Merge pull request #277 from TorkelE/cataly_doc_update

Chaneg doc mentions of DiffEqBiological to Catalyst and update syntax

assets/Project.toml

@@ -1,5 +1,5 @@
 [deps]
-DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0"
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 ParameterizedFunctions = "65888b18-ceab-5e60-b2b9-181511a3b968"

assets/assets.jl

@@ -1,5 +1,5 @@
 # Generate the assets (pngs for README)
-using Latexify, LaTeXStrings, ParameterizedFunctions, DiffEqBiological
+using Latexify, LaTeXStrings, ParameterizedFunctions, Catalyst
 
 struct Ket{T}
     x::T
@@ -20,12 +20,12 @@ things = [
                                (r_bind, r_unbind), A + B ↔ C
                                Hill(C, v, k, n), 0 --> X
                                d_x, X --> 0
-                           end r_bind r_unbind v k n d_x),
+                           end; form=:ode),
           "demo_rn_arrow" => latexify(@reaction_network demoNetwork begin
                                      (r_bind, r_unbind), A + B ↔ C
                                      Hill(C, v, k, n), 0 --> X
                                      d_x, X --> 0
-                                 end r_bind r_unbind v k n d_x; env=:arrow),
+                                 end),
          ]
 
 cd("$(pkgdir(Latexify))/assets") do

docs/make.jl

@@ -19,7 +19,7 @@ makedocs(
         "tutorials/recipes.md",
         "Use with other packages" => [
             "tutorials/parameterizedfunctions.md",
-            "tutorials/DiffEqBiological.md"
+            "tutorials/Catalyst.md"
         ],
         "tutorials/notebooks.md",
         "arguments.md",

docs/src/arguments.md

@@ -43,7 +43,7 @@ latexify(args, env=:mdtable)
 ```
 
 ## Chemical arrow notation
-Available with `ReactionNetwork`s from `DiffEqBiological`.
+Available with `ReactionNetwork`s from `Catalyst`.
 ```@eval
 Base.include(@__MODULE__, "src/table_generator.jl")
 args = [arg for arg in keyword_arguments if :arrow in arg.env]

docs/src/table_generator.jl

@@ -39,7 +39,7 @@ keyword_arguments = [
     KeywordArgument(:convert_unicode, [:mdtable, :tabular, :align, :array, :raw, :inline], "`Bool`", "`true`", "Convert unicode characters to latex commands, for example `α` to `\\alpha`", [:Any]),
     KeywordArgument(:cdot, [:mdtable, :tabular, :align, :array, :raw, :inline], "`Bool`", "`true`", "Toggle between using `\\cdot` or just a space to represent multiplication.", [:Any]),
     KeywordArgument(:symbolic, [:align], "`Bool`", "`false`", "Use symbolic calculations to clean up the expression.", [:ReactionNetwork]),
-    KeywordArgument(:clean, [:align], "`Bool`", "`false`", "Clean out `1*` terms. Only useful for DiffEqBiological versions 3.4 or below.", [:ReactionNetwork]),
+    KeywordArgument(:clean, [:align], "`Bool`", "`false`", "Clean out `1*` terms. Only useful for Catalyst (then named DiffEqBiological) versions 3.4 or below.", [:ReactionNetwork]),
     KeywordArgument(:rows, [:align], "Iterable or symol", ":all", "Which rows to include in the output.", [:Any]),
     KeywordArgument(:booktabs, [:tabular], "`Bool`", "`false`", "Add top, mid and bottom booktabs rule", [:Any]),
     KeywordArgument(:index, [:mdtable, :tabular, :align, :array, :raw, :inline], "`Symb`", "`:bracket`", "Represent index specification with `:bracket` (`u[1]`) or `:subscript` (`u_1`). ", [:Any]),

docs/src/tutorials/DiffEqBiological.md → docs/src/tutorials/Catalyst.md

@@ -1,22 +1,21 @@
-# Use with @reaction_network from DiffEqBiological.jl.
+# Use with @reaction_network from Catalyst.jl.
 
-Latexify.jl has methods for dealing with AbstractReactionNetworks. For more information regarding this DSL, turn to its [docs](http://docs.juliadiffeq.org/latest/models/biological.html). The latexify end of things are pretty simple: feed a reaction network to `latexify()` and let it do its magic.
+Latexify.jl has methods for dealing with the `ReactionNetwork` models generated by Catalyst.jl. More information regarding these can be found [here](https://github.com/SciML/Catalyst.jl). The latexify end of things are pretty simple: feed a reaction network to `latexify()` and let it do its magic.
 
 ```julia
-using DiffEqBiological
+using Catalyst
 using Latexify
 copy_to_clipboard(true)
 
-@reaction_func hill2(x, v, k) = v*x^2/(k^2 + x^2)
-
-rn = @reaction_network MyRnType begin
+hill2(x, v, k) = v*x^2/(k^2 + x^2)
+rn = @reaction_network begin
   hill2(y, v_x, k_x), 0 --> x
   p_y, 0 --> y
   (d_x, d_y), (x, y) --> 0
   (r_b, r_u), x ↔ y
-end v_x k_x p_y d_x d_y r_b r_u
+end
 
-latexify(rn)
+latexify(rn; form=:ode)
 ```
 ```math
 \begin{align}
@@ -25,25 +24,25 @@ latexify(rn)
 \end{align}
 ```
 
-The method has a keyword for choosing between outputting the ODE or the noise term. While it is not obvious from the latexify output, the noise in the reaction network is correlated.
-
+Alternatively, the SDEs generated through the chemical Langevin equations can be displayed by setting the `form` argument to `:sde`. Here, the noise in the reaction network is correlated/
 ```julia
-latexify(rn; noise=true)
+latexify(rn; form=:sde)
 ```
-
 ```math
 \begin{align}
 \frac{dx}{dt} =& \sqrt{\frac{v_{x} \cdot y^{2}}{k_{x}^{2} + y^{2}}} - \sqrt{d_{x} \cdot x} - \sqrt{r_{b} \cdot x} + \sqrt{r_{u} \cdot y} \\
 \frac{dy}{dt} =& \sqrt{p_{y}} - \sqrt{d_{y} \cdot y} + \sqrt{r_{b} \cdot x} - \sqrt{r_{u} \cdot y} \\
 \end{align}
 ```
 
+Note: On the current version of Latexify, generation of SDEs from reaction networks is broken.
+
 
 ## Chemical arrow notation
 
-DiffEqBiologicals reaction network is all about chemical arrow notation, so why should we not be able to render arrows?
+Catalyst reaction network is all about chemical arrow notation, so why should we not be able to render arrows?
 
-Use `latexify`'s `env` keyword argument to specify that you want `:chemical` (or the equivalent `:arrow`, `:arrows` or `:chem`).
+This is the default output (when no value to `form` is given).
 
 ```julia
 latexify(rn; env=:chemical)

paper/paper.md

@@ -41,7 +41,7 @@ Latexify.jl itself. This becomes especially powerful in combination with
 Julia's metaprogramming facilities and easily generated domain-specific
 languages (DSLs). Latexify.jl can, for example, output the system of
 differential equations (and much more) that is automatically generated by a
-chemical reaction arrow DSL provided by DiffEqBiological.jl [@diffeq].  
+chemical reaction arrow DSL provided by Catalyst.jl [@diffeq].  
 
 The package aims to support the scientific work-flow through facilitating
 inspection, automation and representation. Simple inspection of the equations