Merge d1658d3 into 4feb634

Project.toml

@@ -3,6 +3,7 @@ uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
 version = "5.0"
 
 [deps]
+Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -26,4 +27,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [targets]
-test = ["DiffEqBase","DiffEqJump","OrdinaryDiffEq","Random","SafeTestsets", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "UnPack"]
+test = ["DiffEqBase", "DiffEqJump", "OrdinaryDiffEq", "Random", "SafeTestsets", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "UnPack"]

README.md

@@ -62,7 +62,8 @@ the current master branch.
 - Julia `Expr`s can be obtained for all rate laws and functions determining the
   deterministic and stochastic terms within resulting ODE, SDE or jump models.
 - [`Latexify`](https://github.com/korsbo/Latexify.jl) can be used to generate
-  LaTeX expressions corresponding to generated mathematical models.
+  LaTeX expressions corresponding to generated mathematical models or the
+  underlying set of reactions.
 
 ## Illustrative Examples
 #### Gillespie Simulations of Michaelis-Menten Enzyme Kinetics

docs/make.jl

@@ -1,6 +1,37 @@
 using Documenter
 using Catalyst, ModelingToolkit
 
+
+# supposed hack to get mhchem but doesn't seem to work yet...
+# const katex_version = "0.11.1"
+# function Documenter.Writers.HTMLWriter.RD.mathengine!(r::Documenter.Utilities.JSDependencies.RequireJS, engine::Documenter.KaTeX)
+#     push!(r, Documenter.Utilities.JSDependencies.RemoteLibrary(
+#         "katex",
+#         "https://cdnjs.cloudflare.com/ajax/libs/KaTeX/$(katex_version)/katex.min.js"
+#     ))
+#     push!(r, Documenter.Utilities.JSDependencies.RemoteLibrary(
+#         "mhchem",
+#         "https://cdnjs.cloudflare.com/ajax/libs/KaTeX/$(katex_version)/contrib/mhchem.min.js"
+#     ))
+#     push!(r, Documenter.Utilities.JSDependencies.RemoteLibrary(
+#         "katex-auto-render",
+#         "https://cdnjs.cloudflare.com/ajax/libs/KaTeX/$(katex_version)/contrib/auto-render.min.js",
+#         deps = ["katex"],
+#     ))
+#     push!(r, Documenter.Utilities.JSDependencies.Snippet(
+#         ["jquery", "katex", "mhchem", "katex-auto-render"],
+#         ["\$", "katex", "renderMathInElement"],
+#         """
+#         \$(document).ready(function() {
+#           renderMathInElement(
+#             document.body,
+#             $(Documenter.Utilities.JSDependencies.json_jsescape(engine.config, 2))
+#           );
+#         })
+#         """
+#     ))
+# end
+
 makedocs(
     sitename = "Catalyst.jl",
     authors = "Samuel Isaacson",

docs/src/index.md

@@ -35,7 +35,8 @@ estimation, machine learning applications, etc).
 - Julia `Expr`s can be obtained for all rate laws and functions determining the
   deterministic and stochastic terms within resulting ODE, SDE or jump models.
 - [`Latexify`](https://github.com/korsbo/Latexify.jl) can be used to generate
-  LaTeX expressions corresponding to generated mathematical models.
+  LaTeX expressions corresponding to generated mathematical models or the
+  underlying set of reactions.
 
 ## Installation
 Catalyst can be installed through the Julia package manager:
@@ -46,15 +47,19 @@ using Catalyst
 ```
 
 ## Illustrative Example
-Here is a simple example of generating and solving an SIR ODE model:
-
+Here is a simple example of generating and solving an SIR ODE model. We first
+define the SIR reaction model using Catalyst
 ```julia
-using Catalyst, DiffEqBase, OrdinaryDiffEq
+using Catalyst
 rn = @reaction_network begin
-    k1, S + I --> 2I
-    k2, I --> R
-end k1 k2
-p     = [.1/1000, .01]           # [k1,k2]
+    α, S + I --> 2I
+    β, I --> R
+end α β
+```
+To generate and solve a mass action ODE version of the model we use
+```julia
+using DiffEqBase, OrdinaryDiffEq
+p     = [.1/1000, .01]           # [α,β]
 tspan = (0.0,250.0)
 u0    = [999.0,1.0,0.0]          # [S,I,R] at t=0
 op    = ODEProblem(rn, u0, tspan, p)
@@ -66,3 +71,4 @@ using Plots
 plot(sol, lw=2)
 ```
 ![SIR Solution](assets/SIR.svg)
+

src/Catalyst.jl

@@ -4,6 +4,7 @@ using Reexport, ModelingToolkit
 @reexport using ModelingToolkit
 import MacroTools
 import Base: (==), merge!, merge
+using Latexify
 
 const ExprValues = Union{Expr,Symbol,Float64,Int}
 
@@ -21,4 +22,7 @@ export species, params, reactions, speciesmap, paramsmap, numspecies, numreactio
 export make_empty_network, addspecies!, addparam!, addreaction!
 export dependants, dependents
 
+# for Latex printing of ReactionSystems
+include("latexify_recipes.jl")
+
 end # module

src/latexify_recipes.jl

@@ -0,0 +1,118 @@
+# #Recursively traverses an expression and removes things like X^1, 1*X. Will not actually have any affect on the expression when used as a function, but will make it much easier to look at it for debugging, as well as if it is transformed to LaTeX code.
+function recursive_clean!(expr)
+    (expr isa Symbol) && (expr == :no___noise___scaling) && (return 1)
+    (typeof(expr)!=Expr) && (return expr)
+    for i = 1:length(expr.args)
+        expr.args[i] = recursive_clean!(expr.args[i])
+    end
+    (expr.args[1] == :^) && (expr.args[3] == 1) && (return expr.args[2])
+    if expr.args[1] == :*
+        in(0,expr.args) && (return 0)
+        i = 1
+        while (i = i + 1) <= length(expr.args)
+             if (typeof(expr.args[i]) == Expr) && (expr.args[i].head == :call) && (expr.args[i].args[1] == :*)
+                 for arg in expr.args[i].args
+                     (arg != :*) && push!(expr.args, arg)
+                 end
+             end
+        end
+        for i = length(expr.args):-1:2
+            (typeof(expr.args[i]) == Expr) && (expr.args[i].head == :call) && (expr.args[i].args[1] == :*) && deleteat!(expr.args,i)
+            (expr.args[i] == 1) && deleteat!(expr.args,i)
+        end
+        (length(expr.args) == 2) && (return expr.args[2])                   # We have a multiplication of only one thing, return only that thing.
+        (length(expr.args) == 1) && (return 1)                              #We have only * and no real argumenys.
+        (length(expr.args) == 3) && (expr.args[2] == -1) && return :(-$(expr.args[3]))
+        (length(expr.args) == 3) && (expr.args[3] == -1) && return :(-$(expr.args[2]))
+    end
+    if expr.head == :call
+        (expr.args[1] == :/) && (expr.args[3] == 1) && (return expr.args[2])
+        haskey(funcdict, expr.args[1]) && return funcdict[expr.args[1]](expr.args[2:end])
+        in(expr.args[1],hill_name) && return hill(expr)
+        in(expr.args[1],hillR_name) && return hillR(expr)
+        in(expr.args[1],mm_name) && return mm(expr)
+        in(expr.args[1],mmR_name) && return mmR(expr)
+        (expr.args[1] == :binomial) && (expr.args[3] == 1) && return expr.args[2]
+        #@isdefined($(expr.args[1])) || error("Function $(expr.args[1]) not defined.")
+    end
+    return expr
+end
+
+
+function chemical_arrows(rn::ModelingToolkit.ReactionSystem;
+    expand = true, double_linebreak=false, mathjax=true, starred=false, kwargs...)
+    str = starred ? "\\begin{align*}\n" : "\\begin{align}\n"
+    eol = double_linebreak ? "\\\\\\\\\n" : "\\\\\n"
+
+    mathjax && (str *= "\\require{mhchem}\n")
+
+
+    backwards_reaction = false
+    rxs = ModelingToolkit.equations(rn)
+    for (i, r) in enumerate(rxs)
+        if backwards_reaction
+            backwards_reaction = false
+            continue
+        end
+        str *= "\\ce{ "
+
+        ### Expand functions to maths expressions
+        rate = Expr(r.rate)
+        expand && (rate = recursive_clean!(rate))
+        expand && (rate = recursive_clean!(rate))
+
+        ### Generate formatted string of substrates
+        substrates = [latexraw("$(substrate[2]== 1 ? "" : "$(substrate[2]) * ") $(substrate[1].op.name)"; kwargs...) for substrate in zip(r.substrates,r.substoich)]
+        isempty(substrates) && (substrates = ["\\varnothing"])
+
+        str *= join(substrates, " + ")
+
+        ### Generate reaction arrows
+        if i + 1 <= length(rxs) && issetequal(r.products,rxs[i+1].substrates) && issetequal(r.substrates,rxs[i+1].products)
+            ### Bi-directional arrows
+            rate_backwards = Expr(rxs[i+1].rate)
+            expand && (rate_backwards = recursive_clean!(rate_backwards))
+            expand && (rate_backwards = recursive_clean!(rate_backwards))
+            str *= " &<=>"
+            str *= "[" * latexraw(rate; kwargs...) * "]"
+            str *= "[" * latexraw(rate_backwards; kwargs...) * "] "
+            backwards_reaction = true
+        else
+            ### Uni-directional arrows
+            str *= " &->"
+            str *= "[" * latexraw(rate; kwargs...) * "] "
+        end
+
+        ### Generate formatted string of products
+        products = [latexraw("$(product[2]== 1 ? "" : "$(product[2]) * ") $(product[1].op.name)"; kwargs...) for product in zip(r.products,r.prodstoich) ]
+        isempty(products) && (products = ["\\varnothing"])
+        str *= join(products, " + ")
+        str *= "}$eol"
+    end
+    str = str[1:end-length(eol)] * "\n"
+
+    str *= starred ? "\\end{align*}\n" : "\\end{align}\n"
+
+    latexstr = Latexify.LaTeXString(str)
+    Latexify.COPY_TO_CLIPBOARD && clipboard(latexstr)
+    return latexstr
+end
+
+
+@latexrecipe function f(sys::ModelingToolkit.ReactionSystem)
+    # Set default option values.
+    env --> :chem
+    cdot --> false
+
+    return sys
+end
+
+
+function Latexify.infer_output(env, rs::ReactionSystem, args...)
+    env in [:arrows, :chem, :chemical, :arrow] && return chemical_arrows
+
+    error("The environment $env is not defined.")
+    latex_function = Latexify.get_latex_function(rs, args...)
+
+    return latex_function
+end

test/latexify.jl

@@ -34,67 +34,37 @@ r = @reaction_network begin
     (d1,d2,d3,d4,d5), (X1,X2,X3,X4,X5)  ⟶ ∅
 end v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4 v5 K5 n5 k1 k2 k3 k4 k5 k6 d1 d2 d3 d4 d5
 
-@test latexify(r; noise=true, cdot=false) ==
+@test latexify(r) == 
 raw"\begin{align}
-\mathrm{dX1}\left( t \right) =& \left( \frac{v1 K1^{n1}}{K1^{n1} + X2^{n1}} \frac{v1 X4^{n1}}{K1^{n1} + X4^{n1}} + k1 X2 - \frac{k2}{2} X1 X4^{2} - \frac{k5}{6} X5^{3} X1 + k6 X2 - d1 X1 \right) dt + \sqrt{\left\|\frac{v1 K1^{n1}}{K1^{n1} + X2^{n1}} \frac{v1 X4^{n1}}{K1^{n1} + X4^{n1}}\right\|} dW_{1(t)} + \sqrt{\left\|k1 X2\right\|} dW_{6(t)} + \left(  - \sqrt{\left\|\frac{k2}{2} X1 X4^{2}\right\|} \right) dW_{7(t)} + \left(  - \sqrt{\left\|\frac{k5}{6} X5^{3} X1\right\|} \right) dW_{10(t)} + \sqrt{\left\|k6 X2\right\|} dW_{11(t)} + \left(  - \sqrt{\left\|d1 X1\right\|} \right) dW_{12(t)} \\
-\mathrm{dX2}\left( t \right) =& \left( \frac{v2 X5^{n2}}{K2^{n2} + X5^{n2}} - k1 X2 + \frac{k2}{2} X1 X4^{2} + \frac{k5}{6} X5^{3} X1 - k6 X2 - d2 X2 \right) dt + \sqrt{\left\|\frac{v2 X5^{n2}}{K2^{n2} + X5^{n2}}\right\|} dW_{2(t)} + \left(  - \sqrt{\left\|k1 X2\right\|} \right) dW_{6(t)} + \sqrt{\left\|\frac{k2}{2} X1 X4^{2}\right\|} dW_{7(t)} + \sqrt{\left\|\frac{k5}{6} X5^{3} X1\right\|} dW_{10(t)} + \left(  - \sqrt{\left\|k6 X2\right\|} \right) dW_{11(t)} + \left(  - \sqrt{\left\|d2 X2\right\|} \right) dW_{13(t)} \\
-\mathrm{dX3}\left( t \right) =& \left( \frac{v3 X3^{n3}}{K3^{n3} + X3^{n3}} + k3 X4 - k4 X3 - d3 X3 \right) dt + \sqrt{\left\|\frac{v3 X3^{n3}}{K3^{n3} + X3^{n3}}\right\|} dW_{3(t)} + \sqrt{\left\|k3 X4\right\|} dW_{8(t)} + \left(  - \sqrt{\left\|k4 X3\right\|} \right) dW_{9(t)} + \left(  - \sqrt{\left\|d3 X3\right\|} \right) dW_{14(t)} \\
-\mathrm{dX4}\left( t \right) =& \left( \frac{v4 K4^{n4}}{K4^{n4} + X1^{n4}} + 2 k1 X2 -2 \frac{k2}{2} X1 X4^{2} - k3 X4 + k4 X3 - d4 X4 \right) dt + \sqrt{\left\|\frac{v4 K4^{n4}}{K4^{n4} + X1^{n4}}\right\|} dW_{4(t)} + 2 \sqrt{\left\|k1 X2\right\|} dW_{6(t)} -2 \sqrt{\left\|\frac{k2}{2} X1 X4^{2}\right\|} dW_{7(t)} + \left(  - \sqrt{\left\|k3 X4\right\|} \right) dW_{8(t)} + \sqrt{\left\|k4 X3\right\|} dW_{9(t)} + \left(  - \sqrt{\left\|d4 X4\right\|} \right) dW_{15(t)} \\
-\mathrm{dX5}\left( t \right) =& \left( \frac{v5 X2^{n5}}{K5^{n5} + X2^{n5}} -3 \frac{k5}{6} X5^{3} X1 + 3 k6 X2 - d5 X5 \right) dt + \sqrt{\left\|\frac{v5 X2^{n5}}{K5^{n5} + X2^{n5}}\right\|} dW_{5(t)} -3 \sqrt{\left\|\frac{k5}{6} X5^{3} X1\right\|} dW_{10(t)} + 3 \sqrt{\left\|k6 X2\right\|} dW_{11(t)} + \left(  - \sqrt{\left\|d5 X5\right\|} \right) dW_{16(t)}
+\require{mhchem}
+\ce{ \varnothing &->[\frac{v1 K1^{n1}}{K1^{n1} + \left( \mathrm{X2}\left( t \right) \right)^{n1}} \frac{v1 \left( \mathrm{X4}\left( t \right) \right)^{n1}}{K1^{n1} + \left( \mathrm{X4}\left( t \right) \right)^{n1}}] X1}\\
+\ce{ \varnothing &->[\frac{v2 \left( \mathrm{X5}\left( t \right) \right)^{n2}}{K2^{n2} + \left( \mathrm{X5}\left( t \right) \right)^{n2}}] X2}\\
+\ce{ \varnothing &->[\frac{v3 \left( \mathrm{X3}\left( t \right) \right)^{n3}}{K3^{n3} + \left( \mathrm{X3}\left( t \right) \right)^{n3}}] X3}\\
+\ce{ \varnothing &->[\frac{v4 K4^{n4}}{K4^{n4} + \left( \mathrm{X1}\left( t \right) \right)^{n4}}] X4}\\
+\ce{ \varnothing &->[\frac{v5 \left( \mathrm{X2}\left( t \right) \right)^{n5}}{K5^{n5} + \left( \mathrm{X2}\left( t \right) \right)^{n5}}] X5}\\
+\ce{ X2 &<=>[k1][k2] X1 + 2 X4}\\
+\ce{ X4 &<=>[k3][k4] X3}\\
+\ce{ 3 X5 + X1 &<=>[k5][k6] X2}\\
+\ce{ X1 &->[d1] \varnothing}\\
+\ce{ X2 &->[d2] \varnothing}\\
+\ce{ X3 &->[d3] \varnothing}\\
+\ce{ X4 &->[d4] \varnothing}\\
+\ce{ X5 &->[d5] \varnothing}
 \end{align}
 "
 
-
 r = @reaction_network begin
     (hill(B, p_a, k, n), d_a), 0 ↔ A
     (p_b, d_b), 0 ↔ B
     (r_a, r_b), 3B ↔ A
 end p_a k n d_a p_b d_b r_a r_b
 
-
-@test latexify(r; noise=true, bracket=true) ==
-raw"\begin{align}
-\mathrm{\mathrm{d}\left[A\right]}\left( t \right) =& \left( \frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}} - d_{a} \cdot \left[ A \right] + \frac{r_{a}}{6} \cdot \left[ B \right]^{3} - r_{b} \cdot \left[ A \right] \right) \cdot dt + \sqrt{\left\|\frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}}\right\|} \cdot dW_{1(t)} + \left(  - \sqrt{\left\|d_{a} \cdot \left[ A \right]\right\|} \right) \cdot dW_{2(t)} + \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dW_{5(t)} + \left(  - \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \right) \cdot dW_{6(t)} \\
-\mathrm{\mathrm{d}\left[B\right]}\left( t \right) =& \left( p_{b} - d_{b} \cdot \left[ B \right] -3 \cdot \frac{r_{a}}{6} \cdot \left[ B \right]^{3} + 3 \cdot r_{b} \cdot \left[ A \right] \right) \cdot dt + \sqrt{\left\|p_{b}\right\|} \cdot dW_{3(t)} + \left(  - \sqrt{\left\|d_{b} \cdot \left[ B \right]\right\|} \right) \cdot dW_{4(t)} -3 \cdot \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dW_{5(t)} + 3 \cdot \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \cdot dW_{6(t)}
-\end{align}
-"
-
-
-@test latexify(r; noise_only=true, bracket=true) ==
-raw"\begin{align}
-\mathrm{\mathrm{d}\left[A\right]}\left( t \right) ∝& \sqrt{\left\|\frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}}\right\|} \cdot dW_{1(t)} + \left(  - \sqrt{\left\|d_{a} \cdot \left[ A \right]\right\|} \right) \cdot dW_{2(t)} + \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dW_{5(t)} + \left(  - \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \right) \cdot dW_{6(t)} \\
-\mathrm{\mathrm{d}\left[B\right]}\left( t \right) ∝& \sqrt{\left\|p_{b}\right\|} \cdot dW_{3(t)} + \left(  - \sqrt{\left\|d_{b} \cdot \left[ B \right]\right\|} \right) \cdot dW_{4(t)} -3 \cdot \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dW_{5(t)} + 3 \cdot \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \cdot dW_{6(t)}
-\end{align}
-"
-
-
-@test latexify(r; noise_only=true, bracket=true, cdot=false) ==
-raw"\begin{align}
-\mathrm{\mathrm{d}\left[A\right]}\left( t \right) ∝& \sqrt{\left\|\frac{p_{a} \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}}\right\|} dW_{1(t)} + \left(  - \sqrt{\left\|d_{a} \left[ A \right]\right\|} \right) dW_{2(t)} + \sqrt{\left\|\frac{r_{a}}{6} \left[ B \right]^{3}\right\|} dW_{5(t)} + \left(  - \sqrt{\left\|r_{b} \left[ A \right]\right\|} \right) dW_{6(t)} \\
-\mathrm{\mathrm{d}\left[B\right]}\left( t \right) ∝& \sqrt{\left\|p_{b}\right\|} dW_{3(t)} + \left(  - \sqrt{\left\|d_{b} \left[ B \right]\right\|} \right) dW_{4(t)} -3 \sqrt{\left\|\frac{r_{a}}{6} \left[ B \right]^{3}\right\|} dW_{5(t)} + 3 \sqrt{\left\|r_{b} \left[ A \right]\right\|} dW_{6(t)}
-\end{align}
-"
-
-
-@test latexify(r; noise=true, noise_var=:Noise, bracket=true) ==
+@test latexify(r) == 
 raw"\begin{align}
-\mathrm{\mathrm{d}\left[A\right]}\left( t \right) =& \left( \frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}} - d_{a} \cdot \left[ A \right] + \frac{r_{a}}{6} \cdot \left[ B \right]^{3} - r_{b} \cdot \left[ A \right] \right) \cdot dt + \sqrt{\left\|\frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}}\right\|} \cdot dNoise_{1(t)} + \left(  - \sqrt{\left\|d_{a} \cdot \left[ A \right]\right\|} \right) \cdot dNoise_{2(t)} + \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dNoise_{5(t)} + \left(  - \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \right) \cdot dNoise_{6(t)} \\
-\mathrm{\mathrm{d}\left[B\right]}\left( t \right) =& \left( p_{b} - d_{b} \cdot \left[ B \right] -3 \cdot \frac{r_{a}}{6} \cdot \left[ B \right]^{3} + 3 \cdot r_{b} \cdot \left[ A \right] \right) \cdot dt + \sqrt{\left\|p_{b}\right\|} \cdot dNoise_{3(t)} + \left(  - \sqrt{\left\|d_{b} \cdot \left[ B \right]\right\|} \right) \cdot dNoise_{4(t)} -3 \cdot \sqrt{\left\|\frac{r_{a}}{6} \cdot \left[ B \right]^{3}\right\|} \cdot dNoise_{5(t)} + 3 \cdot \sqrt{\left\|r_{b} \cdot \left[ A \right]\right\|} \cdot dNoise_{6(t)}
+\require{mhchem}
+\ce{ \varnothing &<=>[\frac{p_{a} \left( \mathrm{B}\left( t \right) \right)^{n}}{k^{n} + \left( \mathrm{B}\left( t \right) \right)^{n}}][d_{a}] A}\\
+\ce{ \varnothing &<=>[p_{b}][d_{b}] B}\\
+\ce{ 3 B &<=>[r_{a}][r_{b}] A}
 \end{align}
 "
 
-
-@test latexify(r; bracket=true) ==
-raw"\begin{align}
-\frac{d\left[ A \right](t)}{dt} =& \frac{p_{a} \cdot \left[ B \right]^{n}}{k^{n} + \left[ B \right]^{n}} - d_{a} \cdot \left[ A \right] + \frac{r_{a}}{6} \cdot \left[ B \right]^{3} - r_{b} \cdot \left[ A \right] \\
-\frac{d\left[ B \right](t)}{dt} =& p_{b} - d_{b} \cdot \left[ B \right] -3 \cdot \frac{r_{a}}{6} \cdot \left[ B \right]^{3} + 3 \cdot r_{b} \cdot \left[ A \right]
-\end{align}
-"
-
-
-@test latexify(r; bracket=false) ==
-raw"\begin{align}
-\frac{dA(t)}{dt} =& \frac{p_{a} \cdot B^{n}}{k^{n} + B^{n}} - d_{a} \cdot A + \frac{r_{a}}{6} \cdot B^{3} - r_{b} \cdot A \\
-\frac{dB(t)}{dt} =& p_{b} - d_{b} \cdot B -3 \cdot \frac{r_{a}}{6} \cdot B^{3} + 3 \cdot r_{b} \cdot A
-\end{align}
-"

test/runtests.jl

@@ -29,6 +29,6 @@ using SafeTestsets
 
 # Miscellaneous tests
 #@time @safetestset "Basic Plotting" begin include("plotting.jl") end
-#@time @safetestset "Latexify" begin include("latexify.jl") end
+@time @safetestset "Latexify" begin include("latexify.jl") end
 
 end # @time