Merge pull request #18 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

@@ -17,7 +17,7 @@ makedocs(;
     pages = [
         "Home" => "index.md",
         "Examples" => "examples.md",
-        "Mathematical Details" => "math.md"
+        "Mathematical Details" => "math.md",
     ]
 )
 

docs/make.jl

@@ -25,4 +25,4 @@ include("solve.jl")
     (obj::Returns)(@nospecialize(args...); @nospecialize(kw...)) = obj.value
 end
 
-end # module 
+end # module

src/FiniteVolumeMethod1D.jl

@@ -29,9 +29,9 @@ Base.@kwdef struct Dirichlet{F, P} <: AbstractBoundaryCondition{F, P}
 end
 Dirichlet(f::Function) = Dirichlet(f, nothing)
 Dirichlet(v::Number) =
-    let v = v
-        Dirichlet((u, t, p) -> oftype(u, v))
-    end
+let v = v
+    Dirichlet((u, t, p) -> oftype(u, v))
+end
 
 @doc raw"""
     Neumann{F,P} <: AbstractBoundaryCondition{F,P}
@@ -60,9 +60,9 @@ Base.@kwdef struct Neumann{F, P} <: AbstractBoundaryCondition{F, P}
     Neumann(f::F, p::P = nothing) where {F, P} = new{F, P}(f, p)
 end
 Neumann(v::Number) =
-    let v = v
-        Neumann((u, t, p) -> oftype(u, v))
-    end
+let v = v
+    Neumann((u, t, p) -> oftype(u, v))
+end
 
 is_dirichlet(::AbstractBoundaryCondition) = false
 is_dirichlet(::Dirichlet) = true

src/boundary_conditions.jl

@@ -37,10 +37,12 @@ function pde_odes!(dudt, u, prob::P, t) where {P}
         hᵢ = h[i]
         hᵢ₋₁ = h[i - 1]
         Rᵢ = R(u[i], xᵢ, t, Rp)
-        dudt[i] = inv(Vᵢ) * (D̄ᵢᵢ₊₁ * ((u[i + 1] - u[i]) / hᵢ) -
-                   D̄ᵢ₋₁ᵢ * ((u[i] - u[i - 1]) / hᵢ₋₁)) + Rᵢ
+        dudt[i] = inv(Vᵢ) * (
+            D̄ᵢᵢ₊₁ * ((u[i + 1] - u[i]) / hᵢ) -
+                D̄ᵢ₋₁ᵢ * ((u[i] - u[i - 1]) / hᵢ₋₁)
+        ) + Rᵢ
     end
-    if !is_dirichlet(rhs)
+    return if !is_dirichlet(rhs)
         b = mesh_points[end]
         xₙ₋₁ = mesh_points[end - 1]
         Vₙ = V[end]
@@ -58,16 +60,16 @@ end
 
 jacobian_sparsity(prob::FVMProblem) = jacobian_sparsity(prob.geometry.mesh_points)
 function jacobian_sparsity(pts)
-    num_nnz = 3(length(pts) - 2) + 4 # 3 neighbours for each interior node, 2 from each boundary node 
+    num_nnz = 3(length(pts) - 2) + 4 # 3 neighbours for each interior node, 2 from each boundary node
     I = zeros(Int64, num_nnz)
     J = zeros(Int64, num_nnz)
     V = ones(num_nnz)
-    # The left boundary node 
+    # The left boundary node
     I[1] = firstindex(pts)
     J[1] = firstindex(pts)
     I[2] = firstindex(pts)
     J[2] = firstindex(pts) + 1
-    # The interior nodes 
+    # The interior nodes
     ctr = 3
     for i in (firstindex(pts) + 1):(lastindex(pts) - 1)
         I[ctr] = i
@@ -80,7 +82,7 @@ function jacobian_sparsity(pts)
         J[ctr] = i - 1
         ctr += 1
     end
-    # The right boundary node 
+    # The right boundary node
     I[ctr] = lastindex(pts)
     J[ctr] = lastindex(pts)
     ctr += 1

src/equations.jl

@@ -56,8 +56,9 @@ Base.@kwdef struct FVMProblem{T, DF, DP, RF, RP, L, R, IC, FT}
     final_time::FT
 end
 function FVMProblem(mesh_points, lhs, rhs; kwargs...)
-    FVMProblem(;
+    return FVMProblem(;
         geometry = FVMGeometry(mesh_points),
         boundary_conditions = BoundaryConditions(lhs, rhs),
-        kwargs...)
+        kwargs...
+    )
 end

src/problem.jl

@@ -1,7 +1,9 @@
-function SciMLBase.ODEProblem(prob::FVMProblem;
+function SciMLBase.ODEProblem(
+        prob::FVMProblem;
         specialization::Type{S} = SciMLBase.AutoSpecialize,
         jac_prototype = jacobian_sparsity(prob),
-        kwargs...) where {S}
+        kwargs...
+    ) where {S}
     initial_time = prob.initial_time
     final_time = prob.final_time
     time_span = (initial_time, final_time)
@@ -12,7 +14,8 @@ function SciMLBase.ODEProblem(prob::FVMProblem;
     cb = CallbackSet(lhs_cb, rhs_cb)
     f = ODEFunction{true, S}(pde_odes!; jac_prototype = jac_prototype)
     ode_problem = ODEProblem{true, S}(
-        f, initial_condition, time_span, prob; callback = cb, kwargs...)
+        f, initial_condition, time_span, prob; callback = cb, kwargs...
+    )
     return ode_problem
 end
 
@@ -60,5 +63,5 @@ function update_rhs!(integrator)
 end
 
 function CommonSolve.init(prob::FVMProblem, alg; kwargs...)
-    CommonSolve.init(ODEProblem(prob; kwargs...), alg; kwargs...)
+    return CommonSolve.init(ODEProblem(prob; kwargs...), alg; kwargs...)
 end

src/solve.jl

@@ -5,14 +5,14 @@ using OrdinaryDiffEq
 using CairoMakie
 using ReferenceTests
 
-# p. 145 Constanda 
-# uₜ = uₓₓ + π²exp[-24π²t]sin(5πx), 0 < x < 1 
+# p. 145 Constanda
+# uₜ = uₓₓ + π²exp[-24π²t]sin(5πx), 0 < x < 1
 # u(0, t) = 0
 # u(1, t) = 0
 # u(x, 0) = 3sin(4πx)
 
 function exact_u(x, t)
-    return 3exp(-16π^2*t)*sin(4π*x) + exp(-25π^2*t)*(exp(π^2*t)-1)*sin(5π*x)
+    return 3exp(-16π^2 * t) * sin(4π * x) + exp(-25π^2 * t) * (exp(π^2 * t) - 1) * sin(5π * x)
 end
 
 reaction_function = (u, x, t, p) -> p[1] * exp(-p[2] * t) * sin(p[3] * x)
@@ -21,18 +21,20 @@ diffusion_function = (u, x, t, p) -> one(u)
 lhs = Dirichlet(0.0)
 rhs = Dirichlet(0.0)
 mesh_points = LinRange(0, 1, 500)
-ic_ff = x -> 3sin(4π*x)
+ic_ff = x -> 3sin(4π * x)
 initial_condition = ic_ff.(mesh_points)
 final_time = 0.05
-prob = FVMProblem(mesh_points, lhs, rhs;
+prob = FVMProblem(
+    mesh_points, lhs, rhs;
     diffusion_function,
     reaction_function,
     reaction_parameters,
     initial_condition,
-    final_time)
+    final_time
+)
 sol = solve(prob, TRBDF2(linsolve = KLUFactorization()), saveat = 0.001)
 exact_sol = [exact_u.(mesh_points, sol.t[i]) for i in eachindex(sol)]
-@test reduce(hcat, sol.u) ≈ reduce(hcat, exact_sol) rtol = 1e-1
+@test reduce(hcat, sol.u) ≈ reduce(hcat, exact_sol) rtol = 1.0e-1
 
 let t_range = LinRange(0.0, final_time, 250)
     fig = Figure(fontsize = 33)

test/dirichlet_source.jl

@@ -23,17 +23,23 @@ ic_f(x) = x < 0 ? 1.0 : 1 / 2
 Dt = Differential(t)
 Dx = Differential(x)
 Dxx = Differential(x)^2
-eqs = [Dt(u(t, x)) ~
-       Dx(
-    (inv(θ₁ * u(t, x)) + θ₂ * inv(u(t, x)^2) + θ₃ * inv(u(t, x)^3)) *
-    Dx(u(t, x))
-) +
-       β * K * u(t, x) * (1 - u(t, x) / K)]
-bcs = [Dx(u(t, 2π)) ~ 0.0,
+eqs = [
+    Dt(u(t, x)) ~
+        Dx(
+        (inv(θ₁ * u(t, x)) + θ₂ * inv(u(t, x)^2) + θ₃ * inv(u(t, x)^3)) *
+            Dx(u(t, x))
+    ) +
+        β * K * u(t, x) * (1 - u(t, x) / K),
+]
+bcs = [
+    Dx(u(t, 2π)) ~ 0.0,
     Dx(u(t, -2π)) ~ 0.0,
-    u(0, x) ~ ic_f(x)]
-domains = [t ∈ Interval(0.0, 1.0),
-    x ∈ Interval(-2π, 2π)]
+    u(0, x) ~ ic_f(x),
+]
+domains = [
+    t ∈ Interval(0.0, 1.0),
+    x ∈ Interval(-2π, 2π),
+]
 @named pdesys = PDESystem(
     eqs,
     bcs,
@@ -44,8 +50,8 @@ domains = [t ∈ Interval(0.0, 1.0),
         θ₁ => 1.0,
         θ₂ => 50.0,
         θ₃ => 3.0,
-        β => 1e-3,
-        K => 2.0
+        β => 1.0e-3,
+        K => 2.0,
     ]
 )
 discretisation = MOLFiniteDifference([x => 0.1], t)
@@ -59,7 +65,7 @@ solu = sol[u(t, x)]
 diffusion_function = (u, x, t, p) -> inv(p[1] * u) + p[2] * inv(u^2) + p[3] * inv(u^3)
 reaction_function = (u, x, t, p) -> p[1] * p[2] * u * (1 - u / p[2])
 diffusion_parameters = [1.0, 50.0, 3.0]
-reaction_parameters = [1e-3, 2.0]
+reaction_parameters = [1.0e-3, 2.0]
 mesh_points = solx
 initial_condition = ic_f.(mesh_points)
 final_time = 1.0
@@ -78,7 +84,7 @@ fvm_prob = FVMProblem(
 )
 fvm_sol = solve(fvm_prob, TRBDF2(), saveat = solt)
 fvm_solu = reduce(hcat, fvm_sol.u)'
-@test solu ≈ fvm_solu rtol = 1e-2
+@test solu ≈ fvm_solu rtol = 1.0e-2
 
 let sol = fvm_sol, t_range = LinRange(0.0, final_time, 250)
     fig = Figure(fontsize = 33)