Merge pull request #251 from isaacsas/graph-tweak

Switch Catlab to imports

Author: isaacsas

src/Catalyst.jl

@@ -27,8 +27,7 @@ include("latexify_recipes.jl")
 
 # for making and saving graphs
 import Base.Iterators: flatten
-using Catlab.Graphics.Graphviz
-import Catlab.Graphics.Graphviz: Graph, Edge
+import Catlab.Graphics.Graphviz: Graph, Edge, Attributes, Node, Digraph, run_graphviz
 include("graphs.jl")
 export Graph, savegraph
 

src/graphs.jl

@@ -63,7 +63,7 @@ function Graph(rn::ReactionSystem)
     (!isempty(es)) && push!(edges, es)
 
     stmts = vcat(stmts, collect(flatten(edges)))
-    g = Graphviz.Digraph("G", stmts; graph_attrs=graph_attrs, node_attrs=node_attrs, edge_attrs=edge_attrs)
+    g = Digraph("G", stmts; graph_attrs=graph_attrs, node_attrs=node_attrs, edge_attrs=edge_attrs)
     return g
 end
 

src/latexify_recipes.jl

@@ -45,10 +45,16 @@ function chemical_arrows(rn::ModelingToolkit.ReactionSystem;
     eol = double_linebreak ? "\\\\\\\\\n" : "\\\\\n"
 
     mathjax && (str *= "\\require{mhchem}\n")
-
-
     backwards_reaction = false
     rxs = ModelingToolkit.equations(rn)
+    @variables t
+    
+    # this should replace A(t) with A in equations however, currently substituter rewrites 
+    # things like x/y as inv(y)*x^1 which looks worse... for now we leave a stub that can 
+    # be updated when substitution preserves expressions better.
+    # subber = ModelingToolkit.substituter([s(t) => s() for s in states(rn)])        
+    subber = x -> x
+
     for (i, r) in enumerate(rxs)
         if backwards_reaction
             backwards_reaction = false
@@ -57,7 +63,7 @@ function chemical_arrows(rn::ModelingToolkit.ReactionSystem;
         str *= "\\ce{ "
 
         ### Expand functions to maths expressions
-        rate = r.rate isa Operation ? Expr(r.rate) : r.rate
+        rate = r.rate isa Operation ? Expr(subber(r.rate)) : r.rate
         expand && (rate = recursive_clean!(rate))
         expand && (rate = recursive_clean!(rate))
 
@@ -72,7 +78,7 @@ function chemical_arrows(rn::ModelingToolkit.ReactionSystem;
         poststr = mathjax ? "]" : "\$]"    
         if i + 1 <= length(rxs) && issetequal(r.products,rxs[i+1].substrates) && issetequal(r.substrates,rxs[i+1].products)
             ### Bi-directional arrows
-            rate_backwards = Expr(rxs[i+1].rate)
+            rate_backwards = rxs[i+1].rate isa Operation ? Expr(subber(rxs[i+1].rate)) : rxs[i+1].rate             
             expand && (rate_backwards = recursive_clean!(rate_backwards))
             expand && (rate_backwards = recursive_clean!(rate_backwards))
             str *= " &<=>"