Reworking the API and Docs to merge in DynamicalSystems.jl

.gitignore

@@ -9,4 +9,6 @@ Manifest.toml
 *.scss
 test/*.png
 test/*.bson
-*style.jl
+*style.jl
+tutorial.md
+examples.md

Project.toml

@@ -1,10 +1,9 @@
 name = "RecurrenceMicrostatesAnalysis"
 uuid = "cb83a08b-85c6-4e94-91aa-4e946c7d4f0c"
-repo = "https://github.com/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl"
 version = "0.4.0"
+repo = "https://github.com/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl"
 
 [deps]
-Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 Atomix = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 ComplexityMeasures = "ab4b797d-85ee-42ba-b621-05d793b346a2"
@@ -15,9 +14,9 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-Adapt = "4.4.0"
 Atomix = "1.1.2"
 Combinatorics = "1.1.0"
 ComplexityMeasures = "3.8.5"
@@ -28,6 +27,7 @@ Random = "1.10.9"
 Reexport = "1.2.2"
 StateSpaceSets = "2.5.3"
 StaticArrays = "1.9.15"
+Statistics = "1.11.1"
 julia = "1.8"
 
 [extras]

README.md

@@ -1,7 +1,7 @@
 # RecurrenceMicrostatesAnalysis.jl
 
-[![CI](https://github.com/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl/workflows/CI/badge.svg)](https://github.com/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl/actions)
-[![codecov](https://codecov.io/gh/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl/graph/badge.svg?token=NR3S4JOE4R)](https://codecov.io/gh/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl)
+[![CI](https://github.com/JuliaDynamics/RecurrenceMicrostatesAnalysis.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/RecurrenceMicrostatesAnalysis.jl/actions)
+[![codecov](https://codecov.io/gh/JuliaDynamics/RecurrenceMicrostatesAnalysis.jl/graph/badge.svg?token=NR3S4JOE4R)](https://codecov.io/gh/JuliaDynamics/RecurrenceMicrostatesAnalysis.jl)
 [![Package Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Ftotal_downloads%2FRecurrenceMicrostatesAnalysis&query=total_requests&label=Downloads)](http://juliapkgstats.com/pkg/RecurrenceMicrostatesAnalysis)
 [![Publication](https://img.shields.io/badge/publication-Chaos-blue.svg)](https://doi.org/10.1063/5.0293708)
 
@@ -24,5 +24,5 @@ import Pkg
 Pkg.add("RecurrenceMicrostatesAnalysis")
 ```
 
-The package documentation is available [online](https://dynamicsufpr.github.io/RecurrenceMicrostatesAnalysis.jl/), or you can build it
+The package documentation is available [online](https://juliadynamics.github.io/RecurrenceMicrostatesAnalysis.jl/stable/), or you can build it
 locally by running `julia docs/make.jl`.

docs/Project.toml

@@ -8,10 +8,16 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
+DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+PredefinedDynamicalSystems = "31e2f376-db9e-427a-b76e-a14f56347a14"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RecurrenceAnalysis = "639c3291-70d9-5ea2-8c5b-839eba1ee399"
 RecurrenceMicrostatesAnalysis = "cb83a08b-85c6-4e94-91aa-4e946c7d4f0c"
 StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

docs/make.jl

@@ -5,45 +5,40 @@ using DocumenterCitations
 using RecurrenceMicrostatesAnalysis
 using StateSpaceSets
 
+# Convert tutorial file to markdown
+import Literate
+Literate.markdown("src/tutorial.jl", "src"; credit = false)
+Literate.markdown("src/examples.jl", "src"; credit = false)
+
 pages = [
     "Welcome" => "index.md",
-    "Tutorial" => [
-        "Distributions" => "tutorial/distributions.md",
-        "Quantifiers" => "tutorial/quantifiers.md",
-        "Recurrence Functions" => "tutorial/recurrences.md",
-        "Shapes and Sampling" => "tutorial/shapes_and_sampling.md",
-        "GPU" => "tutorial/gpu.md",
-        "Utils" => "tutorial/utils.md",
-    ],
-    "Examples" => [
-            "Machine Learning" => "examples/ml.md",
-        ],
-    "Developers" => "dev.md",
+    "Tutorial" => "tutorial.md",
+    "API" => "api.md",
+    "GPU" => "gpu.md",
+    "Examples" => "examples.md",
+    "Developers docs" => "dev.md",
     "References" => "refs.md",
 ]
 
+# Apply JuliaDynamics theme, choosing a specific branch (easier debugging)
+github_user = "JuliaDynamics"
+branch = "master"
+download_path = "https://raw.githubusercontent.com/$github_user/doctheme/$branch/"
+
+import Downloads
+Downloads.download(
+    "$download_path/build_docs_with_style.jl",
+    joinpath(@__DIR__, "build_docs_with_style.jl")
+)
+include("build_docs_with_style.jl")
+
+using DocumenterCitations
+
 bib = CitationBibliography(
     joinpath(@__DIR__, "refs.bib");
     style=:authoryear
 )
 
-makedocs(
-    sitename = "RecurrenceMicrostatesAnalysis.jl",
-    format = Documenter.HTML(
-        prettyurls = true,
-        collapselevel = 3,
-    ),
-    modules = [RecurrenceMicrostatesAnalysis, StateSpaceSets, ComplexityMeasures],
-    pages = pages,
-    doctest = false,
-    checkdocs = :exported,
-    warnonly = [:doctest, :missing_docs],
-    plugins = [bib]
+build_docs_with_style(pages, RecurrenceMicrostatesAnalysis, ComplexityMeasures, StateSpaceSets;
+    expandfirst = ["index.md"], bib,
 )
-
-deploydocs(
-    repo = "github.com/DynamicsUFPR/RecurrenceMicrostatesAnalysis.jl.git",
-    target = "build",
-    push_preview = true,
-    versions = ["stable" => "v^", "v#.#", "dev" => "dev"]
-)

docs/refs.bib

@@ -137,6 +137,15 @@ @article{Ferreira2025RMALib
    month = {11},
    title = {RecurrenceMicrostatesAnalysis.jl: A Julia library for analyzing dynamical systems with recurrence microstates},
    volume = {35},
-   url = {https://pubs.aip.org/cha/article/35/11/113123/3372778/RecurrenceMicrostatesAnalysis-jl-A-Julia-library},
    year = {2025}
 }
+
+@article{Silveira2025ML,
+  author = {Silveira, J. V. M and Costa, H. C and Spezzatto, G. S and Prado, T. L and Lopes, S. R},
+  journal = {Braz. J. Phys.},
+  number = {56},
+  title = {Classifying Complex Dynamical and Stochastic Systems via Physics-Based Recurrence Features},
+  volume = {37},
+  year = {2025},
+  doi = {10.1007/s13538-025-01969-6}
+}

docs/src/api.md

@@ -0,0 +1,77 @@
+# API
+
+## Recurrence Microstates
+```@docs
+RecurrenceMicrostates
+```
+
+### Recurrence expressions
+```@docs
+RecurrenceExpression
+recurrence
+ThresholdRecurrence
+CorridorRecurrence
+```
+
+### Microstate shapes
+```@docs
+MicrostateShape
+RectMicrostate
+DiagonalMicrostate
+TriangleMicrostate
+```
+
+### Sampling modes
+```@docs
+SamplingMode
+SRandom
+Full
+```
+
+### Sampling space
+!!! todo "Future implementation"
+    We pretend to expand the [`RecurrenceMicrostates`](@ref) structure to also consider
+    a setted space from the recurrence plot as source of information to construct
+    the RMA distribution.
+
+```@docs
+SamplingSpace
+```
+
+## Recurrence Quantification Analysis
+```@docs
+RecurrenceRate
+RecurrenceDeterminism
+RecurrenceLaminarity
+Disorder
+WindowedDisorder
+
+rma
+```
+
+## Optimization
+```@docs
+Parameter
+optimize
+Threshold
+```
+
+## Operations
+```@docs
+Operation
+operate
+PermuteRows
+PermuteColumns
+Transpose
+```
+
+## Utils
+
+### GPU Metrics
+**Distances.jl** is not compatible with GPU execution; therefore, distance evaluations must be reimplemented
+for GPU usage. This is done using a [`GPUMetric`](@ref).
+
+```@docs
+GPUMetric
+GPUEuclidean
+```