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DOC: fix documentation for package extensions #132

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Oct 31, 2023
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DOC: fix documentation for package extensions #132

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1 change: 1 addition & 0 deletions docs/Project.toml
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Original file line number Diff line number Diff line change
@@ -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"
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7 changes: 6 additions & 1 deletion docs/make.jl
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Expand Up @@ -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
Expand Down Expand Up @@ -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"],
),
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30 changes: 26 additions & 4 deletions docs/src/api.md
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@@ -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
Expand All @@ -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
```