docs: add docstrings, restructure api manual

Author: MartinuzziFrancesco

README.md

@@ -109,7 +109,7 @@ esn = ReservoirChain(
     StatefulLayer(ESNCell(input_size => res_size; init_reservoir=rand_sparse(; radius=1.2, sparsity=6/300))),
     NLAT2(),
     Readout(res_size => input_size)
-)
+) #or ESN(input_size, res_size, input_size; init_reservoir=rand_sparse(; radius=1.2, sparsity=6/300))
 ```
 
 The echo state network can now be trained and tested.

docs/Project.toml

@@ -3,6 +3,7 @@ CellularAutomata = "878138dc-5b27-11ea-1a71-cb95d38d6b29"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

docs/make.jl

@@ -1,7 +1,7 @@
 using Documenter, DocumenterCitations, ReservoirComputing
 
-cp("./docs/Manifest.toml", "./docs/src/assets/Manifest.toml"; force = true)
-cp("./docs/Project.toml", "./docs/src/assets/Project.toml"; force = true)
+cp("./docs/Manifest.toml", "./docs/src/assets/Manifest.toml"; force=true)
+cp("./docs/Project.toml", "./docs/src/assets/Project.toml"; force=true)
 
 ENV["PLOTS_TEST"] = "true"
 ENV["GKSwstype"] = "100"
@@ -10,19 +10,23 @@ mathengine = Documenter.MathJax()
 
 bib = CitationBibliography(
     joinpath(@__DIR__, "src", "refs.bib");
-    style = :authoryear
+    style=:authoryear
 )
 
-makedocs(; modules = [ReservoirComputing],
-    sitename = "ReservoirComputing.jl",
-    clean = true, doctest = false, linkcheck = true,
-    plugins = [bib],
-    format = Documenter.HTML(;
+links = InterLinks(
+    "Lux" => "https://lux.csail.mit.edu/stable/"
+)
+
+makedocs(; modules=[ReservoirComputing],
+    sitename="ReservoirComputing.jl",
+    clean=true, doctest=false, linkcheck=true,
+    plugins=[links, bib],
+    format=Documenter.HTML(;
         mathengine,
-        assets = ["assets/favicon.ico"],
-        canonical = "https://docs.sciml.ai/ReservoirComputing/stable/"),
-    pages = pages
+        assets=["assets/favicon.ico"],
+        canonical="https://docs.sciml.ai/ReservoirComputing/stable/"),
+    pages=pages
 )
 
-deploydocs(; repo = "github.com/SciML/ReservoirComputing.jl.git",
-    push_preview = true)
+deploydocs(; repo="github.com/SciML/ReservoirComputing.jl.git",
+    push_preview=true)

docs/pages.jl

@@ -1,24 +1,24 @@
 pages = [
     "ReservoirComputing.jl" => "index.md",
     "General Settings" => Any[
-        "Changing Training Algorithms" => "general/different_training.md",
-        "Altering States" => "general/states_variation.md",
-        "Generative vs Predictive" => "general/predictive_generative.md"],
+        "Changing Training Algorithms"=>"general/different_training.md",
+        "Altering States"=>"general/states_variation.md",
+        "Generative vs Predictive"=>"general/predictive_generative.md"],
     "Echo State Network Tutorials" => Any[
-        "Lorenz System Forecasting" => "esn_tutorials/lorenz_basic.md",
+        "Lorenz System Forecasting"=>"esn_tutorials/lorenz_basic.md",
         #"Mackey-Glass Forecasting on GPU" => "esn_tutorials/mackeyglass_basic.md",
-        "Using Different Layers" => "esn_tutorials/change_layers.md",
-        "Using Different Reservoir Drivers" => "esn_tutorials/different_drivers.md",
+        "Using Different Layers"=>"esn_tutorials/change_layers.md",
+        "Using Different Reservoir Drivers"=>"esn_tutorials/different_drivers.md",
         #"Using Different Training Methods" => "esn_tutorials/different_training.md",
-        "Deep Echo State Networks" => "esn_tutorials/deep_esn.md",
-        "Hybrid Echo State Networks" => "esn_tutorials/hybrid.md"],
+        "Deep Echo State Networks"=>"esn_tutorials/deep_esn.md",
+        "Hybrid Echo State Networks"=>"esn_tutorials/hybrid.md"],
     "Reservoir Computing with Cellular Automata" => "reca_tutorials/reca.md",
-    "API Documentation" => Any["Training Algorithms" => "api/training.md",
-        "States Modifications" => "api/states.md",
-        "Prediction Types" => "api/predict.md",
-        "Echo State Networks" => "api/esn.md",
-        "ESN Initializers" => "api/inits.md",
-        "ESN Drivers" => "api/esn_drivers.md",
-        "ESN Variations" => "api/esn_variations.md",
-        "ReCA" => "api/reca.md"]    #"References" => "references.md"
+    "API Documentation" => Any[
+        "Layers"=>"api/layers.md",
+        "Models"=>"api/models.md",
+        "States"=>"api/states.md",
+        "Train"=>"api/training.md",
+        "Predict"=>"api/predict.md",
+        "Initializers"=>"api/inits.md",
+        "ReCA"=>"api/reca.md"]    #"References" => "references.md"
 ]

docs/src/api/esn.md

@@ -0,0 +1,15 @@
+# Layers
+
+## Base Layers
+```@doc
+    ReservoirChain
+    Readout
+    Collect
+    StatefulLayer
+```
+
+## Echo State Networks
+
+```@doc
+    ESNCell
+```

docs/src/api/esn_drivers.md

@@ -0,0 +1,6 @@
+# Models
+
+```@docs
+    ESN
+    DeepESN
+```

docs/src/api/esn_variations.md

@@ -1,6 +1,5 @@
-# Prediction Types
+# Predict
 
 ```@docs
-    Generative
-    Predictive
+    predict
 ```