Final cleanup

src/simulation.jl

@@ -375,18 +375,20 @@ function compile(d::SummationDecapode, inputs::Vector{Symbol}, alloc_vectors::Ve
   # Get the Vars of the inputs (probably state Vars).
   visited_Var = falses(nparts(d, :Var))
 
-  # input_numbers = incident(d, inputs, :name)
+  # TODO: Pass in state indices instead of names
   input_numbers = reduce(vcat, incident(d, inputs, :name))
-  # visited_Var[collect(flatten(input_numbers))] .= true
+
   visited_Var[input_numbers] .= true
   visited_Var[incident(d, :Literal, :type)] .= true
 
+  # TODO: Collect these visited arrays into one structure indexed by :Op1, :Op2, and :Σ
   visited_1 = falses(nparts(d, :Op1))
   visited_2 = falses(nparts(d, :Op2))
   visited_Σ = falses(nparts(d, :Σ))
 
   # FIXME: this is a quadratic implementation of topological_sort inlined in here.
-  op_order = []
+  op_order = AbstractCall[]
+
   for _ in 1:(nparts(d, :Op1) + nparts(d,:Op2) + nparts(d, :Σ))
     for op in parts(d, :Op1)
       s = d[op, :src]
@@ -581,10 +583,10 @@ end
 A combined `infer_types` and `resolve_overloads` pipeline with default DEC rules.
 """
 function infer_overload_compiler!(d::SummationDecapode, dimension::Int)
-  if(dimension == 1)
+  if dimension == 1
     infer_types!(d, op1_inf_rules_1D, op2_inf_rules_1D)
     resolve_overloads!(d, op1_res_rules_1D, op2_res_rules_1D)
-  elseif(dimension == 2)
+  elseif dimension == 2
     infer_types!(d, op1_inf_rules_2D, op2_inf_rules_2D)
     resolve_overloads!(d, op1_res_rules_2D, op2_res_rules_2D)
   end
@@ -596,16 +598,9 @@ end
 Collects all DEC operators that are concrete matrices.
 """
 function init_dec_matrices!(d::SummationDecapode, dec_matrices::Vector{Symbol}, optimizable_dec_operators::Set{Symbol})
-
-  for op1_name in d[:op1]
-    if(op1_name ∈ optimizable_dec_operators)
-      push!(dec_matrices, op1_name)
-    end
-  end
-
-  for op2_name in d[:op2]
-    if(op2_name ∈ optimizable_dec_operators)
-      push!(dec_matrices, op2_name)
+  for op_name in vcat(d[:op1], d[:op2])
+    if(op_name in optimizable_dec_operators)
+      push!(dec_matrices, op_name)
     end
   end
 end
@@ -696,10 +691,13 @@ function gensim(user_d::SummationDecapode, input_vars::Vector{Symbol}; dimension
   (stateeltype == Float32 || stateeltype == Float64) ||
     throw(UnsupportedStateeltypeException(stateeltype))
 
-  recognize_types(user_d)
+  # Explicit copy for safety
+  gen_d = deepcopy(user_d)
+
+  recognize_types(gen_d)
 
   # Makes copy
-  gen_d = expand_operators(user_d)
+  gen_d = expand_operators(gen_d)
 
   dec_matrices = Vector{Symbol}()
   alloc_vectors = Vector{AllocVecCall}()