Merge pull request #323 from ChrisRackauckas-Claude/runic-formatting

Switch from JuliaFormatter to Runic.jl for code formatting

Author: ChrisRackauckas

.JuliaFormatter.toml

@@ -0,0 +1,19 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'main'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  runic:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: fredrikekre/runic-action@v1
+        with:
+          version: '1'

.github/workflows/FormatCheck.yml

@@ -17,10 +17,10 @@ makedocs(;
         "Examples" => [
             "examples/DiffEqFlux.md",
             "examples/adaptive_control.md",
+            "examples/ODE_jac.md",
             "examples/coulomb_control.md",
-            "examples/ODE_jac.md"
         ],
-        "API" => "api.md"
+        "API" => "api.md",
     ],
     repo = GitHub("SciML/ComponentArrays.jl"),
     sitename = "ComponentArrays.jl",

docs/make.jl

@@ -23,12 +23,12 @@ tspan2 = (0.0f0, 25.0f0)
 # Make truth data
 function trueODEfunc(du, u, p, t)
     true_A = [-0.1 2.0; -2.0 -0.1]
-    du .= ((u .^ 3)'true_A)'
+    return du .= ((u .^ 3)'true_A)'
 end
 
 t = range(tspan[1], tspan[2], length = datasize)
 # t = Float32.(vcat(range(0.0, 0.9, length=10), 10 .^ range(log10(tspan[1]+1), log10(tspan[2]), length=datasize-10)))
-t = Float32.([0; 10 .^ range(log10(tspan[1] + 0.01), log10(tspan[2]), length = datasize-1)])
+t = Float32.([0; 10 .^ range(log10(tspan[1] + 0.01), log10(tspan[2]), length = datasize - 1)])
 prob = ODEProblem(trueODEfunc, u0, tspan2)
 ode_sol = solve(prob, Tsit5())
 ode_data = Array(ode_sol(t)) + MeasurementNoise(0.1)
@@ -39,7 +39,7 @@ neural_layer(in, out) = ComponentArray{Float32}(W = glorot_uniform(out, in), b =
 # Dense neural layer function
 dense(layer, activation = identity) = u -> activation.(layer.W * u + layer.b)
 
-# Neural ODE function 
+# Neural ODE function
 dudt(u, p, t) = u .^ 3 |> dense(p.L1, σ) |> dense(p.L2)
 
 prob = ODEProblem(dudt, u0, tspan2)
@@ -56,7 +56,7 @@ full_sol(θ) = solve(prob, Tsit5(), u0 = θ.u, p = θ.p)
 function loss_n_ode(θ)
     pred = predict_n_ode(θ)
 
-    loss = sum(abs2, ode_data .- pred)/datasize + 0.1*(sum(abs, θ.p)/length(θ.p))
+    loss = sum(abs2, ode_data .- pred) / datasize + 0.1 * (sum(abs, θ.p) / length(θ.p))
     return loss, pred
 end
 loss_n_ode(θ)
@@ -83,12 +83,18 @@ cb = function (θ, loss, pred; doplot = false)
     plot!(pl_3, ode_sol, vars = (1, 2), label = "truth")
     scatter!(pl_3, pred[1, :], pred[2, :], label = "predicted data")
     scatter!(pl_3, ode_data[1, :], ode_data[2, :], label = "measured data")
-    plot!(pl_3, hcat(pred[1, :], ode_data[1, :])', hcat(pred[2, :], ode_data[2, :])',
-        label = false, color = :lightgray, legend = :bottomright)
-
-    display(plot(
-        plot(pl_1, pl_2, layout = (2, 1), size = (400, 500)), pl_3, layout = (1, 2), size = (
-            950, 500)))
+    plot!(
+        pl_3, hcat(pred[1, :], ode_data[1, :])', hcat(pred[2, :], ode_data[2, :])',
+        label = false, color = :lightgray, legend = :bottomright
+    )
+
+    display(
+        plot(
+            plot(pl_1, pl_2, layout = (2, 1), size = (400, 500)), pl_3, layout = (1, 2), size = (
+                950, 500,
+            )
+        )
+    )
     # frame(anim)
     return false
 end

examples/DiffEqFlux_example.jl

@@ -9,13 +9,13 @@ function lorenz!(D, u, p, t; f = 0.0)
     @unpack σ, ρ, β = p
     @unpack x, y, z = u
 
-    D.x = σ*(y - x)
-    D.y = x*(ρ - z) - y - f
-    D.z = x*y - β*z
+    D.x = σ * (y - x)
+    D.y = x * (ρ - z) - y - f
+    D.z = x * y - β * z
     return nothing
 end
 
-lorenz_p = (σ = 10.0, ρ = 28.0, β = 8/3)
+lorenz_p = (σ = 10.0, ρ = 28.0, β = 8 / 3)
 lorenz_ic = ComponentArray(x = 0.0, y = 0.0, z = 0.0)
 lorenz_prob = ODEProblem(lorenz!, lorenz_ic, tspan, lorenz_p)
 
@@ -24,12 +24,12 @@ function lotka!(D, u, p, t; f = 0.0)
     @unpack α, β, γ, δ = p
     @unpack x, y = u
 
-    D.x = α*x - β*x*y + f
-    D.y = -γ*y + δ*x*y
+    D.x = α * x - β * x * y + f
+    D.y = -γ * y + δ * x * y
     return nothing
 end
 
-lotka_p = (α = 2/3, β = 4/3, γ = 1.0, δ = 1.0)
+lotka_p = (α = 2 / 3, β = 4 / 3, γ = 1.0, δ = 1.0)
 lotka_ic = ComponentArray(x = 1.0, y = 1.0)
 lotka_prob = ODEProblem(lotka!, lotka_ic, tspan, lotka_p)
 
@@ -38,8 +38,8 @@ function composed!(D, u, p, t)
     c = p.c #coupling parameter
     @unpack lorenz, lotka = u
 
-    lorenz!(D.lorenz, lorenz, p.lorenz, t, f = c*lotka.x)
-    lotka!(D.lotka, lotka, p.lotka, t, f = c*lorenz.x)
+    lorenz!(D.lorenz, lorenz, p.lorenz, t, f = c * lotka.x)
+    lotka!(D.lotka, lotka, p.lotka, t, f = c * lorenz.x)
     return nothing
 end
 

examples/ODE_example.jl

@@ -9,9 +9,9 @@ function lorenz!(D, u, p, t; f = 0.0)
     @unpack σ, ρ, β = p
     @unpack x, y, z = u
 
-    D.x = σ*(y - x)
-    D.y = x*(ρ - z) - y - f
-    D.z = x*y - β*z
+    D.x = σ * (y - x)
+    D.y = x * (ρ - z) - y - f
+    D.z = x * y - β * z
     return nothing
 end
 function lorenz_jac!(D, u, p, t)
@@ -31,7 +31,7 @@ function lorenz_jac!(D, u, p, t)
     return nothing
 end
 
-lorenz_p = (σ = 10.0, ρ = 28.0, β = 8/3)
+lorenz_p = (σ = 10.0, ρ = 28.0, β = 8 / 3)
 lorenz_ic = ComponentArray(x = 0.0, y = 0.0, z = 0.0)
 lorenz_fun = ODEFunction(lorenz!, jac = lorenz_jac!)
 lorenz_prob = ODEProblem(lorenz_fun, lorenz_ic, tspan, lorenz_p)
@@ -41,23 +41,23 @@ function lotka!(D, u, p, t; f = 0.0)
     @unpack α, β, γ, δ = p
     @unpack x, y = u
 
-    D.x = α*x - β*x*y + f
-    D.y = -γ*y + δ*x*y
+    D.x = α * x - β * x * y + f
+    D.y = -γ * y + δ * x * y
     return nothing
 end
 function lotka_jac!(D, u, p, t)
     @unpack α, β, γ, δ = p
     @unpack x, y = u
 
-    D[:x, :x] = α - β*y
-    D[:x, :y] = -β*x
+    D[:x, :x] = α - β * y
+    D[:x, :y] = -β * x
 
-    D[:y, :x] = δ*y
-    D[:y, :y] = -γ + δ*x
+    D[:y, :x] = δ * y
+    D[:y, :y] = -γ + δ * x
     return nothing
 end
 
-lotka_p = (α = 2/3, β = 4/3, γ = 1.0, δ = 1.0)
+lotka_p = (α = 2 / 3, β = 4 / 3, γ = 1.0, δ = 1.0)
 lotka_ic = ComponentArray(x = 1.0, y = 1.0)
 lotka_fun = ODEFunction(lotka!, jac = lotka_jac!)
 lotka_prob = ODEProblem(lotka_fun, lotka_ic, tspan, lotka_p)
@@ -67,8 +67,8 @@ function composed!(D, u, p, t)
     c = p.c #coupling parameter
     @unpack lorenz, lotka = u
 
-    lorenz!(D.lorenz, lorenz, p.lorenz, t, f = c*lotka.x)
-    lotka!(D.lotka, lotka, p.lotka, t, f = c*lorenz.x)
+    lorenz!(D.lorenz, lorenz, p.lorenz, t, f = c * lotka.x)
+    lotka!(D.lotka, lotka, p.lotka, t, f = c * lorenz.x)
     return nothing
 end
 function composed_jac!(D, u, p, t)

examples/ODE_jac_example.jl

@@ -12,8 +12,9 @@ maybe_apply(f, x, p, t) = f
 
 function apply_inputs(func; kwargs...)
     simfun(dx, x, p, t) = func(
-        dx, x, p, t; map(f->maybe_apply(f, x, p, t), (; kwargs...))...)
-    simfun(x, p, t) = func(x, p, t; map(f->maybe_apply(f, x, p, t), (; kwargs...))...)
+        dx, x, p, t; map(f -> maybe_apply(f, x, p, t), (; kwargs...))...
+    )
+    simfun(x, p, t) = func(x, p, t; map(f -> maybe_apply(f, x, p, t), (; kwargs...))...)
     return simfun
 end
 
@@ -27,7 +28,7 @@ SISO_simulator(P::TransferFunction) = SISO_simulator(ss(P))
 function SISO_simulator(P::AbstractStateSpace)
     @unpack A, B, C, D = P
 
-    if size(D)!=(1, 1)
+    if size(D) != (1, 1)
         error("This is not a SISO system")
     end
 
@@ -37,8 +38,8 @@ function SISO_simulator(P::AbstractStateSpace)
     DD = D[1, 1]
 
     return function sim!(dx, x, p, t; u = 0.0)
-        dx .= A*x + BB*u
-        return CC*x + DD*u
+        dx .= A * x + BB * u
+        return CC * x + DD * u
     end
 end
 
@@ -60,13 +61,13 @@ nominal_sim! = SISO_simulator(nominal_plant)
 
 # To test robustness to uncertainty, we'll also include unmodeled dynamics with an entirely
 # different structure than our nominal plant model.
-unmodeled_dynamics = 229/(s^2 + 30s + 229)
+unmodeled_dynamics = 229 / (s^2 + 30s + 229)
 truth_plant = nominal_plant * unmodeled_dynamics
 truth_sim! = SISO_simulator(truth_plant)
 
 # We'll make a first-order sensor as well so we can add noise to our measurement
 τ = 0.005
-sensor_plant = 1 / (τ*s + 1)
+sensor_plant = 1 / (τ * s + 1)
 sensor_sim! = SISO_simulator(sensor_plant)
 
 ## Derivative functions
@@ -76,7 +77,7 @@ control(θ, w) = θ'w
 
 # We'll use a simple gradient descent adaptation law
 function adapt!(Dθ, θ, γ, t; e, w)
-    Dθ .= -γ*e*w
+    Dθ .= -γ * e * w
     return nothing
 end
 
@@ -98,7 +99,7 @@ function feedback_sys!(D, vars, p, t; ym, r, n)
     return yp
 end
 # Now the full system takes in an input signal `r`, feeds it through the reference model,
-# and feeds the output of the reference model `ym` and the input signal to `feedback_sys`. 
+# and feeds the output of the reference model `ym` and the input signal to `feedback_sys`.
 function system!(D, vars, p, t; r = 0.0, n = 0.0)
     @unpack reference_model, feedback_loop = vars
 
@@ -122,31 +123,33 @@ sensor_ic = zeros(1)
 θ_est_ic = ComponentArray(θr = 0.0, θy = 0.0)
 
 ## Set up and run Simulation
-function simulate(plant_fun, plant_ic;
+function simulate(
+        plant_fun, plant_ic;
         tspan = tspan,
         input_signal = input_signal,
         adapt_gain = 1.5,
         noise_param = nothing,
-        deterministic_noise = 0.0)
+        deterministic_noise = 0.0
+    )
     noise(D, vars, p, t) = (D.feedback_loop.sensor[1] = noise_param)
 
     # Truth control parameters
-    θ_truth = (r = bm/bp, y = (ap-am)/bp)
+    θ_truth = (r = bm / bp, y = (ap - am) / bp)
 
     # Initial conditions
     ic = ComponentArray(
         reference_model = ref_ic,
         feedback_loop = (
             parameter_estimates = θ_est_ic,
             sensor = sensor_ic,
-            plant_model = plant_ic
+            plant_model = plant_ic,
         )
     )
 
     # Model parameters
     p = (
         gamma = adapt_gain,
-        plant_fun = plant_fun
+        plant_fun = plant_fun,
     )
 
     sim_fun = apply_inputs(system!; r = input_signal, n = deterministic_noise)
@@ -172,9 +175,14 @@ function simulate(plant_fun, plant_ic;
     )
 
     # Parameter estimate tracking
-    bottom = plot(sol,
-        vars = Symbol.([
-            "feedback_loop.parameter_estimates.θr", "feedback_loop.parameter_estimates.θy"]))
+    bottom = plot(
+        sol,
+        vars = Symbol.(
+            [
+                "feedback_loop.parameter_estimates.θr", "feedback_loop.parameter_estimates.θy",
+            ]
+        )
+    )
     plot!(
         bottom,
         [tspan...], [θ_truth.r θ_truth.y; θ_truth.r θ_truth.y],
@@ -184,8 +192,10 @@ function simulate(plant_fun, plant_ic;
     )
 
     # Combine both plots
-    plot(top, bottom, layout = (2, 1), size = (800, 800))
+    return plot(top, bottom, layout = (2, 1), size = (800, 800))
 end
 
-simulate(truth_sim!, truth_ic; input_signal = 2.0,
-    deterministic_noise = (x, p, t)->0.5sin(16.1t), noise_param = nothing)
+simulate(
+    truth_sim!, truth_ic; input_signal = 2.0,
+    deterministic_noise = (x, p, t) -> 0.5sin(16.1t), noise_param = nothing
+)