fix latex display of symbolic stoich

.gitignore

@@ -8,4 +8,6 @@ Manifest.toml
 
 # vscode stuff
 .vscode
-.vscode/*
+.vscode/*
+
+LocalPreferences.toml

Project.toml

@@ -1,6 +1,6 @@
 name = "Catalyst"
 uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
-version = "10.6"
+version = "10.6.0"
 
 [deps]
 AbstractAlgebra = "c3fe647b-3220-5bb0-a1ea-a7954cac585d"
@@ -9,6 +9,7 @@ DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqJump = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
@@ -25,6 +26,7 @@ DiffEqBase = "6.54.0"
 DiffEqJump = "7.0, 8.0"
 DocStringExtensions = "0.8"
 Graphs = "1.4"
+LaTeXStrings = "v1.3.0"
 Latexify = "0.14, 0.15"
 MacroTools = "0.5.5"
 ModelingToolkit = "6.3, 7.0, 8.0"

src/Catalyst.jl

@@ -5,7 +5,7 @@ module Catalyst
 
 using DocStringExtensions
 using SparseArrays, DiffEqBase, Reexport, DiffEqJump
-using Latexify, Requires
+using LaTeXStrings, Latexify, Requires
 
 # ModelingToolkit imports and convenience functions we use
 using ModelingToolkit; const MT = ModelingToolkit

src/latexify_recipes.jl

@@ -61,6 +61,22 @@ function any_nonrx_subsys(rn::MT.AbstractSystem)
     false
 end
 
+function make_stoich_str(spec, stoich, subber; kwargs...)
+    if isequal(stoich,one(stoich)) 
+        latexraw(subber(spec); kwargs...) 
+    else
+        if Symbolics.istree(stoich)
+            LaTeXString("(") * 
+            latexraw(subber(stoich); kwargs...) * 
+            LaTeXString(")") * 
+            latexraw(subber(spec); kwargs...) 
+        else
+            latexraw(subber(stoich); kwargs...) * LaTeXString(" ") * 
+            latexraw(subber(spec); kwargs...) 
+        end
+    end
+end
+
 function chemical_arrows(rn::ReactionSystem;
     expand = true, double_linebreak=false, mathjax=true, starred=false, kwargs...)
 
@@ -79,7 +95,7 @@ function chemical_arrows(rn::ReactionSystem;
     mathjax && (str *= "\\require{mhchem}\n")
     backwards_reaction = false
 
-    subber = ModelingToolkit.substituter([s => MT.operation(s) for s in species(rn)])
+    subber = ModelingToolkit.substituter([s => value(Symbolics.variable(MT.getname(s))) for s in species(rn)])
 
     for (i, r) in enumerate(rxs)
         if backwards_reaction
@@ -94,7 +110,9 @@ function chemical_arrows(rn::ReactionSystem;
         expand && (rate = recursive_clean!(rate))
 
         ### Generate formatted string of substrates
-        substrates = [latexraw("$(substrate[2]== 1 ? "" : "$(substrate[2]) * ") $(substrate[1].f.name)"; kwargs...) for substrate in zip(r.substrates,r.substoich)]
+        substrates = [make_stoich_str(substrate[1],substrate[2],subber; kwargs...) for substrate in zip(r.substrates,r.substoich)]
+        @show substrates
+        #substrates = [latexraw("$(substrate[2]== 1 ? "" : "$(substrate[2]) * ") $(substrate[1].f.name)"; kwargs...) for substrate in zip(r.substrates,r.substoich)]
         isempty(substrates) && (substrates = ["\\varnothing"])
 
         str *= join(substrates, " + ")
@@ -119,7 +137,8 @@ function chemical_arrows(rn::ReactionSystem;
         end
 
         ### Generate formatted string of products
-        products = [latexraw("$(product[2]== 1 ? "" : "$(product[2]) * ") $(product[1].f.name)"; kwargs...) for product in zip(r.products,r.prodstoich) ]
+        products = [make_stoich_str(product[1],product[2],subber; kwargs...) for product in zip(r.products,r.prodstoich)]
+        #products = [latexraw("$(product[2]== 1 ? "" : "$(product[2]) * ") $(product[1].f.name)"; kwargs...) for product in zip(r.products,r.prodstoich) ]
         isempty(products) && (products = ["\\varnothing"])
         str *= join(products, " + ")
         str *= "}$eol"