Merge pull request #835 from SciML/test_restructure

Test restructure and parallelisation

.github/workflows/CI.yml

@@ -3,11 +3,9 @@ on:
   pull_request:
     branches:
       - master
-      - Catalyst_version_14
   push:
     branches:
       - master
-      - Catalyst_version_14
 jobs:
   test:
     runs-on: ubuntu-latest

test/programmatic_model_creation/component_based_model_creation.jl → test/compositional_modelling/component_based_model_creation.jl

@@ -6,7 +6,7 @@
 using Catalyst, LinearAlgebra, OrdinaryDiffEq, SciMLNLSolve, Test
 using ModelingToolkit: nameof
 
-# Fetch test networks.
+# Sets the default `t` to use.
 t = default_t()
 
 

test/dsl/dsl_basics.jl → test/dsl/dsl_advanced_model_construction.jl

@@ -1,6 +1,6 @@
 #! format: off
 
-### Fetch Packages and Set Global Variables ###
+### Prepares Tests ###
 
 # Fetch packages.
 using Catalyst, ModelingToolkit
@@ -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)
@@ -67,12 +76,12 @@ end
 
 ### Test Interpolation Within the DSL ###
 
-# Tests basic interpolation cases.
 
 # Declares parameters and species used across the test.
 @parameters α k k1 k2
 @species A(t) B(t) C(t) D(t)
 
+# Tests basic interpolation cases.
 let
     AA = A
     AAA = A^2 + B
@@ -92,7 +101,6 @@ let
     rn2 = ReactionSystem([Reaction(k, [AA,C], [D])], t; name=:rn)
     @test rn == rn2
 end
-
 let
     BB = B; A2 = A
     rn = @reaction_network rn begin
@@ -104,7 +112,6 @@ let
                         t; name=:rn)
     @test rn == rn2
 end
-
 let
     AA = A
     kk1 = k^2*A
@@ -323,58 +330,6 @@ 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_model_construction.jl → test/dsl/dsl_basic_model_construction.jl

@@ -4,12 +4,14 @@
 using DiffEqBase, Catalyst, Random, Test
 using ModelingToolkit: operation, istree, get_unknowns, get_ps, get_eqs, get_systems,
                        get_iv, nameof
-t = default_t()
 
-# Sets rnd number.
+# Sets stable rng number.
 using StableRNGs
 rng = StableRNG(12345)
 
+# Sets the default `t` to use.
+t = default_t()
+
 # Fetch test networks and functions.
 include("../test_networks.jl")
 include("../test_functions.jl")
@@ -33,7 +35,7 @@ function all_reactants(eqs)
     return Set{Symbol}(unique(all_reactants))
 end
 
-# Gets all parameters (where every reaction rate is constant)
+# Gets all parameters (where every reaction rate is constant).
 function all_parameters(eqs)
     return Set(unique(map(eq -> opname(eq.rate), eqs)))
 end
@@ -371,7 +373,7 @@ let
     end
 end
 
-# Test that I works as a name.
+# Test that the `I` symbol works as a quantity name.
 let
     rn = @reaction_network begin
         k1, S + I --> 2I
@@ -382,7 +384,7 @@ let
     @test any(isequal(I), unknowns(rn))
 end
 
-# Tests backwards and double arrows.
+# Tests backwards and bi-directional arrows.
 let
     rn1 = @reaction_network arrowtest begin
         (a1, a2), C <--> 0
@@ -401,7 +403,7 @@ let
     @test rn1 == rn2
 end
 
-# Tests arrow variants in "@reaction" macro .
+# Tests arrow variants in `@reaction`` macro .
 let
     @test isequal((@reaction k, 0 --> X), (@reaction k, X <-- 0))
     @test isequal((@reaction k, 0 --> X), (@reaction k, X ⟻ 0))
@@ -435,15 +437,3 @@ 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_options.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 Designations ###
+
+# 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.
@@ -596,7 +651,7 @@ let
     @test length(unknowns(rn2)) == 2
 end
 
-# Tests specific declaration of Observables as species/variables
+# Tests specific declaration of observables as species/variables.
 let
     rn = @reaction_network begin
         @species X(t)
@@ -687,7 +742,7 @@ let
 end
 
 
-### Coupled CRN/Equations Models ###
+### Test `@equations` Option for Coupled CRN/Equations Models ###
 
 # Checks creation of basic network.
 # Check indexing of output solution.