Format code

benchmark/benchmarks.jl

@@ -21,13 +21,15 @@ for structure in [:nonsymmetric, :symmetric],
 
     problem = ColoringProblem(; structure, partition)
     algo = GreedyColoringAlgorithm(
-        RandomOrder(StableRNG(0), 0); decompression, postprocessing=true
+        RandomOrder(StableRNG(0), 0);
+        decompression,
+        postprocessing = true,
     )
 
     # use several random matrices to reduce variance
     nb_samples = 5
-    As = [sparse(Symmetric(sprand(StableRNG(i), Bool, n, n, p))) for i in 1:nb_samples]
-    results = [coloring(A, problem, algo; decompression_eltype=Float64) for A in As]
+    As = [sparse(Symmetric(sprand(StableRNG(i), Bool, n, n, p))) for i = 1:nb_samples]
+    results = [coloring(A, problem, algo; decompression_eltype = Float64) for A in As]
     Bs = [compress(Float64.(A), result) for (A, result) in zip(As, results)]
 
     bench_col = @benchmarkable begin
@@ -57,7 +59,7 @@ for structure in [:nonsymmetric, :symmetric],
     p in [2 / n, 5 / n, 10 / n]
 
     nb_samples = 5
-    As = [sparse(Symmetric(sprand(StableRNG(i), Bool, n, n, p))) for i in 1:nb_samples]
+    As = [sparse(Symmetric(sprand(StableRNG(i), Bool, n, n, p))) for i = 1:nb_samples]
     if structure == :symmetric
         gs = [SMC.AdjacencyGraph(A) for A in As]
         bench_ord = @benchmarkable begin

docs/make.jl

@@ -4,24 +4,28 @@ using SparseMatrixColorings
 
 links = InterLinks("ADTypes" => "https://sciml.github.io/ADTypes.jl/stable/")
 
-cp(joinpath(@__DIR__, "..", "README.md"), joinpath(@__DIR__, "src", "index.md"); force=true)
+cp(
+    joinpath(@__DIR__, "..", "README.md"),
+    joinpath(@__DIR__, "src", "index.md");
+    force = true,
+)
 
 makedocs(;
-    modules=[SparseMatrixColorings],
-    authors="Guillaume Dalle and Alexis Montoison",
-    sitename="SparseMatrixColorings.jl",
-    format=Documenter.HTML(),
-    pages=[
+    modules = [SparseMatrixColorings],
+    authors = "Guillaume Dalle and Alexis Montoison",
+    sitename = "SparseMatrixColorings.jl",
+    format = Documenter.HTML(),
+    pages = [
         "Home" => "index.md",
         "tutorial.md",
         "api.md",
         "Developer Documentation" => ["dev.md", "vis.md"],
     ],
-    plugins=[links],
+    plugins = [links],
 )
 
 deploydocs(;
-    repo="github.com/JuliaDiff/SparseMatrixColorings.jl",
-    push_preview=true,
-    devbranch="main",
+    repo = "github.com/JuliaDiff/SparseMatrixColorings.jl",
+    push_preview = true,
+    devbranch = "main",
 )

ext/SparseMatrixColoringsCUDAExt.jl

@@ -8,22 +8,31 @@ using cuSPARSE: AbstractCuSparseMatrix, CuSparseMatrixCSC, CuSparseMatrixCSR
 ## CSC Result
 
 function SMC.ColumnColoringResult(
-    A::CuSparseMatrixCSC, bg::SMC.BipartiteGraph{T}, color::Vector{<:Integer}
+    A::CuSparseMatrixCSC,
+    bg::SMC.BipartiteGraph{T},
+    color::Vector{<:Integer},
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.column_csc_indices(bg, color)
-    additional_info = (; compressed_indices_gpu_csc=CuVector(compressed_indices))
+    additional_info = (; compressed_indices_gpu_csc = CuVector(compressed_indices))
     return SMC.ColumnColoringResult(
-        A, bg, color, group, compressed_indices, additional_info
+        A,
+        bg,
+        color,
+        group,
+        compressed_indices,
+        additional_info,
     )
 end
 
 function SMC.RowColoringResult(
-    A::CuSparseMatrixCSC, bg::SMC.BipartiteGraph{T}, color::Vector{<:Integer}
+    A::CuSparseMatrixCSC,
+    bg::SMC.BipartiteGraph{T},
+    color::Vector{<:Integer},
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.row_csc_indices(bg, color)
-    additional_info = (; compressed_indices_gpu_csc=CuVector(compressed_indices))
+    additional_info = (; compressed_indices_gpu_csc = CuVector(compressed_indices))
     return SMC.RowColoringResult(A, bg, color, group, compressed_indices, additional_info)
 end
 
@@ -35,33 +44,47 @@ function SMC.StarSetColoringResult(
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.star_csc_indices(ag, color, star_set)
-    additional_info = (; compressed_indices_gpu_csc=CuVector(compressed_indices))
+    additional_info = (; compressed_indices_gpu_csc = CuVector(compressed_indices))
     return SMC.StarSetColoringResult(
-        A, ag, color, group, compressed_indices, additional_info
+        A,
+        ag,
+        color,
+        group,
+        compressed_indices,
+        additional_info,
     )
 end
 
 ## CSR Result
 
 function SMC.ColumnColoringResult(
-    A::CuSparseMatrixCSR, bg::SMC.BipartiteGraph{T}, color::Vector{<:Integer}
+    A::CuSparseMatrixCSR,
+    bg::SMC.BipartiteGraph{T},
+    color::Vector{<:Integer},
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.column_csc_indices(bg, color)
     compressed_indices_csr = SMC.column_csr_indices(bg, color)
-    additional_info = (; compressed_indices_gpu_csr=CuVector(compressed_indices_csr))
+    additional_info = (; compressed_indices_gpu_csr = CuVector(compressed_indices_csr))
     return SMC.ColumnColoringResult(
-        A, bg, color, group, compressed_indices, additional_info
+        A,
+        bg,
+        color,
+        group,
+        compressed_indices,
+        additional_info,
     )
 end
 
 function SMC.RowColoringResult(
-    A::CuSparseMatrixCSR, bg::SMC.BipartiteGraph{T}, color::Vector{<:Integer}
+    A::CuSparseMatrixCSR,
+    bg::SMC.BipartiteGraph{T},
+    color::Vector{<:Integer},
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.row_csc_indices(bg, color)
     compressed_indices_csr = SMC.row_csr_indices(bg, color)
-    additional_info = (; compressed_indices_gpu_csr=CuVector(compressed_indices_csr))
+    additional_info = (; compressed_indices_gpu_csr = CuVector(compressed_indices_csr))
     return SMC.RowColoringResult(A, bg, color, group, compressed_indices, additional_info)
 end
 
@@ -73,9 +96,14 @@ function SMC.StarSetColoringResult(
 ) where {T<:Integer}
     group = SMC.group_by_color(T, color)
     compressed_indices = SMC.star_csc_indices(ag, color, star_set)
-    additional_info = (; compressed_indices_gpu_csr=CuVector(compressed_indices))
+    additional_info = (; compressed_indices_gpu_csr = CuVector(compressed_indices))
     return SMC.StarSetColoringResult(
-        A, ag, color, group, compressed_indices, additional_info
+        A,
+        ag,
+        color,
+        group,
+        compressed_indices,
+        additional_info,
     )
 end
 
@@ -84,15 +112,19 @@ end
 for R in (:ColumnColoringResult, :RowColoringResult)
     # loop to avoid method ambiguity
     @eval function SMC.decompress!(
-        A::CuSparseMatrixCSC, B::CuMatrix, result::SMC.$R{<:CuSparseMatrixCSC}
+        A::CuSparseMatrixCSC,
+        B::CuMatrix,
+        result::SMC.$R{<:CuSparseMatrixCSC},
     )
         compressed_indices = result.additional_info.compressed_indices_gpu_csc
         copyto!(A.nzVal, view(B, compressed_indices))
         return A
     end
 
     @eval function SMC.decompress!(
-        A::CuSparseMatrixCSR, B::CuMatrix, result::SMC.$R{<:CuSparseMatrixCSR}
+        A::CuSparseMatrixCSR,
+        B::CuMatrix,
+        result::SMC.$R{<:CuSparseMatrixCSR},
     )
         compressed_indices = result.additional_info.compressed_indices_gpu_csr
         copyto!(A.nzVal, view(B, compressed_indices))
@@ -104,12 +136,12 @@ function SMC.decompress!(
     A::CuSparseMatrixCSC,
     B::CuMatrix,
     result::SMC.StarSetColoringResult{<:CuSparseMatrixCSC},
-    uplo::Symbol=:F,
+    uplo::Symbol = :F,
 )
     if uplo != :F
         throw(
             SMC.UnsupportedDecompressionError(
-                "Single-triangle decompression is not supported on GPU matrices"
+                "Single-triangle decompression is not supported on GPU matrices",
             ),
         )
     end
@@ -122,12 +154,12 @@ function SMC.decompress!(
     A::CuSparseMatrixCSR,
     B::CuMatrix,
     result::SMC.StarSetColoringResult{<:CuSparseMatrixCSR},
-    uplo::Symbol=:F,
+    uplo::Symbol = :F,
 )
     if uplo != :F
         throw(
             SMC.UnsupportedDecompressionError(
-                "Single-triangle decompression is not supported on GPU matrices"
+                "Single-triangle decompression is not supported on GPU matrices",
             ),
         )
     end

ext/SparseMatrixColoringsCliqueTreesExt.jl

@@ -15,7 +15,7 @@ function vertices(g::AdjacencyGraph{T}, order::PerfectEliminationOrder) where {T
 
     # construct a perfect elimination order
     # self-loops are ignored
-    order, _ = permutation(M; alg=order.elimination_algorithm)
+    order, _ = permutation(M; alg = order.elimination_algorithm)
 
     return reverse!(order)
 end

ext/SparseMatrixColoringsColorsExt.jl

@@ -37,13 +37,13 @@ const DEFAULT_PAD = 0
 
 function SparseMatrixColorings.show_colors(
     res::AbstractColoringResult;
-    colorscheme=nothing,
-    background_color::Colorant=DEFAULT_BACKGROUND_COLOR, # color used for zero matrix entries and pad
-    border_color::Colorant=DEFAULT_BORDER_COLOR, # color used for zero matrix entries and pad
-    scale::Int=DEFAULT_SCALE, # scale size of matrix entries to `scale × scale` pixels
-    border::Int=DEFAULT_BORDER,  # border around matrix entries
-    pad::Int=DEFAULT_PAD, # pad between matrix entries
-    warn::Bool=true,
+    colorscheme = nothing,
+    background_color::Colorant = DEFAULT_BACKGROUND_COLOR, # color used for zero matrix entries and pad
+    border_color::Colorant = DEFAULT_BORDER_COLOR, # color used for zero matrix entries and pad
+    scale::Int = DEFAULT_SCALE, # scale size of matrix entries to `scale × scale` pixels
+    border::Int = DEFAULT_BORDER,  # border around matrix entries
+    pad::Int = DEFAULT_PAD, # pad between matrix entries
+    warn::Bool = true,
 )
     scale < 1 && throw(ArgumentError("`scale` has to be ≥ 1."))
     border < 0 && throw(ArgumentError("`border` has to be ≥ 0."))
@@ -53,15 +53,14 @@ function SparseMatrixColorings.show_colors(
         if warn && ncolors(res) > length(colorscheme)
             @warn "`show_colors` will reuse colors since the provided `colorscheme` has $(length(colorscheme)) colors and the matrix needs $(ncolors(res)). You can turn off this warning via the keyword argument `warn = false`, or choose a larger `colorscheme` from ColorSchemes.jl."
         end
-        colorscheme, background_color, border_color = promote_colors(
-            colorscheme, background_color, border_color
-        )
+        colorscheme, background_color, border_color =
+            promote_colors(colorscheme, background_color, border_color)
     else
         # Sample n distinguishable colors, excluding the background and border color
         colorscheme = distinguishable_colors(
             ncolors(res),
             [convert(RGB, background_color), convert(RGB, border_color)];
-            dropseed=true,
+            dropseed = true,
         )
     end
     outs = allocate_outputs(res, background_color, border_color, scale, border, pad)
@@ -86,7 +85,7 @@ function matrix_entry_area(I::CartesianIndex, scale, border, pad)
 end
 
 function matrix_entry_plus_border_area(I::CartesianIndex, scale, border, pad)
-    stencil = CartesianIndices((1:(scale + 2border), 1:(scale + 2border)))
+    stencil = CartesianIndices((1:(scale+2border), 1:(scale+2border)))
     return CartesianIndex(1, 1) * pad +
            (I - CartesianIndex(1, 1)) * (scale + 2border + pad) .+ stencil
 end
@@ -272,7 +271,7 @@ function show_colors!(
     A_rcolor_indices = mod1.(row_shift .+ row_colors(res), length(colorscheme))
     B_ccolor_indices = mod1.(1:maximum(column_colors(res)), length(colorscheme))
     B_rcolor_indices =
-        mod1.((row_shift + 1):(row_shift + maximum(row_colors(res))), length(colorscheme))
+        mod1.((row_shift+1):(row_shift+maximum(row_colors(res))), length(colorscheme))
     A_ccolors = colorscheme[A_ccolor_indices]
     A_rcolors = colorscheme[A_rcolor_indices]
     B_ccolors = colorscheme[B_ccolor_indices]

ext/SparseMatrixColoringsGPUArraysExt.jl

@@ -9,7 +9,8 @@ SMC.matrix_versions(A::AbstractGPUSparseMatrix) = (A,)
 ## Compression (slow, through CPU)
 
 function SMC.compress(
-    A::AbstractGPUSparseMatrix, result::SMC.AbstractColoringResult{structure,:column}
+    A::AbstractGPUSparseMatrix,
+    result::SMC.AbstractColoringResult{structure,:column},
 ) where {structure}
     A_cpu = SparseMatrixCSC(A)
     B_cpu = SMC.compress(A_cpu, result)
@@ -18,7 +19,8 @@ function SMC.compress(
 end
 
 function SMC.compress(
-    A::AbstractGPUSparseMatrix, result::SMC.AbstractColoringResult{structure,:row}
+    A::AbstractGPUSparseMatrix,
+    result::SMC.AbstractColoringResult{structure,:row},
 ) where {structure}
     A_cpu = SparseMatrixCSC(A)
     B_cpu = SMC.compress(A_cpu, result)

ext/SparseMatrixColoringsJuMPExt.jl

@@ -21,8 +21,8 @@ function optimal_distance2_coloring(
     bg::BipartiteGraph,
     ::Val{side},
     optimizer::O;
-    silent::Bool=true,
-    assert_solved::Bool=true,
+    silent::Bool = true,
+    assert_solved::Bool = true,
 ) where {side,O}
     other_side = 3 - side
     n = nb_vertices(bg, Val(side))
@@ -66,14 +66,22 @@ end
 function ADTypes.column_coloring(A::AbstractMatrix, algo::OptimalColoringAlgorithm)
     bg = BipartiteGraph(A)
     return optimal_distance2_coloring(
-        bg, Val(2), algo.optimizer; algo.silent, algo.assert_solved
+        bg,
+        Val(2),
+        algo.optimizer;
+        algo.silent,
+        algo.assert_solved,
     )
 end
 
 function ADTypes.row_coloring(A::AbstractMatrix, algo::OptimalColoringAlgorithm)
     bg = BipartiteGraph(A)
     return optimal_distance2_coloring(
-        bg, Val(1), algo.optimizer; algo.silent, algo.assert_solved
+        bg,
+        Val(1),
+        algo.optimizer;
+        algo.silent,
+        algo.assert_solved,
     )
 end
 

src/adtypes.jl

@@ -4,8 +4,8 @@ function coloring(
     A::AbstractMatrix,
     problem::ColoringProblem{structure,partition},
     algo::ADTypes.AbstractColoringAlgorithm;
-    decompression_eltype::Type{R}=Float64,
-    symmetric_pattern::Bool=false,
+    decompression_eltype::Type{R} = Float64,
+    symmetric_pattern::Bool = false,
 ) where {structure,partition,R}
     symmetric_pattern = symmetric_pattern || A isa Union{Symmetric,Hermitian}
     if structure == :nonsymmetric