Merge pull request #208 from ArnoStrouwen/master

SciML style formatting

Author: ChrisRackauckas

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style = "sciml"

.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

@@ -2,17 +2,14 @@ using Documenter, SparseDiffTools
 
 include("pages.jl")
 
-makedocs(
-    sitename = "SparseDiffTools.jl",
-    authors = "Chris Rackauckas",
-    modules = [SparseDiffTools],
-    clean = true,
-    doctest = false,
-    format = Documenter.HTML(
-        assets = ["assets/favicon.ico"],
-        canonical = "https://docs.sciml.ai/SparseDiffTools/stable/",
-    ),
-    pages = pages,
-)
+makedocs(sitename = "SparseDiffTools.jl",
+         authors = "Chris Rackauckas",
+         modules = [SparseDiffTools],
+         clean = true,
+         doctest = false,
+         format = Documenter.HTML(assets = ["assets/favicon.ico"],
+                                  canonical = "https://docs.sciml.ai/SparseDiffTools/stable/"),
+         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

@@ -19,31 +19,30 @@ 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")
 include("coloring/backtracking_coloring.jl")
@@ -63,8 +62,9 @@ parameterless_type(x) = parameterless_type(typeof(x))
 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!
+    @require Zygote="e88e6eb3-aa80-5325-afca-941959d7151f" begin
+        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 +30,8 @@ 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 +42,7 @@ 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 +51,7 @@ 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
@@ -60,7 +61,6 @@ function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
     return color
 end
 
-
 """
         prevent_cycle!(first_visit_to_tree::AbstractVector{<:Tuple{Integer,Integer}},
                         forbidden_colors::AbstractVector{<:Integer},
@@ -76,7 +76,7 @@ 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}},
+function prevent_cycle!(first_visit_to_tree::AbstractVector{<:Tuple{Integer, Integer}},
                         forbidden_colors::AbstractVector{<:Integer},
                         v::Integer,
                         w::Integer,
@@ -88,13 +88,12 @@ function prevent_cycle!(first_visit_to_tree::AbstractVector{<:Tuple{Integer,Inte
     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
 end
 
-
 """
         grow_star!(two_colored_forest::DisjointSets{<:Integer},
                     first_neighbor::AbstractVector{<: Tuple{Integer,Integer}},
@@ -109,24 +108,23 @@ 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}},
+                    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)
+    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
 
-
 """
         merge_trees!(two_colored_forest::DisjointSets{<:Integer},
                       v::Integer,
@@ -142,14 +140,13 @@ function merge_trees!(two_colored_forest::DisjointSets{<:Integer},
                       w::Integer,
                       x::Integer,
                       g::Graphs.AbstractGraph)
-    e1 = find(v,w,g,two_colored_forest)
-    e2 = find(w,x,g,two_colored_forest)
+    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
 end
 
-
 """
         insert_new_tree!(two_colored_forest::DisjointSets{<:Integer},
                           v::Integer,
@@ -163,11 +160,10 @@ 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)
+    edge_index = find_edge_index(v, w, g)
+    push!(two_colored_forest, edge_index)
 end
 
-
 """
         min_index(forbidden_colors::AbstractVector{<:Integer}, v::Integer)
 
@@ -177,7 +173,6 @@ function min_index(forbidden_colors::AbstractVector{<:Integer}, v::Integer)
     return findfirst(!isequal(v), forbidden_colors)
 end
 
-
 """
         find(w::Integer,
              x::Integer,
@@ -195,7 +190,6 @@ function find(w::Integer,
     return find_root!(two_colored_forest, edge_index)
 end
 
-
 """
         find_edge(g::Graphs.AbstractGraph, v::Integer, w::Integer)
 
@@ -205,7 +199,6 @@ v and w in the graph g
 function find_edge_index(v::Integer, w::Integer, g::Graphs.AbstractGraph)
     pos = 1
     for i in edges(g)
-
         if (src(i) == v && dst(i) == w) || (src(i) == w && dst(i) == v)
             return pos
         end