SciML style formatting

Author: ArnoStrouwen

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

docs/make.jl

@@ -15,4 +15,7 @@ makedocs(
     pages = pages,
 )
 
-deploydocs(repo = "https://github.com/JuliaDiff/SparseDiffTools.jl.git"; push_preview = true)
+deploydocs(
+    repo = "https://github.com/JuliaDiff/SparseDiffTools.jl.git";
+    push_preview = true,
+)

src/SparseDiffTools.jl

@@ -19,30 +19,40 @@ using DataStructures: DisjointSets, find_root!, union!
 
 using ArrayInterfaceCore: matrix_colors
 
-export  contract_color,
-        greedy_d1,
-        greedy_star1_coloring,
-        greedy_star2_coloring,
-        matrix2graph,
-        matrix_colors,
-        forwarddiff_color_jacobian!,
-        forwarddiff_color_jacobian,
-        ForwardColorJacCache,
-        numauto_color_hessian!,
-        numauto_color_hessian,
-        autoauto_color_hessian!,
-        autoauto_color_hessian,
-        ForwardColorHesCache,
-        ForwardAutoColorHesCache,
-        auto_jacvec,auto_jacvec!,
-        num_jacvec,num_jacvec!,
-        num_vecjac,num_vecjac!,
-        num_hesvec,num_hesvec!,
-        numauto_hesvec,numauto_hesvec!,
-        autonum_hesvec,autonum_hesvec!,
-        num_hesvecgrad,num_hesvecgrad!,
-        auto_hesvecgrad,auto_hesvecgrad!,
-        JacVec,HesVec,HesVecGrad
+export contract_color,
+    greedy_d1,
+    greedy_star1_coloring,
+    greedy_star2_coloring,
+    matrix2graph,
+    matrix_colors,
+    forwarddiff_color_jacobian!,
+    forwarddiff_color_jacobian,
+    ForwardColorJacCache,
+    numauto_color_hessian!,
+    numauto_color_hessian,
+    autoauto_color_hessian!,
+    autoauto_color_hessian,
+    ForwardColorHesCache,
+    ForwardAutoColorHesCache,
+    auto_jacvec,
+    auto_jacvec!,
+    num_jacvec,
+    num_jacvec!,
+    num_vecjac,
+    num_vecjac!,
+    num_hesvec,
+    num_hesvec!,
+    numauto_hesvec,
+    numauto_hesvec!,
+    autonum_hesvec,
+    autonum_hesvec!,
+    num_hesvecgrad,
+    num_hesvecgrad!,
+    auto_hesvecgrad,
+    auto_hesvecgrad!,
+    JacVec,
+    HesVec,
+    HesVecGrad
 
 
 include("coloring/high_level.jl")
@@ -64,7 +74,8 @@ parameterless_type(x::Type) = __parameterless_type(x)
 
 function __init__()
     @require Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" begin
-        export numback_hesvec, numback_hesvec!, autoback_hesvec, autoback_hesvec!, auto_vecjac, auto_vecjac!
+        export numback_hesvec,
+            numback_hesvec!, autoback_hesvec, autoback_hesvec!, auto_vecjac, auto_vecjac!
 
         include("differentiation/vecjac_products_zygote.jl")
         include("differentiation/jaches_products_zygote.jl")

src/coloring/acyclic_coloring.jl

@@ -13,8 +13,8 @@ function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
     color = zeros(Int, nv(g))
     two_colored_forest = DisjointSets{Int}(())
 
-    first_visit_to_tree = fill((0,0), ne(g))
-    first_neighbor = fill((0,0), ne(g))
+    first_visit_to_tree = fill((0, 0), ne(g))
+    first_neighbor = fill((0, 0), ne(g))
 
     forbidden_colors = zeros(Int, nv(g))
 
@@ -30,7 +30,16 @@ function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
                 for x in outneighbors(g, w)
                     if color[x] != 0
                         if forbidden_colors[color[x]] != v
-                            prevent_cycle!(first_visit_to_tree,forbidden_colors,v, w, x, g, two_colored_forest,color)
+                            prevent_cycle!(
+                                first_visit_to_tree,
+                                forbidden_colors,
+                                v,
+                                w,
+                                x,
+                                g,
+                                two_colored_forest,
+                                color,
+                            )
                         end
                     end
                 end
@@ -41,7 +50,7 @@ function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
 
         for w in outneighbors(g, v)
             if color[w] != 0
-                grow_star!(two_colored_forest,first_neighbor,v, w, g, color)
+                grow_star!(two_colored_forest, first_neighbor, v, w, g, color)
             end
         end
 
@@ -50,7 +59,7 @@ function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
                 for x in outneighbors(g, w)
                     if color[x] != 0 && x != v
                         if color[x] == color[v]
-                            merge_trees!(two_colored_forest,v,w,x,g)
+                            merge_trees!(two_colored_forest, v, w, x, g)
                         end
                     end
                 end
@@ -76,19 +85,21 @@ which is adjacent to vertices w and x in graph g. Disjoint set is used to store
 the induced 2-colored subgraphs/trees where the id of set is an integer
 representing an edge of graph 'g'
 """
-function prevent_cycle!(first_visit_to_tree::AbstractVector{<:Tuple{Integer,Integer}},
-                        forbidden_colors::AbstractVector{<:Integer},
-                        v::Integer,
-                        w::Integer,
-                        x::Integer,
-                        g::Graphs.AbstractGraph,
-                        two_colored_forest::DisjointSets{<:Integer},
-                        color::AbstractVector{<:Integer})
+function prevent_cycle!(
+    first_visit_to_tree::AbstractVector{<:Tuple{Integer,Integer}},
+    forbidden_colors::AbstractVector{<:Integer},
+    v::Integer,
+    w::Integer,
+    x::Integer,
+    g::Graphs.AbstractGraph,
+    two_colored_forest::DisjointSets{<:Integer},
+    color::AbstractVector{<:Integer},
+)
     e = find(w, x, g, two_colored_forest)
     p, q = first_visit_to_tree[e]
 
     if p != v
-        first_visit_to_tree[e] = (v,w)
+        first_visit_to_tree[e] = (v, w)
     elseif q != w
         forbidden_colors[color[x]] = v
     end
@@ -108,20 +119,22 @@ previously uncolored vertex v, by comparing it with the adjacent vertex w.
 Disjoint set is used to store stars in sets, which are identified through key
 edges present in g.
 """
-function grow_star!(two_colored_forest::DisjointSets{<:Integer},
-                    first_neighbor::AbstractVector{<: Tuple{Integer,Integer}},
-                    v::Integer,
-                    w::Integer,
-                    g::Graphs.AbstractGraph,
-                    color::AbstractVector{<:Integer})
-    insert_new_tree!(two_colored_forest,v,w,g)
+function grow_star!(
+    two_colored_forest::DisjointSets{<:Integer},
+    first_neighbor::AbstractVector{<:Tuple{Integer,Integer}},
+    v::Integer,
+    w::Integer,
+    g::Graphs.AbstractGraph,
+    color::AbstractVector{<:Integer},
+)
+    insert_new_tree!(two_colored_forest, v, w, g)
     p, q = first_neighbor[color[w]]
 
     if p != v
-        first_neighbor[color[w]] = (v,w)
+        first_neighbor[color[w]] = (v, w)
     else
-        e1 = find(v,w,g,two_colored_forest)
-        e2 = find(p,q,g,two_colored_forest)
+        e1 = find(v, w, g, two_colored_forest)
+        e2 = find(p, q, g, two_colored_forest)
         union!(two_colored_forest, e1, e2)
     end
 end
@@ -137,13 +150,15 @@ end
 Subroutine to merge trees present in the disjoint set which have a
 common edge.
 """
-function merge_trees!(two_colored_forest::DisjointSets{<:Integer},
-                      v::Integer,
-                      w::Integer,
-                      x::Integer,
-                      g::Graphs.AbstractGraph)
-    e1 = find(v,w,g,two_colored_forest)
-    e2 = find(w,x,g,two_colored_forest)
+function merge_trees!(
+    two_colored_forest::DisjointSets{<:Integer},
+    v::Integer,
+    w::Integer,
+    x::Integer,
+    g::Graphs.AbstractGraph,
+)
+    e1 = find(v, w, g, two_colored_forest)
+    e2 = find(w, x, g, two_colored_forest)
     if e1 != e2
         union!(two_colored_forest, e1, e2)
     end
@@ -159,12 +174,14 @@ end
 creates a new singleton set in the disjoint set 'two_colored_forest' consisting
 of the edge connecting v and w in the graph g
 """
-function insert_new_tree!(two_colored_forest::DisjointSets{<:Integer},
-                          v::Integer,
-                          w::Integer,
-                          g::Graphs.AbstractGraph)
-    edge_index = find_edge_index(v,w,g)
-    push!(two_colored_forest,edge_index)
+function insert_new_tree!(
+    two_colored_forest::DisjointSets{<:Integer},
+    v::Integer,
+    w::Integer,
+    g::Graphs.AbstractGraph,
+)
+    edge_index = find_edge_index(v, w, g)
+    push!(two_colored_forest, edge_index)
 end
 
 
@@ -187,10 +204,12 @@ end
 Returns the root of the disjoint set to which the edge connecting vertices w and x
 in the graph g belongs to
 """
-function find(w::Integer,
-              x::Integer,
-              g::Graphs.AbstractGraph,
-              two_colored_forest::DisjointSets{<:Integer})
+function find(
+    w::Integer,
+    x::Integer,
+    g::Graphs.AbstractGraph,
+    two_colored_forest::DisjointSets{<:Integer},
+)
     edge_index = find_edge_index(w, x, g)
     return find_root!(two_colored_forest, edge_index)
 end