Fix namespacing of mixed equations and reactions

Author: YingboMa

src/systems/abstractsystem.jl

@@ -472,15 +472,18 @@ function namespace_defaults(sys)
          for (k, v) in pairs(defs))
 end
 
-function namespace_equations(sys::AbstractSystem)
+function namespace_equations(sys::AbstractSystem, ivs = nothing)
     eqs = equations(sys)
     isempty(eqs) && return Equation[]
-    map(eq -> namespace_equation(eq, sys), eqs)
+    map(eq -> namespace_equation(eq, sys; ivs), eqs)
 end
 
-function namespace_equation(eq::Equation, sys, n = nameof(sys))
-    _lhs = namespace_expr(eq.lhs, sys, n)
-    _rhs = namespace_expr(eq.rhs, sys, n)
+function namespace_equation(eq::Equation,
+    sys,
+    n = nameof(sys);
+    ivs = independent_variables(sys))
+    _lhs = namespace_expr(eq.lhs, sys, n; ivs)
+    _rhs = namespace_expr(eq.rhs, sys, n; ivs)
     _lhs ~ _rhs
 end
 
@@ -490,15 +493,14 @@ function namespace_assignment(eq::Assignment, sys)
     Assignment(_lhs, _rhs)
 end
 
-function namespace_expr(O, sys, n = nameof(sys))
-    ivs = independent_variables(sys)
+function namespace_expr(O, sys, n = nameof(sys); ivs = independent_variables(sys))
     O = unwrap(O)
     if any(isequal(O), ivs)
         return O
     elseif istree(O)
         T = typeof(O)
         renamed = let sys = sys, n = n, T = T
-            map(a -> namespace_expr(a, sys, n)::Any, arguments(O))
+            map(a -> namespace_expr(a, sys, n; ivs)::Any, arguments(O))
         end
         if isvariable(O)
             # Use renamespace so the scope is correct, and make sure to use the
@@ -513,7 +515,7 @@ function namespace_expr(O, sys, n = nameof(sys))
         renamespace(n, O)
     elseif O isa Array
         let sys = sys, n = n
-            map(o -> namespace_expr(o, sys, n), O)
+            map(o -> namespace_expr(o, sys, n; ivs), O)
         end
     else
         O