formatting and version bump

SciML · Dec 13, 2023 · 195f61b · 195f61b
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "ReservoirComputing"
 uuid = "7c2d2b1e-3dd4-11ea-355a-8f6a8116e294"
 authors = ["Francesco Martinuzzi"]
-version = "0.9.4"
+version = "0.9.5"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

diff --git a/README.md b/README.md
@@ -2,13 +2,13 @@
 
 [![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
 [![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/ReservoirComputing/stable/)
- [![arXiv](https://img.shields.io/badge/arXiv-2204.05117-00b300.svg)](https://arxiv.org/abs/2204.05117)
+[![arXiv](https://img.shields.io/badge/arXiv-2204.05117-00b300.svg)](https://arxiv.org/abs/2204.05117)
 
 [![codecov](https://codecov.io/gh/SciML/ReservoirComputing.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/SciML/ReservoirComputing.jl)
 [![Build Status](https://github.com/SciML/ReservoirComputing.jl/workflows/CI/badge.svg)](https://github.com/SciML/ReservoirComputing.jl/actions?query=workflow%3ACI)
 [![Build status](https://badge.buildkite.com/db8f91b89a10ad79bbd1d9fdb1340e6f6602a1c0ed9496d4d0.svg)](https://buildkite.com/julialang/reservoircomputing-dot-jl)
 
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
 ![rc_full_logo_large_white_cropped](https://user-images.githubusercontent.com/10376688/144242116-8243f58a-5ac6-4e0e-88d5-3409f00e20b4.png)
@@ -23,58 +23,68 @@ To illustrate the workflow of this library we will showcase how it is possible t
 using ReservoirComputing, OrdinaryDiffEq
 
 #lorenz system parameters
-u0 = [1.0,0.0,0.0]                       
-tspan = (0.0,200.0)                      
-p = [10.0,28.0,8/3]
+u0 = [1.0, 0.0, 0.0]
+tspan = (0.0, 200.0)
+p = [10.0, 28.0, 8 / 3]
 
 #define lorenz system
-function lorenz(du,u,p,t)
-    du[1] = p[1]*(u[2]-u[1])
-    du[2] = u[1]*(p[2]-u[3]) - u[2]
-    du[3] = u[1]*u[2] - p[3]*u[3]
+function lorenz(du, u, p, t)
+    du[1] = p[1] * (u[2] - u[1])
+    du[2] = u[1] * (p[2] - u[3]) - u[2]
+    du[3] = u[1] * u[2] - p[3] * u[3]
 end
 #solve and take data
-prob = ODEProblem(lorenz, u0, tspan, p)  
-data = solve(prob, ABM54(), dt=0.02)   
+prob = ODEProblem(lorenz, u0, tspan, p)
+data = solve(prob, ABM54(), dt = 0.02)
 
 shift = 300
 train_len = 5000
 predict_len = 1250
 
 #one step ahead for generative prediction
-input_data = data[:, shift:shift+train_len-1]
-target_data = data[:, shift+1:shift+train_len]
+input_data = data[:, shift:(shift + train_len - 1)]
+target_data = data[:, (shift + 1):(shift + train_len)]
 
-test = data[:,shift+train_len:shift+train_len+predict_len-1]
+test = data[:, (shift + train_len):(shift + train_len + predict_len - 1)]
 ```
+
 Now that we have the data we can initialize the ESN with the chosen parameters. Given that this is a quick example we are going to change the least amount of possible parameters. For more detailed examples and explanations of the functions please refer to the documentation.
+
 ```julia
 res_size = 300
-esn = ESN(input_data; 
-          reservoir = RandSparseReservoir(res_size, radius=1.2, sparsity=6/res_size),
-          input_layer = WeightedLayer(),
-          nla_type = NLAT2())
+esn = ESN(input_data;
+    reservoir = RandSparseReservoir(res_size, radius = 1.2, sparsity = 6 / res_size),
+    input_layer = WeightedLayer(),
+    nla_type = NLAT2())
 ```
 
 The echo state network can now be trained and tested. If not specified, the training will always be Ordinary Least Squares regression. The full range of training methods is detailed in the documentation.
+
 ```julia
 output_layer = train(esn, target_data)
 output = esn(Generative(predict_len), output_layer)
 ```
 
 The data is returned as a matrix, `output` in the code above, that contains the predicted trajectories. The results can now be easily plotted (for the actual script used to obtain this plot please refer to the documentation):
+
 ```julia
 using Plots
-plot(transpose(output),layout=(3,1), label="predicted")
-plot!(transpose(test),layout=(3,1), label="actual")
+plot(transpose(output), layout = (3, 1), label = "predicted")
+plot!(transpose(test), layout = (3, 1), label = "actual")
 ```
+
 ![lorenz_basic](https://user-images.githubusercontent.com/10376688/166227371-8bffa318-5c49-401f-9c64-9c71980cb3f7.png)
 
 One can also visualize the phase space of the attractor and the comparison with the actual one:
+
 ```julia
-plot(transpose(output)[:,1], transpose(output)[:,2], transpose(output)[:,3], label="predicted")
-plot!(transpose(test)[:,1], transpose(test)[:,2], transpose(test)[:,3], label="actual")
+plot(transpose(output)[:, 1],
+    transpose(output)[:, 2],
+    transpose(output)[:, 3],
+    label = "predicted")
+plot!(transpose(test)[:, 1], transpose(test)[:, 2], transpose(test)[:, 3], label = "actual")
 ```
+
 ![lorenz_attractor](https://user-images.githubusercontent.com/10376688/81470281-5a34b580-91ea-11ea-9eea-d2b266da19f4.png)
 
 ## Citing

diff --git a/docs/make.jl b/docs/make.jl
@@ -8,13 +8,12 @@ ENV["GKSwstype"] = "100"
 include("pages.jl")
 
 makedocs(modules = [ReservoirComputing],
-         sitename = "ReservoirComputing.jl",
-         clean = true, doctest = false, linkcheck = true,
-         warnonly = [:missing_docs],
-         format = Documenter.HTML(
-                                  assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/ReservoirComputing/stable/"),
-         pages = pages)
+    sitename = "ReservoirComputing.jl",
+    clean = true, doctest = false, linkcheck = true,
+    warnonly = [:missing_docs],
+    format = Documenter.HTML(assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/ReservoirComputing/stable/"),
+    pages = pages)
 
 deploydocs(repo = "github.com/SciML/ReservoirComputing.jl.git";
-           push_preview = true)
+    push_preview = true)
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -1,21 +1,21 @@
 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"],
+        "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",
-                                          #"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 Training Methods" => "esn_tutorials/different_training.md",
-                                          "Deep Echo State Networks" => "esn_tutorials/deep_esn.md",
-                                          "Hybrid Echo State Networks" => "esn_tutorials/hybrid.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 Training Methods" => "esn_tutorials/different_training.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 Layers" => "api/esn_layers.md",
-                               "ESN Drivers" => "api/esn_drivers.md",
-                               "ReCA" => "api/reca.md"],
+        "States Modifications" => "api/states.md",
+        "Prediction Types" => "api/predict.md",
+        "Echo State Networks" => "api/esn.md",
+        "ESN Layers" => "api/esn_layers.md",
+        "ESN Drivers" => "api/esn_drivers.md",
+        "ReCA" => "api/reca.md"],
 ]
diff --git a/docs/src/api/esn.md b/docs/src/api/esn.md
@@ -1,23 +1,28 @@
 # Echo State Networks
+
 The core component of an ESN is the `ESN` type. It represents the entire Echo State Network and includes parameters for configuring the reservoir, input scaling, and output weights. Here's the documentation for the `ESN` type:
 
 ```@docs
     ESN
 ```
 
 ## Variations
+
 In addition to the standard `ESN` model, there are variations that allow for deeper customization of the underlying model. Currently, there are two available variations: `Default` and `Hybrid`. These variations provide different ways to configure the ESN. Here's the documentation for the variations:
 
 ```@docs
     Default
     Hybrid
 ```
+
 The `Hybrid` variation is the most complex option and offers additional customization. Note that more variations may be added in the future to provide even greater flexibility.
 
 ## Training
 
 To train an ESN model, you can use the `train` function. It takes the ESN model, training data, and other optional parameters as input and returns a trained model. Here's the documentation for the train function:
+
 ```@docs
     train
 ```
-With these components and variations, you can configure and train ESN models for various time series and sequential data prediction tasks.
+
+With these components and variations, you can configure and train ESN models for various time series and sequential data prediction tasks.
diff --git a/docs/src/api/esn_drivers.md b/docs/src/api/esn_drivers.md
@@ -1,13 +1,16 @@
 # ESN Drivers
+
 ```@docs
     RNN
     MRNN
     GRU
 ```
-The ```GRU``` driver also provides the user with the choice of the possible variants:
+
+The `GRU` driver also provides the user with the choice of the possible variants:
+
 ```@docs
     FullyGated
     Minimal
 ```
-Please refer to the original papers for more detail about these architectures.
 
+Please refer to the original papers for more detail about these architectures.
diff --git a/docs/src/api/esn_layers.md b/docs/src/api/esn_layers.md
@@ -1,6 +1,7 @@
 # ESN Layers
 
 ## Input Layers
+
 ```@docs
     WeightedLayer
     DenseLayer
@@ -9,16 +10,22 @@
     MinimumLayer
     NullLayer
 ```
-The signs in the ```MinimumLayer``` are chosen based on the following methods:
+
+The signs in the `MinimumLayer` are chosen based on the following methods:
+
 ```@docs
     BernoulliSample
     IrrationalSample
 ```
+
 To derive the matrix one can call the following function:
+
 ```@docs
     create_layer
 ```
-To create new input layers, it suffices to define a new struct containing the needed parameters of the new input layer. This struct will need to be an ```AbstractLayer```, so the ```create_layer``` function can be dispatched over it. The workflow should follow this snippet:
+
+To create new input layers, it suffices to define a new struct containing the needed parameters of the new input layer. This struct will need to be an `AbstractLayer`, so the `create_layer` function can be dispatched over it. The workflow should follow this snippet:
+
 ```julia
 #creation of the new struct for the layer
 struct MyNewLayer <: AbstractLayer
@@ -32,6 +39,7 @@ end
 ```
 
 ## Reservoirs
+
 ```@docs
     RandSparseReservoir
     PseudoSVDReservoir
@@ -43,11 +51,13 @@ end
 ```
 
 Like for the input layers, to actually build the matrix of the reservoir, one can call the following function:
+
 ```@docs
     create_reservoir
 ```
 
-To create a new reservoir, the procedure is similar to the one for the input layers. First, the definition of the new struct of type ```AbstractReservoir``` with the reservoir parameters is needed. Then the dispatch over the ```create_reservoir``` function makes the model actually build the reservoir matrix. An example of the workflow is given in the following snippet:
+To create a new reservoir, the procedure is similar to the one for the input layers. First, the definition of the new struct of type `AbstractReservoir` with the reservoir parameters is needed. Then the dispatch over the `create_reservoir` function makes the model actually build the reservoir matrix. An example of the workflow is given in the following snippet:
+
 ```julia
 #creation of the new struct for the reservoir
 struct MyNewReservoir <: AbstractReservoir

diff --git a/docs/src/api/predict.md b/docs/src/api/predict.md
@@ -1,4 +1,5 @@
 # Prediction Types
+
 ```@docs
     Generative
     Predictive

diff --git a/docs/src/api/reca.md b/docs/src/api/reca.md
@@ -1,11 +1,13 @@
 # Reservoir Computing with Cellular Automata
+
 ```@docs
     RECA
 ```
 
 The input encodings are the equivalent of the input matrices of the ESNs. These are the available encodings:
+
 ```@docs
     RandomMapping
 ```
 
-The training and prediction follow the same workflow as the ESN. It is important to note that currently we were unable to find any papers using these models with a ```Generative``` approach for the prediction, so full support is given only to the ```Predictive``` method.
+The training and prediction follow the same workflow as the ESN. It is important to note that currently we were unable to find any papers using these models with a `Generative` approach for the prediction, so full support is given only to the `Predictive` method.
diff --git a/docs/src/api/states.md b/docs/src/api/states.md
@@ -1,6 +1,7 @@
 # States Modifications
 
 ## Padding and Estension
+
 ```@docs
     StandardStates
     ExtendedStates
@@ -9,6 +10,7 @@
 ```
 
 ## Non Linear Transformations
+
 ```@docs
     NLADefault
     NLAT1

diff --git a/docs/src/api/training.md b/docs/src/api/training.md
@@ -1,13 +1,16 @@
 # Training Algorithms
 
 ## Linear Models
+
 ```@docs
     StandardRidge
     LinearModel
 ```
 
 ## Gaussian Regression
+
 Currently, v0.9 is unavailable.
 
 ## Support Vector Regression
-Support Vector Regression is possible using a direct call to [LIBSVM](https://github.com/JuliaML/LIBSVM.jl) regression methods. Instead of a wrapper, please refer to the use of ```LIBSVM.AbstractSVR``` in the original library.
+
+Support Vector Regression is possible using a direct call to [LIBSVM](https://github.com/JuliaML/LIBSVM.jl) regression methods. Instead of a wrapper, please refer to the use of `LIBSVM.AbstractSVR` in the original library.