docs: start splitting reca from main docs

Author: MartinuzziFrancesco

Project.toml

@@ -1,7 +1,7 @@
 name = "ReservoirComputing"
 uuid = "7c2d2b1e-3dd4-11ea-355a-8f6a8116e294"
 authors = ["Francesco Martinuzzi"]
-version = "0.11.3"
+version = "0.12.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

docs/make.jl

@@ -15,6 +15,7 @@ bib = CitationBibliography(
 
 makedocs(; modules = [ReservoirComputing],
     sitename = "ReservoirComputing.jl",
+    authors = "Francesco Martinuzzi",
     clean = true, doctest = false, linkcheck = true,
     plugins = [bib],
     format = Documenter.HTML(;

docs/pages.jl

@@ -19,6 +19,5 @@ pages = [
         "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"
+        "ESN Variations" => "api/esn_variations.md"]
 ]

lib/ReservoirCellularAutomata/Project.toml

@@ -14,7 +14,7 @@ Aqua = "0.8"
 CellularAutomata = "0.0.6"
 Random = "1.11.0"
 Reexport = "1.2.2"
-ReservoirComputing = "0.11.3"
+ReservoirComputing = "0.12.0"
 SafeTestsets = "0.1.0"
 Test = "1"
 julia = "1.10"

lib/ReservoirCellularAutomata/docs/make.jl

@@ -1,24 +1,29 @@
-using ReservoirCellularAutomata
-using Documenter
+using Documenter, DocumenterCitations, ReservoirCellularAutomata
 
-DocMeta.setdocmeta!(ReservoirCellularAutomata, :DocTestSetup,
-    :(using ReservoirCellularAutomata); recursive = true)
+cp("./docs/Manifest.toml", "./docs/src/assets/Manifest.toml"; force = true)
+cp("./docs/Project.toml", "./docs/src/assets/Project.toml"; force = true)
 
-makedocs(;
-    modules = [ReservoirCellularAutomata],
-    authors = "Francesco Martinuzzi",
+ENV["PLOTS_TEST"] = "true"
+ENV["GKSwstype"] = "100"
+include("pages.jl")
+mathengine = Documenter.MathJax()
+
+bib = CitationBibliography(
+    joinpath(@__DIR__, "src", "refs.bib");
+    style = :authoryear
+)
+
+makedocs(; modules = [ReservoirCellularAutomata],
     sitename = "ReservoirCellularAutomata.jl",
+    authors = "Francesco Martinuzzi",
+    clean = true, doctest = false, linkcheck = true,
+    plugins = [bib],
     format = Documenter.HTML(;
-        canonical = "https://MartinuzziFrancesco.github.io/ReservoirCellularAutomata.jl",
-        edit_link = "main",
-        assets = String[]
-    ),
-    pages = [
-        "Home" => "index.md"
-    ]
+        mathengine,
+        assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/ReservoirComputing/stable/"),
+    pages = pages
 )
 
-deploydocs(;
-    repo = "github.com/MartinuzziFrancesco/ReservoirCellularAutomata.jl",
-    devbranch = "main"
-)
+deploydocs(; repo = "github.com/SciML/ReservoirComputing.jl.git",
+    push_preview = true)

lib/ReservoirCellularAutomata/docs/pages.jl

@@ -0,0 +1,4 @@
+pages = [
+    "ReservoirCellularAutomata.jl" => "index.md",
+    "API Manual" => "api/reca.md"
+]

docs/src/api/reca.md renamed to lib/ReservoirCellularAutomata/docs/src/api/reca.md

@@ -0,0 +1,21 @@
+@misc{Yilmaz2014,
+  doi = {10.48550/ARXIV.1410.0162},
+  url = {https://arxiv.org/abs/1410.0162},
+  author = {Yilmaz,  Ozgur},
+  keywords = {Neural and Evolutionary Computing (cs.NE),  FOS: Computer and information sciences,  FOS: Computer and information sciences},
+  title = {Reservoir Computing using Cellular Automata},
+  publisher = {arXiv},
+  year = {2014},
+  copyright = {arXiv.org perpetual,  non-exclusive license}
+}
+
+@misc{Nichele2017,
+  doi = {10.48550/ARXIV.1703.02806},
+  url = {https://arxiv.org/abs/1703.02806},
+  author = {Nichele,  Stefano and Molund,  Andreas},
+  keywords = {Neural and Evolutionary Computing (cs.NE),  Emerging Technologies (cs.ET),  FOS: Computer and information sciences,  FOS: Computer and information sciences},
+  title = {Deep Reservoir Computing Using Cellular Automata},
+  publisher = {arXiv},
+  year = {2017},
+  copyright = {arXiv.org perpetual,  non-exclusive license}
+}

lib/ReservoirCellularAutomata/docs/src/refs.bib

@@ -18,11 +18,8 @@ end
         nla_type = NLADefault(),
         states_type = StandardStates())
 
-[1] Yilmaz, Ozgur. “_Reservoir computing using cellular automata._”
-arXiv preprint arXiv:1410.0162 (2014).
-
-[2] Nichele, Stefano, and Andreas Molund. “_Deep reservoir computing using cellular
-automata._” arXiv preprint arXiv:1703.02806 (2017).
+Builds a Resercoir Computing model with cellular automata [Yilmaz2014](@cite)
+[Nichele2017](@cite).
 """
 function RECA(train_data,
         automata;

lib/ReservoirCellularAutomata/src/reca.jl

@@ -14,10 +14,7 @@ end
 Random mapping of the input data directly in the reservoir. The `expansion_size`
 determines the dimension of the single reservoir, and `permutations` determines the
 number of total reservoirs that will be connected, each with a different mapping.
-The detail of this implementation can be found in [1].
-
-[1] Nichele, Stefano, and Andreas Molund. “Deep reservoir computing using cellular
-automata.” arXiv preprint arXiv:1703.02806 (2017).
+The detail of this implementation can be found in [Nichele2017](@cite).
 """
 function RandomMapping(; permutations = 8, expansion_size = 40)
     RandomMapping(permutations, expansion_size)