DOC: add package extension documentation

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 DisplayAs = "0b91fe84-8a4c-11e9-3e1d-67c38462b6d6"
@@ -8,6 +9,7 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"

docs/make.jl

@@ -6,6 +6,9 @@ const generated_dir = joinpath(@__DIR__, "src", "generated")
 
 @info "Loading AlgebraicPetri"
 using AlgebraicPetri
+using Catalyst
+using ModelingToolkit
+using OrdinaryDiffEq
 
 const no_literate = "--no-literate" in ARGS
 if !no_literate
@@ -30,11 +33,16 @@ if !no_literate
       end
     end
   end
+else
+  @info "Literate.jl: skipped"
 end
 
+extensions = ["Catalyst", "ModelingToolkit", "OrdinaryDiffEq"]
+extension_modules = [Base.get_extension(AlgebraicPetri, Symbol("AlgebraicPetri"*ext*"Ext")) for ext in extensions]
+
 @info "Building Documenter.jl docs"
 makedocs(
-  modules   = [AlgebraicPetri],
+  modules   = vcat([AlgebraicPetri], extension_modules),
   format    = Documenter.HTML(
     assets = ["assets/analytics.js"],
   ),

docs/src/api.md

@@ -1,5 +1,57 @@
 # Library Reference
 
+## `AlgebraicPetri`
+
+```@autodocs
+Modules = [AlgebraicPetri]
+```
+
+## `AlgebraicPetri.BilayerNetworks`
+
+```@autodocs
+Modules = [AlgebraicPetri.BilayerNetworks]
+```
+
+## `AlgebraicPetri.Epidemiology`
+
+```@autodocs
+Modules = [AlgebraicPetri.Epidemiology]
+```
+
+## `AlgebraicPetri.ModelComparison`
+
 ```@autodocs
-Modules = [AlgebraicPetri, AlgebraicPetri.Epidemiology, AlgebraicPetri.OpenTransitions]
+Modules = [AlgebraicPetri.ModelComparison]
+```
+
+## `AlgebraicPetri.OpenTransitions`
+
+```@autodocs
+Modules = [AlgebraicPetri.OpenTransitions]
+```
+
+## `AlgebraicPetri.TypedPetri`
+
+```@autodocs
+Modules = [AlgebraicPetri.TypedPetri]
+```
+
+## Package Extensions
+
+### [Catalyst.jl](https://github.com/SciML/Catalyst.jl)
+
+```@docs
+Catalyst.ReactionSystem
+```
+
+### [ModelngToolkit.jl](https://github.com/SciML/ModelingToolkit.jl)
+
+```@docs
+ModelingToolkit.ODESystem
+```
+
+### [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl)
+
+```@docs
+OrdinaryDiffEq.ODEProblem
 ```

ext/AlgebraicPetriCatalystExt.jl

@@ -8,8 +8,9 @@ import Catalyst: ReactionSystem
 
 counter(a) = [count(==(i),a) for i in unique(a)]
 
-""" Convert a general PetriNet to a ReactionSystem
+""" ReactionSystem(pn::AbstractPetriNet)
 
+Convert a general PetriNet to a ReactionSystem
 This conversion forgets any labels or rates provided, and converts all
 parameters and variables into symbols. It does preserve the ordering of
 transitions and states though (Transition 1 has a rate of k[1], state 1 has a

ext/AlgebraicPetriModelingToolkitExt.jl

@@ -7,7 +7,10 @@ using ModelingToolkit
 import ModelingToolkit: ODESystem
 
 
-""" Convert a general PetriNet to an ODESystem
+"""
+  ODESystem(p::AbstractPetriNet; name=:PetriNet, kws...)
+
+Convert a general PetriNet to an ODESystem
 This conversion forgets any labels or rates provided, and converts all
 parameters and variables into symbols. It does preserve the ordering of
 transitions and states though (Transition 1 has a rate of k[1], state 1 has a

ext/AlgebraicPetriOrdinaryDiffEqExt.jl

@@ -3,7 +3,19 @@ module AlgebraicPetriOrdinaryDiffEqExt
 using AlgebraicPetri
 import OrdinaryDiffEq: ODEProblem
 
+""" ODEProblem(m::AbstractPetriNet, u0, tspan, β)
+
+Convert a general PetriNet to an ODEProblem
+This takes the initial conditions and rates as parameters and will ignore
+any initial conditions and rates embedded in the Petri Net if they exist.
+"""
 ODEProblem(m::AbstractPetriNet, u0, tspan, β) = ODEProblem(vectorfield(m), u0, tspan, β)
+
+""" ODEProblem(m::AbstractPetriNet, tspan)
+
+Convert a general PetriNet to an ODEProblem
+This assumes the concentrations and weights are embedded in the Petri Net.
+"""
 ODEProblem(m::AbstractPetriNet, tspan) = ODEProblem(vectorfield(m), concentrations(m), tspan, rates(m))
 
 end