Merge branch 'main' into isaacsas-update-doc-ci

Author: vyudu

Project.toml

@@ -51,6 +51,8 @@ julia = "1.10"
 SBMLImporter = "210efffb-c3c8-456d-a807-6f55560b12fe"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
+UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [targets]
-test = ["Test", "SBMLImporter", "SafeTestsets"]
+test = ["Test", "SBMLImporter", "SafeTestsets", "StableRNGs", "UnPack"]

docs/make.jl

@@ -10,8 +10,8 @@ makedocs(
     clean = true,
     pages = Any[
         "Home" => "index.md",
-        "Network Analysis Algorithms" => "algorithms.md",
-        "Roadmap" => "roadmap.md"
+        "Network Analysis Algorithms" => "Algorithms.md",
+        "Roadmap" => "ROADMAP.md"
     ],
     warnonly = [:missing_docs]
 )

docs/src/index.md

@@ -38,3 +38,11 @@ pmap = Dict(zip(parameters(edelstein), ones(6))) # Creates dict from symbolic pa
 In order to convert from a symbol dictionary to a Symbolics dictionary, one can use the `symmap_to_varmap` function from Catalyst. 
 
 ### Comparisons to existing packages
+A variety of packages for network analysis exist, including the following: 
+1. [Chemical Reaction Network Toolbox](https://zenodo.org/records/5149266) (Feinberg et al.) 
+2. [CoNTRoL](https://control.math.wvu.edu/) (Johnston et al.) 
+
+### Starting with Julia and Catalyst
+Please see the [starting with Julia](https://docs.sciml.ai/Catalyst/stable/introduction_to_catalyst/catalyst_for_new_julia_users/) section of Catalyst.jl's documentation for tips on getting started with Julia in general. 
+
+If you have a reaction network stored in some other file format, such as `.net`, SBML, and others, please reference the [loading chemical reaction networks](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/) tutorial in the Catalyst documentation. There are sections for loading `.net` and SBML files. Once the reaction network is loaded as a Catalyst `ReactionSystem`, it can be passed to the network analysis algorithms defined in this function.