Merge pull request #616 from isaacsas/avoid_repeated_reactants

Disallow repeated reactants and making hashing order independent

Author: isaacsas

src/networkapi.jl

@@ -1302,11 +1302,15 @@ end
 
 function hash(rx::Reaction, h::UInt)
     h = Base.hash(rx.rate, h)
-    h = Base.hash(rx.substrates, h)
-    h = Base.hash(rx.products, h)
-    h = Base.hash(rx.prodstoich, h)
-    h = Base.hash(rx.substoich, h)
-    h = Base.hash(rx.netstoich, h)
+    for s in Iterators.flatten((rx.substrates, rx.products))
+        h ⊻= hash(s)
+    end
+    for s in Iterators.flatten((rx.substoich, rx.prodstoich))
+        h ⊻= hash(s)
+    end
+    for s in rx.netstoich
+        h ⊻= hash(s)
+    end
     Base.hash(rx.only_use_rate, h)
 end
 

src/reactionsystem.jl

@@ -142,6 +142,8 @@ function Reaction(rate, subs, prods, substoich, prodstoich;
     else
         subs = value.(subs)
     end
+    allunique(subs) ||
+        throw(ArgumentError("Substrates can not be repeated in the list provided to `Reaction`, please modify the stoichiometry for any repeated substrates instead."))
     S = eltype(substoich)
 
     if isnothing(prods)
@@ -152,6 +154,8 @@ function Reaction(rate, subs, prods, substoich, prodstoich;
     else
         prods = value.(prods)
     end
+    allunique(prods) ||
+        throw(ArgumentError("Products can not be repeated in the list provided to `Reaction`, please modify the stoichiometry for any repeated products instead."))
     T = eltype(prodstoich)
 
     # try to get a common type for stoichiometry, using Any if have Syms

test/reactionsystem.jl

@@ -676,3 +676,27 @@ let
     @test issetequal(parameters(osys), [k1, k2])
     @test length(equations(osys)) == 3
 end
+
+# test errors for repeated substrates or products
+let
+    @variables t
+    @species A(t) B(t)
+    @test_throws ArgumentError Reaction(1.0, [A, A, B], [B])
+    @test_throws ArgumentError Reaction(1.0, [B], [A, A])
+    @test_throws ArgumentError Reaction(1.0, [A, A], [B, B])
+end
+
+# test order of species and products doesn't matter for equality or hashing
+let
+    @variables t
+    @species A(t) α(t)
+    rx = Reaction(1.0, [α, A], [α, A], [2, 3], [4, 5])
+    rx2 = Reaction(1.0, [A, α], [A, α], [3, 2], [5, 4])
+    @test rx == rx2
+    @test hash(rx) == hash(rx2)
+
+    rx = Reaction(1.0, [α, A], [α, A], [2, 3], [4, 5]; netstoich = [α => 2, A => 2])
+    rx2 = Reaction(1.0, [A, α], [A, α], [3, 2], [5, 4]; netstoich = [A => 2, α => 2])
+    @test rx == rx2
+    @test hash(rx) == hash(rx2)
+end