From 2680c40d271be391e9f4e13aae025f01c1a3d987 Mon Sep 17 00:00:00 2001
From: Micah Halter <micah@mehalter.com>
Date: Tue, 31 Oct 2023 09:09:23 -0400
Subject: [PATCH] DOC: fix documentation for package extensions

---
 docs/Project.toml |  1 +
 docs/make.jl      |  7 ++++++-
 docs/src/api.md   | 30 ++++++++++++++++++++++++++----
 3 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/docs/Project.toml b/docs/Project.toml
index 9ca2d41..7ef25b0 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 AlgebraicDynamics = "5fd6ff03-a254-427e-8840-ba658f502e32"
+AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
diff --git a/docs/make.jl b/docs/make.jl
index 3dd0dfb..df04e25 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -8,6 +8,8 @@ using AlgebraicDynamics.DWDDynam
 using AlgebraicDynamics.CPortGraphDynam
 using Catlab
 using Catlab.WiringDiagrams
+using AlgebraicPetri
+using DelayDiffEq
 using OrdinaryDiffEq
 
 # This is to resolve method ambiguity and is inlcuded in Base as of 1.8
@@ -40,9 +42,12 @@ for (root, dirs, files) in walkdir(literate_dir)
   end
 end
 
+extensions = ["AlgebraicPetri", "DelayDiffEq", "OrdinaryDiffEq"]
+extension_modules = [Base.get_extension(AlgebraicDynamics, Symbol("AlgebraicDynamics"*ext*"Ext")) for ext in extensions]
+
 @info "Building Documenter.jl docs"
 makedocs(
-  modules   = [AlgebraicDynamics],
+  modules   = vcat([AlgebraicDynamics], extension_modules),
   format    = Documenter.HTML(
     assets = ["assets/analytics.js"],
   ),
diff --git a/docs/src/api.md b/docs/src/api.md
index 907d062..63e5f9e 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -1,14 +1,18 @@
 # Library Reference
 
 ## Types of Dynamical Systems
+
 ### Machines
+
 ```@docs
 AlgebraicDynamics.DWDDynam.AbstractMachine
 AlgebraicDynamics.DWDDynam.ContinuousMachine
 AlgebraicDynamics.DWDDynam.DelayMachine
 AlgebraicDynamics.DWDDynam.DiscreteMachine
 ```
+
 ### Resource Sharers
+
 ```@docs
 AlgebraicDynamics.UWDDynam.AbstractResourceSharer
 AlgebraicDynamics.UWDDynam.ContinuousResourceSharer
@@ -17,33 +21,51 @@ AlgebraicDynamics.UWDDynam.DiscreteResourceSharer
 ```
 
 ## Composition of Dynamical Systems
+
 ### Operad Algebras
+
 ```@docs
 AlgebraicDynamics.UWDDynam.oapply
 ```
+
 ### Checks
+
 ```@docs
 AlgebraicDynamics.UWDDynam.fills
 AlgebraicDynamics.DWDDynam.fills
 ```
 
 ## Time Evolution
+
 ### Instantaneous Dynamics
+
 ```@docs
 AlgebraicDynamics.UWDDynam.eval_dynamics
 ```
+
 ### Time Discretization
+
 ```@docs
 AlgebraicDynamics.UWDDynam.euler_approx
 ```
+
 ### Discrete Trajectory
+
 ```@docs
 AlgebraicDynamics.UWDDynam.trajectory
 ```
 
-## Integration with [DifferentialEquations.jl](https://diffeq.sciml.ai/stable/#Problem-Types)
+## Package Extensions
+
+### [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl)
+
+```@docs
+OrdinaryDiffEq.ODEProblem
+OrdinaryDiffEq.DiscreteProblem
+```
+
+### [DelayDiffEq.jl](https://github.com/SciML/DelayDiffEq.jl)
+
 ```@docs
-AlgebraicDynamics.UWDDynam.ODEProblem
-AlgebraicDynamics.UWDDynam.DDEProblem
-AlgebraicDynamics.UWDDynam.DiscreteProblem
+DelayDiffEq.DDEProblem
 ```