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Merge pull request #7 from SciML/smc/cleanup
Cleanup
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‎.typos.toml

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[default.extend-words]
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nin = "nin"

‎README.md

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# UDEComponents
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://SebastianM-C.github.io/UDEComponents.jl/stable/)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SebastianM-C.github.io/UDEComponents.jl/dev/)
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[![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)
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[![Coverage](https://codecov.io/gh/SebastianM-C/UDEComponents.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SebastianM-C/UDEComponents.jl)
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://SciML.github.io/UDEComponents.jl/stable/)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SciML.github.io/UDEComponents.jl/dev/)
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[![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)
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[![Coverage](https://codecov.io/gh/SciML/UDEComponents.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SciML/UDEComponents.jl)
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[![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)
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[![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
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‎docs/make.jl

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

‎src/UDEComponents.jl

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include("hacks.jl") # this should be removed / upstreamed
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"""
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create_ude_component(n_input = 1, n_output = 1;
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chain = multi_layer_feed_forward(n_input, n_output),
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rng = Xoshiro(0))

‎src/utils.jl

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

‎test/lotka_volterra.jl

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

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

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