Merge pull request #7 from SciML/smc/cleanup

Cleanup

.typos.toml

@@ -0,0 +1,2 @@
+[default.extend-words]
+nin = "nin"

README.md

@@ -1,9 +1,9 @@
 # UDEComponents
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://SebastianM-C.github.io/UDEComponents.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SebastianM-C.github.io/UDEComponents.jl/dev/)
-[![Build Status](https://github.com/SebastianM-C/UDEComponents.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/SebastianM-C/UDEComponents.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/SebastianM-C/UDEComponents.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SebastianM-C/UDEComponents.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://SciML.github.io/UDEComponents.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SciML.github.io/UDEComponents.jl/dev/)
+[![Build Status](https://github.com/SciML/UDEComponents.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/SciML/UDEComponents.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/SciML/UDEComponents.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SciML/UDEComponents.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)
 [![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 

docs/make.jl

@@ -1,23 +1,23 @@
 using UDEComponents
 using Documenter
 
-DocMeta.setdocmeta!(UDEComponents, :DocTestSetup, :(using UDEComponents); recursive=true)
+DocMeta.setdocmeta!(UDEComponents, :DocTestSetup, :(using UDEComponents); recursive = true)
 
 makedocs(;
-    modules=[UDEComponents],
-    authors="Sebastian Micluța-Câmpeanu <[email protected]> and contributors",
-    sitename="UDEComponents.jl",
-    format=Documenter.HTML(;
-        canonical="https://SebastianM-C.github.io/UDEComponents.jl",
-        edit_link="main",
-        assets=String[],
+    modules = [UDEComponents],
+    authors = "Sebastian Micluța-Câmpeanu <[email protected]> and contributors",
+    sitename = "UDEComponents.jl",
+    format = Documenter.HTML(;
+        canonical = "https://SciML.github.io/UDEComponents.jl",
+        edit_link = "main",
+        assets = String[]
     ),
-    pages=[
-        "Home" => "index.md",
-    ],
+    pages = [
+        "Home" => "index.md"
+    ]
 )
 
 deploydocs(;
-    repo="github.com/SebastianM-C/UDEComponents.jl",
-    devbranch="main",
+    repo = "github.com/SciML/UDEComponents.jl",
+    devbranch = "main"
 )

src/UDEComponents.jl

@@ -15,7 +15,6 @@ include("utils.jl")
 include("hacks.jl") # this should be removed / upstreamed
 
 """
-
     create_ude_component(n_input = 1, n_output = 1;
         chain = multi_layer_feed_forward(n_input, n_output),
         rng = Xoshiro(0))

src/utils.jl

@@ -1,25 +1,6 @@
 function multi_layer_feed_forward(input_length, output_length; width::Int = 5,
-        depth::Int = 1, activation = softplus)
+        depth::Int = 1, activation = softplus, disable_optimizations = false)
     Lux.Chain(Lux.Dense(input_length, width, activation),
         [Lux.Dense(width, width, activation) for _ in 1:(depth)]...,
-        Lux.Dense(width, output_length); disable_optimizations = true)
+        Lux.Dense(width, output_length); disable_optimizations)
 end
-
-# Symbolics.@register_array_symbolic print_input(x) begin
-#     size = size(x)
-#     eltype = eltype(x)
-# end
-
-# function print_input(x)
-#     @info x
-#     x
-# end
-
-# function debug_component(n_input, n_output)
-#     @named input = RealInput(nin = n_input)
-#     @named output = RealOutput(nout = n_output)
-
-#     eqs = [output.u ~ print_input(input.u)]
-
-#     @named dbg_comp = ODESystem(eqs, t_nounits, [], [], systems = [input, output])
-# end

test/lotka_volterra.jl

@@ -43,10 +43,8 @@ end
 model = lotka_ude()
 nn = create_ude_component(2, 2)
 
-eqs = [
-    connect(model.nn_in, nn.output)
-    connect(model.nn_out, nn.input)
-]
+eqs = [connect(model.nn_in, nn.output)
+       connect(model.nn_out, nn.input)]
 
 ude_sys = complete(ODESystem(
     eqs, ModelingToolkit.t_nounits, systems = [model, nn], name = :ude_sys))
@@ -83,7 +81,6 @@ function loss(x, (prob, sol_ref, get_vars, get_refs))
     end
 end
 
-
 of = OptimizationFunction{true}(loss, AutoForwardDiff())
 
 ps = (prob, sol_ref, get_vars, get_refs);
@@ -95,20 +92,19 @@ ps = (prob, sol_ref, get_vars, get_refs);
 
 op = OptimizationProblem(of, x0, (prob, sol_ref, get_vars, get_refs))
 
-
 # using Plots
 
 # oh = []
 
-plot_cb = (opt_state, loss) -> begin
-    @info "step $(opt_state.iter), loss: $loss"
-    # push!(oh, opt_state)
-    # new_p = SciMLStructures.replace(Tunable(), prob.p, opt_state.u)
-    # new_prob = remake(prob, p = new_p)
-    # sol = solve(new_prob, Rodas4())
-    # display(plot(sol))
-    false
-end
+# plot_cb = (opt_state, loss) -> begin
+#     @info "step $(opt_state.iter), loss: $loss"
+#     push!(oh, opt_state)
+#     new_p = SciMLStructures.replace(Tunable(), prob.p, opt_state.u)
+#     new_prob = remake(prob, p = new_p)
+#     sol = solve(new_prob, Rodas4())
+#     display(plot(sol))
+#     false
+# end
 
 res = solve(op, Adam(), maxiters = 2000)#, callback = plot_cb)
 

test/qa.jl

@@ -3,12 +3,12 @@ using UDEComponents
 using Aqua
 using JET
 
-@testset verbose = true "Code quality (Aqua.jl)" begin
+@testset verbose=true "Code quality (Aqua.jl)" begin
     Aqua.find_persistent_tasks_deps(UDEComponents)
     Aqua.test_ambiguities(UDEComponents, recursive = false)
     Aqua.test_deps_compat(UDEComponents)
     # TODO: fix type piracy in propagate_ndims and propagate_shape
-    Aqua.test_piracies(UDEComponents, broken=true)
+    Aqua.test_piracies(UDEComponents, broken = true)
     Aqua.test_project_extras(UDEComponents)
     Aqua.test_stale_deps(UDEComponents, ignore = Symbol[])
     Aqua.test_unbound_args(UDEComponents)