test issetequal(species(rn), [A, B, C, C2])
+    @test isequal(ModelingToolkit.get_iv(rn), s)
+    @test issetequal(Catalyst.get_sivs(rn), [x])
+end
+
+
 ### Observables ###
 
 # Test basic functionality.
@@ -687,7 +742,7 @@ let
 end
 
 
-### Coupled CRN/Equations Models ###
+### Test `@equations` for Coupled CRN/Equations Models ###
 
 # Checks creation of basic network.
 # Check indexing of output solution.