Merge pull request #589 from SciML/latexify_update

Add `form` option to latexify

src/latexify_recipes.jl

@@ -176,12 +176,17 @@ function chemical_arrows(rn::ReactionSystem; expand = true,
     return latexstr
 end
 
-@latexrecipe function f(sys::ReactionSystem)
-    # Set default option values.
-    env --> :chem
-    cdot --> false
-
-    return sys
+@latexrecipe function f(rs::ReactionSystem; form = :reactions)
+    if form == :reactions    # Returns chemical reaction network code.
+        cdot --> false
+        env --> :chem
+        return rs
+    elseif form == :ode      # Returns ODE system code.
+        return convert(ODESystem, rs)
+    elseif form == :sde      # Returns SDE system code.
+        return convert(SDESystem, rs)
+    end
+    error("Unrecognised form argument given: $form. This should be either reactions (default), :ode, or :sde.")
 end
 
 function Latexify.infer_output(env, rs::ReactionSystem, args...)

test/latexify.jl

@@ -2,6 +2,7 @@
 
 ### Fetch required packages and reaction networks ###
 using Catalyst, Latexify
+include("test_networks.jl")
 
 ############################
 ### CURRENTLY NOT ACITVE ###
@@ -122,3 +123,19 @@ raw"\begin{align*}
 \ce{ Y &->[$Y k$] \varnothing}
 \end{align*}
 ", "\r\n"=>"\n")
+
+# Tests the `form` option
+for rn in reaction_networks_standard
+    @test latexify(rn)==latexify(rn; form=:reactions)
+    #@test latexify(convert(ODESystem,rn)) == latexify(rn; form=:ode) # Slight difference due to some latexify weirdity. Both displays fine though
+end
+
+rn = @reaction_network begin 
+    (p,d), 0 <--> X
+    (kB,kD), 2X <--> X2
+end
+@test latexify(rn; form=:ode) == raw"$\begin{align}
+\frac{\mathrm{d} X\left( t \right)}{\mathrm{d}t} =& p - \left( X\left( t \right) \right)^{2} kB - d X\left( t \right) + 2 kD \mathrm{X2}\left( t \right) \\
+\frac{\mathrm{d} \mathrm{X2}\left( t \right)}{\mathrm{d}t} =& \frac{1}{2} \left( X\left( t \right) \right)^{2} kB - kD \mathrm{X2}\left( t \right)
+\end{align}
+$"