Merge pull request #1077 from isaacsas/collect_vars_support

collect_vars support

Author: isaacsas

src/Catalyst.jl

@@ -31,7 +31,8 @@ using ModelingToolkit: Symbolic, value, get_unknowns, get_ps, get_iv, get_system
 import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_variables!,
                         modified_unknowns!, validate, namespace_variables,
                         namespace_parameters, rename, renamespace, getname, flatten,
-                        is_alg_equation, is_diff_equation
+                        is_alg_equation, is_diff_equation, collect_vars!,
+                        eqtype_supports_collect_vars
 
 # internal but needed ModelingToolkit functions
 import ModelingToolkit: check_variables,

src/reaction.jl

@@ -348,6 +348,30 @@ end
 MT.is_diff_equation(rx::Reaction) = false
 MT.is_alg_equation(rx::Reaction) = false
 
+# MTK functions for extracting variables within equation type object
+MT.eqtype_supports_collect_vars(rx::Reaction) = true
+function MT.collect_vars!(unknowns, parameters, rx::Reaction, iv; depth = 0,
+        op = MT.Differential)
+    MT.collect_vars!(unknowns, parameters, rx.rate, iv; depth, op)
+    for sub in rx.substrates
+        MT.collect_vars!(unknowns, parameters, sub, iv; depth, op)
+    end
+    for prod in rx.products
+        MT.collect_vars!(unknowns, parameters, prod, iv; depth, op)
+    end
+    for substoich in rx.substoich
+        MT.collect_vars!(unknowns, parameters, substoich, iv; depth, op)
+    end
+    for prodstoich in rx.prodstoich
+        MT.collect_vars!(unknowns, parameters, prodstoich, iv; depth, op)
+    end
+    if hasnoisescaling(rx)
+        ns = getnoisescaling(rx)
+        MT.collect_vars!(unknowns, parameters, ns, iv; depth, op)
+    end
+    return nothing
+end
+
 """
     get_symbolics(set, rx::Reaction)
 

test/reactionsystem_core/reaction.jl

@@ -3,7 +3,7 @@
 # Fetch packages.
 using Catalyst, Test
 using Catalyst: get_symbolics
-using ModelingToolkit: value, get_variables!
+using ModelingToolkit: value, get_variables!, collect_vars!, eqtype_supports_collect_vars
 
 # Sets the default `t` to use.
 t = default_t()
@@ -235,4 +235,20 @@ let
     @test Catalyst.hasmisc(r2)
     @test_throws Exception Catalyst.getmisc(r1)
     @test isequal(Catalyst.getmisc(r2), ('M', :M))
+end
+
+# tests for collect_vars!
+let
+    t = default_t()
+    @variables E(t) F(t)
+    @species A(t) B(t) C(t) D(t) 
+    @parameters k1, k2, η
+
+    rx = Reaction(k1*E, [A, B], [C], [k2*D, 3], [F], metadata = [:noise_scaling => η])
+    us = Set()
+    ps = Set()
+    @test eqtype_supports_collect_vars(rx) == true
+    collect_vars!(us, ps, rx, t)
+    @test us == Set((A, B, C, D, E, F))
+    @test ps == Set((k1, k2, η))
 end