first tutorial

SciML · Jul 28, 2020 · 482b861 · 482b861
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commit 482b861
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Showing 8 changed files with 62,478 additions and 3 deletions.
diff --git a/docs/make.jl b/docs/make.jl
@@ -20,7 +20,7 @@ using Catalyst, ModelingToolkit
 #     ))
 #     push!(r, Documenter.Utilities.JSDependencies.Snippet(
 #         ["jquery", "katex", "mhchem", "katex-auto-render"],
-#         ["\$", "katex", "renderMathInElement"],
+#         ["\$", "katex", "mhchem", "renderMathInElement"],
 #         """
 #         \$(document).ready(function() {
 #           renderMathInElement(
@@ -35,13 +35,14 @@ using Catalyst, ModelingToolkit
 makedocs(
     sitename = "Catalyst.jl",
     authors = "Samuel Isaacson",
-    format = Documenter.HTML(prettyurls = (get(ENV, "CI", nothing) == "true")),
+    format = Documenter.HTML(mathengine=Documenter.Writers.HTMLWriter.MathJax(), prettyurls = (get(ENV, "CI", nothing) == "true")),
     modules = [Catalyst,ModelingToolkit],
     doctest = false,
     clean = true,
     pages = Any[
         "Home" => "index.md",
         "Tutorials" => Any[
+            "tutorials/using_catalyst.md",
             "tutorials/basics.md",
             "tutorials/models.md",
             "tutorials/basic_examples.md",

diff --git a/docs/src/api/catalyst_api.md b/docs/src/api/catalyst_api.md
@@ -29,7 +29,6 @@ as here `X` is never defined as either a species or parameter.
 ```@docs
 @reaction_network
 make_empty_network
-@add_reactions
 ModelingToolkit.Reaction
 ModelingToolkit.ReactionSystem
 ```
@@ -55,6 +54,7 @@ dependants
 
 ## Functions to extend a Network
 ```@docs
+@add_reactions
 addspecies!
 addparam!
 addreaction!

diff --git a/docs/src/assets/birthdeath_cle.svg b/docs/src/assets/birthdeath_cle.svg
diff --git a/docs/src/assets/repressilator.svg b/docs/src/assets/repressilator.svg