Runic format

.github/workflows/Lint.yml

@@ -26,8 +26,8 @@ jobs:
           version: "1"
       - name: Use Julia cache
         uses: julia-actions/cache@v2
-      - name: Install JuliaFormatter.jl
-        run: julia -e 'using Pkg; pkg"add JuliaFormatter"'
+      - name: Install Runic.jl
+        run: julia -e 'using Pkg; pkg"add Runic"'
       - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
         run: touch requirements.txt
       - name: Setup Python

.pre-commit-config.yaml

@@ -14,9 +14,6 @@ repos:
       - id: check-toml
       - id: check-yaml
       - id: end-of-file-fixer
-      - id: file-contents-sorter
-        files: .JuliaFormatter.toml
-        args: [--unique]
       - id: mixed-line-ending
         args: [--fix=lf]
       # - id: no-commit-to-branch
@@ -43,7 +40,7 @@ repos:
     rev: v1.37.1
     hooks:
       - id: yamllint
-  - repo: https://github.com/domluna/JuliaFormatter.jl
-    rev: v2.1.6
+  - repo: https://github.com/fredrikekre/runic-pre-commit
+    rev: v2.0.1
     hooks:
-      - id: julia-formatter
+      - id: runic

README.md

@@ -5,6 +5,7 @@
 [![Build Status](https://github.com/maltezfaria/LevelSetMethods.jl/workflows/Test/badge.svg)](https://github.com/maltezfaria/LevelSetMethods.jl/actions)
 [![Test workflow status](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Test.yml?query=branch%3Amain)
 [![Lint workflow Status](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Lint.yml/badge.svg?branch=main)](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Lint.yml?query=branch%3Amain)
+[![Runic Badge](https://img.shields.io/badge/Runic-formatting-brightgreen.svg)](https://github.com/fredrikekre/Runic.jl)
 [![Docs workflow Status](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Docs.yml/badge.svg?branch=main)](https://github.com/maltezfaria/LevelSetMethods.jl/actions/workflows/Docs.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/maltezfaria/LevelSetMethods.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/maltezfaria/LevelSetMethods.jl)
 [![BestieTemplate](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/JuliaBesties/BestieTemplate.jl/main/docs/src/assets/badge.json)](https://github.com/JuliaBesties/BestieTemplate.jl)

docs/make.jl

@@ -19,7 +19,7 @@ DocMeta.setdocmeta!(
 const page_rename = Dict("developer.md" => "Developer docs") # Without the numbers
 const numbered_pages = [
     file for file in readdir(joinpath(@__DIR__, "src")) if
-    file != "index.md" && splitext(file)[2] == ".md" && occursin(r"^\d", file)
+        file != "index.md" && splitext(file)[2] == ".md" && occursin(r"^\d", file)
 ]
 
 modules = [LevelSetMethods]

ext/InterpolationsExt.jl

@@ -4,7 +4,7 @@ import Interpolations as Itp
 import LevelSetMethods as LSM
 
 function __init__()
-    @info "Loading Interpolations extension for LevelSetMethods.jl"
+    return @info "Loading Interpolations extension for LevelSetMethods.jl"
 end
 
 Itp.interpolate(ϕ::LSM.LevelSet) = Itp.interpolate(ϕ, Itp.BSpline(Itp.Cubic()))

ext/MMGSurfaceExt.jl

@@ -5,7 +5,7 @@ import MarchingCubes
 import LevelSetMethods as LSM
 
 function __init__()
-    @info "Loading MMGSurface extension for LevelSetMethods.jl"
+    return @info "Loading MMGSurface extension for LevelSetMethods.jl"
 end
 
 """
@@ -37,13 +37,13 @@ boundary and the reconstructed ideal boundary
     Only works for 3 dimensional level-set.
 """
 function LSM.export_surface_mesh(
-    ϕ::LSM.LevelSet,
-    output::String;
-    hgrad = nothing,
-    hmin = nothing,
-    hmax = nothing,
-    hausd = nothing,
-)
+        ϕ::LSM.LevelSet,
+        output::String;
+        hgrad = nothing,
+        hmin = nothing,
+        hmax = nothing,
+        hausd = nothing,
+    )
     N = LSM.dimension(ϕ)
     if N != 3
         throw(ArgumentError("export_mesh of $N dimensional level-set not supported."))
@@ -85,7 +85,7 @@ function LSM.export_surface_mesh(
 end
 
 function _write_3D_triangular_mesh(path, vertices, triangles)
-    open(path, "w") do file
+    return open(path, "w") do file
         write(file, "MeshVersionFormatted 1\n")
         write(file, "Dimension 3\n")
 

ext/MMGVolumeExt.jl

@@ -5,7 +5,7 @@ import LevelSetMethods as LSM
 # using DelimitedFiles # using or import ? # faster with writedlm ?
 
 function __init__()
-    @info "Loading MMGVolume extension for LevelSetMethods.jl"
+    return @info "Loading MMGVolume extension for LevelSetMethods.jl"
 end
 
 """
@@ -39,13 +39,13 @@ For more information, see the official [MMG documentation](http://www.mmgtools.o
     Only works for 2 and 3 dimensional level-set.
 """
 function LSM.export_volume_mesh(
-    ϕ::LSM.LevelSet,
-    output::String;
-    hgrad = nothing,
-    hmin = nothing,
-    hmax = nothing,
-    hausd = nothing,
-)
+        ϕ::LSM.LevelSet,
+        output::String;
+        hgrad = nothing,
+        hmin = nothing,
+        hmax = nothing,
+        hausd = nothing,
+    )
     N = LSM.dimension(ϕ)
     if N != 2 && N != 3
         throw(ArgumentError("export_mesh of $N dimensional level-set not supported."))
@@ -78,7 +78,7 @@ function LSM.export_volume_mesh(
                 num_triangles = 2(nx - 1) * (ny - 1)
                 write(file, "\nTriangles\n")
                 write(file, "$num_triangles\n")
-                for x_id in 1:(nx-1), y_id in 1:(ny-1)
+                for x_id in 1:(nx - 1), y_id in 1:(ny - 1)
                     c00 = (y_id - 1) * nx + x_id
                     c10 = c00 + 1
                     c01 = c00 + nx
@@ -96,7 +96,7 @@ function LSM.export_volume_mesh(
                 num_tetrahedrons = 6(nx - 1) * (ny - 1) * (nz - 1)
                 write(file, "\nTetrahedra\n")
                 write(file, "$num_tetrahedrons\n")
-                for x_id in 1:(nx-1), y_id in 1:(ny-1), z_id in 1:(nz-1)
+                for x_id in 1:(nx - 1), y_id in 1:(ny - 1), z_id in 1:(nz - 1)
                     c000 = (z_id - 1) * nx * ny + (y_id - 1) * nx + x_id
                     c100 = c000 + 1
                     c010 = c000 + nx

ext/MakieExt.jl

@@ -4,7 +4,7 @@ using Makie
 import LevelSetMethods as LSM
 
 function __init__()
-    @info "Loading Makie extension for LevelSetMethods.jl"
+    return @info "Loading Makie extension for LevelSetMethods.jl"
 end
 
 # NOTE: Makie recipes currently can't modify the Axis (https://discourse.julialang.org/t/makie-plot-recipe-collections/86434)
@@ -37,7 +37,10 @@ end
 #     end
 # end
 
-function Makie.convert_arguments(::Union{Type{<:Contour},Type{<:Contourf}}, ϕ::LSM.LevelSet)
+function Makie.convert_arguments(
+        ::Union{Type{<:Contour}, Type{<:Contourf}, Type{<:Heatmap}},
+        ϕ::LSM.LevelSet,
+    )
     LSM.dimension(ϕ) == 2 ||
         throw(ArgumentError("Contour plot only supported for 2D level-sets."))
     return _contour_plot(ϕ)

src/derivatives.jl

@@ -11,7 +11,7 @@ Centered finite difference scheme for first order derivative at grid point `I`
 along dimension `dim`.
 """
 function D⁰(ϕ::CartesianMeshField, I, dim)
-    h  = meshsize(ϕ, dim)
+    h = meshsize(ϕ, dim)
     Im = _decrement_index(I, dim)
     Ip = _increment_index(I, dim)
     return (ϕ[Ip] - ϕ[Im]) / (2h)
@@ -24,14 +24,14 @@ Forward finite difference scheme for first order derivative at grid point `I`
 along dimension `dim`.
 """
 @inline function D⁺(ϕ::CartesianMeshField, I, dim)
-    h  = meshsize(ϕ, dim)
+    h = meshsize(ϕ, dim)
     Ip = _increment_index(I, dim)
     return (ϕ[Ip] - ϕ[I]) / h
 end
 
 function D⁺⁺(ϕ::CartesianMeshField, I, dim)
-    h   = meshsize(ϕ, dim)
-    Ip  = _increment_index(I, dim)
+    h = meshsize(ϕ, dim)
+    Ip = _increment_index(I, dim)
     Ipp = _increment_index(I, dim, 2)
     return (-1.5 * ϕ[I] + 2 * ϕ[Ip] - 1 / 2 * ϕ[Ipp]) / h
 end
@@ -43,7 +43,7 @@ Backward finite difference scheme for first order derivative at grid point `I`
 along dimension `dim`.
 """
 function D⁻(ϕ::CartesianMeshField, I, dim)
-    h  = meshsize(ϕ, dim)
+    h = meshsize(ϕ, dim)
     Im = _decrement_index(I, dim)
     return (ϕ[I] - ϕ[Im]) / h
 end
@@ -57,9 +57,9 @@ end
 
 function weno5⁻(ϕ::CartesianMeshField, I, dim)
     # see section 3.4 of Osher-Fedwik
-    Im  = _decrement_index(I, dim)
+    Im = _decrement_index(I, dim)
     Imm = _decrement_index(Im, dim)
-    Ip  = _increment_index(I, dim)
+    Ip = _increment_index(I, dim)
     Ipp = _increment_index(Ip, dim)
     # finite differences
     v1 = D⁻(ϕ, Imm, dim)
@@ -76,7 +76,7 @@ function weno5⁻(ϕ::CartesianMeshField, I, dim)
     S2 = (13 / 12) * (v2 - 2 * v3 + v4)^2 + (1 / 4) * (v2 - v4)^2
     S3 = (13 / 12) * (v3 - 2 * v4 + v5)^2 + (1 / 4) * (3 * v3 - 4 * v4 + v5)^2
     # fudge factor
-    ϵ = 1e-6 * max(v1^2, v2^2, v3^2, v4^2, v5^2) + 1e-99
+    ϵ = 1.0e-6 * max(v1^2, v2^2, v3^2, v4^2, v5^2) + 1.0e-99
     # weights
     α1 = 0.1 / (S1 + ϵ)^2
     α2 = 0.6 / (S2 + ϵ)^2
@@ -90,9 +90,9 @@ end
 
 function weno5⁺(ϕ::CartesianMeshField, I, dim)
     # see section 3.4 of Osher-Fedwik
-    Im  = _decrement_index(I, dim)
+    Im = _decrement_index(I, dim)
     Imm = _decrement_index(Im, dim)
-    Ip  = _increment_index(I, dim)
+    Ip = _increment_index(I, dim)
     Ipp = _increment_index(Ip, dim)
     # finite differences
     v1 = D⁺(ϕ, Ipp, dim)
@@ -109,7 +109,7 @@ function weno5⁺(ϕ::CartesianMeshField, I, dim)
     S2 = (13 / 12) * (v2 - 2 * v3 + v4)^2 + (1 / 4) * (v2 - v4)^2
     S3 = (13 / 12) * (v3 - 2 * v4 + v5)^2 + (1 / 4) * (3 * v3 - 4 * v4 + v5)^2
     # fudge factor
-    ϵ = 1e-6 * max(v1^2, v2^2, v3^2, v4^2, v5^2) + 1e-99
+    ϵ = 1.0e-6 * max(v1^2, v2^2, v3^2, v4^2, v5^2) + 1.0e-99
     # weights
     α1 = 0.1 / (S1 + ϵ)^2
     α2 = 0.6 / (S2 + ϵ)^2
@@ -128,7 +128,7 @@ Centered finite difference scheme for second order derivative at grid point `I`
 along dimension `dim`. E.g. if `dim=1`, this approximates `∂ₓₓ`.
 """
 function D2⁰(ϕ::CartesianMeshField, I, dim)
-    h  = meshsize(ϕ, dim)
+    h = meshsize(ϕ, dim)
     Im = _decrement_index(I, dim)
     Ip = _increment_index(I, dim)
     return (ϕ[Ip] - 2ϕ[I] + ϕ[Im]) / h^2
@@ -143,7 +143,7 @@ along the dimensions `dims`.
 If `dims[1] == dims[2]`, it is more efficient to call `D2⁰(ϕ,I,dims[1])`.
 """
 function D2(ϕ, I, dims)
-    h  = meshsize(ϕ)
+    h = meshsize(ϕ)
     Ip = _increment_index(I, dims[1])
     Im = _decrement_index(I, dims[1])
     return (D⁰(ϕ, Ip, dims[2]) - D⁰(ϕ, Im, dims[2])) / (2 * h[dims[1]])
@@ -156,8 +156,8 @@ Upward finite difference scheme for second order derivative at grid point `I`
 along dimension `dim`. E.g. if `dim=1`, this approximates `∂ₓₓ`.
 """
 function D2⁺⁺(ϕ::CartesianMeshField, I, dim)
-    h   = meshsize(ϕ, dim)
-    Ip  = _increment_index(I, dim, 1)
+    h = meshsize(ϕ, dim)
+    Ip = _increment_index(I, dim, 1)
     Ipp = _increment_index(I, dim, 2)
     return (ϕ[I] - 2ϕ[Ip] + ϕ[Ipp]) / h^2
 end
@@ -169,8 +169,8 @@ Backward finite difference scheme for second order derivative at grid point `I`
 along dimension `dim`. E.g. if `dim=1`, this approximates `∂ₓₓ`.
 """
 function D2⁻⁻(ϕ::CartesianMeshField, I, dim)
-    h   = meshsize(ϕ, dim)
-    Im  = _decrement_index(I, dim, 1)
+    h = meshsize(ϕ, dim)
+    Im = _decrement_index(I, dim, 1)
     Imm = _decrement_index(I, dim, 2)
     return (ϕ[Imm] - 2ϕ[Im] + ϕ[I]) / h^2
 end

src/levelset.jl

@@ -3,7 +3,7 @@
 
 Alias for [`MeshField`](@ref) with `vals` as an `AbstractArray` of `Real`s.
 """
-const LevelSet{V<:AbstractArray{<:Real},M,B} = MeshField{V,M,B}
+const LevelSet{V <: AbstractArray{<:Real}, M, B} = MeshField{V, M, B}
 
 function LevelSet(f::Function, m)
     vals = map(f, m)
@@ -113,24 +113,24 @@ https://en.wikipedia.org/wiki/Mean_curvature#Implicit_form_of_mean_curvature
 function curvature(ϕ::LevelSet, I)
     N = dimension(ϕ)
     if N == 2
-        ϕx  = D⁰(ϕ, I, 1)
-        ϕy  = D⁰(ϕ, I, 2)
+        ϕx = D⁰(ϕ, I, 1)
+        ϕy = D⁰(ϕ, I, 2)
         ϕxx = D2⁰(ϕ, I, 1)
         ϕyy = D2⁰(ϕ, I, 2)
         ϕxy = D2(ϕ, I, (2, 1))
-        κ   = (ϕxx * (ϕy)^2 - 2 * ϕy * ϕx * ϕxy + ϕyy * ϕx^2) / (ϕx^2 + ϕy^2)^(3 / 2)
+        κ = (ϕxx * (ϕy)^2 - 2 * ϕy * ϕx * ϕxy + ϕyy * ϕx^2) / (ϕx^2 + ϕy^2)^(3 / 2)
         return κ
     elseif N == 3
-        ϕx  = D⁰(ϕ, I, 1)
-        ϕy  = D⁰(ϕ, I, 2)
-        ϕz  = D⁰(ϕ, I, 3)
+        ϕx = D⁰(ϕ, I, 1)
+        ϕy = D⁰(ϕ, I, 2)
+        ϕz = D⁰(ϕ, I, 3)
         ϕxx = D2⁰(ϕ, I, 1)
         ϕyy = D2⁰(ϕ, I, 2)
         ϕzz = D2⁰(ϕ, I, 3)
         ϕxy = D2(ϕ, I, (2, 1))
         ϕxz = D2(ϕ, I, (3, 1))
         ϕyz = D2(ϕ, I, (3, 2))
-        κ   = (ϕxx * ϕy^2 + ϕyy * ϕx^2 + ϕxx * ϕz^2 + ϕzz * ϕx^2 + ϕyy * ϕz^2 + ϕzz  * ϕy^2 - 2 * ϕx * ϕz * ϕxz - 2 * ϕy * ϕz * ϕyz  - 2 * ϕy * ϕx * ϕxy) / (ϕx^2 + ϕy^2 + ϕz^2)^(3 / 2)
+        κ = (ϕxx * ϕy^2 + ϕyy * ϕx^2 + ϕxx * ϕz^2 + ϕzz * ϕx^2 + ϕyy * ϕz^2 + ϕzz * ϕy^2 - 2 * ϕx * ϕz * ϕxz - 2 * ϕy * ϕz * ϕyz - 2 * ϕy * ϕx * ϕxy) / (ϕx^2 + ϕy^2 + ϕz^2)^(3 / 2)
         return κ
     else
         # generic method

src/levelsetequation.jl

@@ -138,8 +138,8 @@ function integrate!(ls::LevelSetEquation, tf, Δt = Inf)
            the level-set equation cannot be solved back in time"
     @assert tf >= tc msg
     # append boundary conditions for integration
-    ϕ         = current_state(ls)
-    buf        = buffers(ls)
+    ϕ = current_state(ls)
+    buf = buffers(ls)
     integrator = time_integrator(ls)
     # dynamic dispatch. Should not be a problem provided enough computation is
     # done inside of the function below
@@ -229,7 +229,7 @@ function _integrate!(ϕ::LevelSet, buffers, integrator::RK3, terms, tc, tf, Δt)
 end
 
 function _compute_terms(terms, ϕ, I, t)
-    sum(terms) do term
+    return sum(terms) do term
         return _compute_term(term, ϕ, I, t)
     end
 end