LightGraphs to Graphs

Project.toml

@@ -10,7 +10,7 @@ Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -24,10 +24,10 @@ Compat = "2.2, 3"
 DataStructures = "0.17, 0.18"
 FiniteDiff = "2.8.1"
 ForwardDiff = "0.10"
-LightGraphs = "1.3"
+Graphs = "1.4"
 Requires = "0.5, 1.0"
 StaticArrays = "1"
-VertexSafeGraphs = "0.1"
+VertexSafeGraphs = "0.2"
 julia = "1.6"
 
 [extras]

src/SparseDiffTools.jl

@@ -3,8 +3,8 @@ module SparseDiffTools
 using Compat
 using FiniteDiff
 using ForwardDiff
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 using Requires
 using VertexSafeGraphs
 using Adapt

src/coloring/acyclic_coloring.jl

@@ -1,5 +1,5 @@
 """
-        color_graph(g::LightGraphs.AbstractGraphs, ::AcyclicColoring)
+        color_graph(g::Graphs.AbstractGraphs, ::AcyclicColoring)
 
 Returns a coloring vector following the acyclic coloring rules (1) the coloring
 corresponds to a distance-1 coloring, and (2) vertices in every cycle of the
@@ -9,7 +9,7 @@ is a collection of trees—and hence is acyclic.
 
 Reference: Gebremedhin AH, Manne F, Pothen A. **New Acyclic and Star Coloring Algorithms with Application to Computing Hessians**
 """
-function color_graph(g::LightGraphs.AbstractGraph, ::AcyclicColoring)
+function color_graph(g::Graphs.AbstractGraph, ::AcyclicColoring)
     color = zeros(Int, nv(g))
     two_colored_forest = DisjointSets{Int}(())
 
@@ -67,7 +67,7 @@ end
                         v::Integer,
                         w::Integer,
                         x::Integer,
-                        g::LightGraphs.AbstractGraph,
+                        g::Graphs.AbstractGraph,
                         two_colored_forest::DisjointSets{<:Integer},
                         color::AbstractVector{<:Integer})
 
@@ -81,7 +81,7 @@ function prevent_cycle!(first_visit_to_tree::AbstractVector{<:Tuple{Integer,Inte
                         v::Integer,
                         w::Integer,
                         x::Integer,
-                        g::LightGraphs.AbstractGraph,
+                        g::Graphs.AbstractGraph,
                         two_colored_forest::DisjointSets{<:Integer},
                         color::AbstractVector{<:Integer})
     e = find(w, x, g, two_colored_forest)
@@ -100,7 +100,7 @@ end
                     first_neighbor::AbstractVector{<: Tuple{Integer,Integer}},
                     v::Integer,
                     w::Integer,
-                    g::LightGraphs.AbstractGraph,
+                    g::Graphs.AbstractGraph,
                     color::AbstractVector{<:Integer})
 
 Grow a 2-colored star after assigning a new color to the
@@ -112,7 +112,7 @@ function grow_star!(two_colored_forest::DisjointSets{<:Integer},
                     first_neighbor::AbstractVector{<: Tuple{Integer,Integer}},
                     v::Integer,
                     w::Integer,
-                    g::LightGraphs.AbstractGraph,
+                    g::Graphs.AbstractGraph,
                     color::AbstractVector{<:Integer})
     insert_new_tree!(two_colored_forest,v,w,g)
     p, q = first_neighbor[color[w]]
@@ -132,7 +132,7 @@ end
                       v::Integer,
                       w::Integer,
                       x::Integer,
-                      g::LightGraphs.AbstractGraph)
+                      g::Graphs.AbstractGraph)
 
 Subroutine to merge trees present in the disjoint set which have a
 common edge.
@@ -141,7 +141,7 @@ function merge_trees!(two_colored_forest::DisjointSets{<:Integer},
                       v::Integer,
                       w::Integer,
                       x::Integer,
-                      g::LightGraphs.AbstractGraph)
+                      g::Graphs.AbstractGraph)
     e1 = find(v,w,g,two_colored_forest)
     e2 = find(w,x,g,two_colored_forest)
     if e1 != e2
@@ -154,15 +154,15 @@ end
         insert_new_tree!(two_colored_forest::DisjointSets{<:Integer},
                           v::Integer,
                           w::Integer,
-                          g::LightGraphs.AbstractGraph)
+                          g::Graphs.AbstractGraph)
 
 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::LightGraphs.AbstractGraph)
+                          g::Graphs.AbstractGraph)
     edge_index = find_edge_index(v,w,g)
     push!(two_colored_forest,edge_index)
 end
@@ -181,28 +181,28 @@ end
 """
         find(w::Integer,
              x::Integer,
-             g::LightGraphs.AbstractGraph,
+             g::Graphs.AbstractGraph,
              two_colored_forest::DisjointSets{<:Integer})
 
 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::LightGraphs.AbstractGraph,
+              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
 
 
 """
-        find_edge(g::LightGraphs.AbstractGraph, v::Integer, w::Integer)
+        find_edge(g::Graphs.AbstractGraph, v::Integer, w::Integer)
 
 Returns an integer equivalent to the index of the edge connecting the vertices
 v and w in the graph g
 """
-function find_edge_index(v::Integer, w::Integer, g::LightGraphs.AbstractGraph)
+function find_edge_index(v::Integer, w::Integer, g::Graphs.AbstractGraph)
     pos = 1
     for i in edges(g)
 

src/coloring/backtracking_coloring.jl

@@ -1,11 +1,11 @@
 """
-    color_graph(g::LightGraphs.AbstractGraph, ::BacktrackingColor)
+    color_graph(g::Graphs.AbstractGraph, ::BacktrackingColor)
 
 Return a tight, distance-1 coloring of graph g
 using the minimum number of colors possible (i.e.
 the chromatic number of graph, `χ(g)`)
 """
-function color_graph(g::LightGraphs.AbstractGraph, ::BacktrackingColor)
+function color_graph(g::Graphs.AbstractGraph, ::BacktrackingColor)
     v = nv(g)
 
     #A is list of vertices in non-increasing order of degree
@@ -96,14 +96,14 @@ function color_graph(g::LightGraphs.AbstractGraph, ::BacktrackingColor)
 end
 
 """
-    sort_by_degree(g::LightGraphs.AbstractGraph)
+    sort_by_degree(g::Graphs.AbstractGraph)
 
 Returns a list of the vertices of graph g sorted
 in non-increasing order of their degrees
 """
-function sort_by_degree(g::LightGraphs.AbstractGraph)
+function sort_by_degree(g::Graphs.AbstractGraph)
     vs = vertices(g)
-    degrees = (LightGraphs.degree(g, v) for v in vs)
+    degrees = (Graphs.degree(g, v) for v in vs)
     vertex_pairs = collect(zip(vs, degrees))
     sort!(vertex_pairs, by = p -> p[2], rev = true)
     return [v[1] for v in vertex_pairs]
@@ -129,7 +129,7 @@ end
                 A::AbstractVector{<:Integer},
                 colors::AbstractVector{<:Integer},
                 F::Array{Integer,1},
-                g::LightGraphs.AbstractGraph,
+                g::Graphs.AbstractGraph,
                 opt::Integer)
 
 Returns set of free colors of x which are less
@@ -149,7 +149,7 @@ function free_colors(x::Integer,
                     A::AbstractVector{<:Integer},
                     colors::AbstractVector{<:Integer},
                     F::Array{Integer,1},
-                    g::LightGraphs.AbstractGraph,
+                    g::Graphs.AbstractGraph,
                     opt::Integer)
     index = -1
 

src/coloring/greedy_star1_coloring.jl

@@ -21,7 +21,7 @@ colors.
 
 Reference: Gebremedhin AH, Manne F, Pothen A. **What color is your Jacobian? Graph coloring for computing derivatives.** SIAM review. 2005;47(4):629-705.
 """
-function color_graph(g::LightGraphs.AbstractGraph, ::GreedyStar1Color)
+function color_graph(g::Graphs.AbstractGraph, ::GreedyStar1Color)
     v = nv(g)
     colorvec = zeros(Int, v)
 

src/coloring/greedy_star2_coloring.jl

@@ -23,7 +23,7 @@ Reference: Gebremedhin AH, Manne F, Pothen A. **What color is your Jacobian? Gra
 
 TODO: add text explaining the difference between star1 and star2
 """
-function color_graph(g::LightGraphs.AbstractGraph, ::GreedyStar2Color)
+function color_graph(g::Graphs.AbstractGraph, ::GreedyStar2Color)
     v = nv(g)
     colorvec = zeros(Int, v)
 

test/test_acyclic.jl

@@ -1,6 +1,6 @@
 using SparseDiffTools
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 using Test
 
 using Random

test/test_bsc.jl

@@ -1,6 +1,6 @@
 using SparseDiffTools
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 using Random
 #=
             Graph g0

test/test_contraction.jl

@@ -1,7 +1,7 @@
 using SparseDiffTools
 using VertexSafeGraphs
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 
 using Random
 Random.seed!(123)

test/test_greedy_d1.jl

@@ -1,7 +1,7 @@
 using SparseDiffTools
 using VertexSafeGraphs
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 using Test
 
 using Random

test/test_greedy_star.jl

@@ -1,6 +1,6 @@
 using SparseDiffTools
-using LightGraphs
-using LightGraphs: SimpleGraph
+using Graphs
+using Graphs: SimpleGraph
 using Test
 
 using Random
@@ -73,7 +73,7 @@ for i in 1:6
 
     #test condition 2
     for j = vertices(g)
-        walk = LightGraphs.self_avoiding_walk(g, j, 4)
+        walk = Graphs.self_avoiding_walk(g, j, 4)
         walk_colors = zeros(Int64, 0)
         if length(walk) >= 4
             for t in walk
@@ -93,7 +93,7 @@ for i in 1:6
 
     #test condition 2
     for j = vertices(g)
-        walk = LightGraphs.self_avoiding_walk(g, j, 4)
+        walk = Graphs.self_avoiding_walk(g, j, 4)
         walk_colors = zeros(Int64, 0)
         if length(walk) >= 4
             for t in walk

test/test_matrix2graph.jl

@@ -1,11 +1,9 @@
 using SparseDiffTools
 using SparseArrays
 using VertexSafeGraphs
-using LightGraphs
+using Graphs
 using Random
 
-const LG = LightGraphs
-
 n = rand(10:100)
 matrices = Array{SparseMatrixCSC, 1}(undef, 0)
 
@@ -19,8 +17,8 @@ for i in 1:20
     matrix = matrices[i]
     g = matrix2graph(matrix, false)
     for e in edges(g)
-        src = LG.src(e)
-        dst = LG.dst(e)
+        src = Graphs.src(e)
+        dst = Graphs.dst(e)
         col1 = abs.(matrix[:, src])
         col2 = abs.(matrix[:, dst])
         pr = col1' * col2
@@ -32,8 +30,8 @@ for i in 1:20
     matrix = matrices[i]
     g = matrix2graph(matrix, true)
     for e in edges(g)
-        src = LG.src(e)
-        dst = LG.dst(e)
+        src = Graphs.src(e)
+        dst = Graphs.dst(e)
         row1 = abs.(matrix[src, :])
         row2 = abs.(matrix[dst, :])
         pr = row1' * row2