Fix adjacency & Laplacian matrices for weighted graph (#48)

* Fix adjacency & Laplacian matrices for weighted graph

* Correct the laplacian_matrix, add degree_matrix, add package dependencies

Test passed

Fix

* Ignore Manifest.toml

* Add dependency

Add dependencies
Add LinearAlgebra
Add Test

* Test degree_matrix

* Refine error and test on error

* Add tests

Author: yuehhua

.gitignore

@@ -1,3 +1,4 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+Manifest.toml

Project.toml

@@ -0,0 +1,10 @@
+name = "SimpleWeightedGraphs"
+uuid = "47aef6b3-ad0c-573a-a1e2-d07658019622"
+version = "1.1.0"
+
+[deps]
+LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/SimpleWeightedGraphs.jl

@@ -15,7 +15,8 @@ import LightGraphs:
     has_vertex, has_edge, inneighbors, outneighbors,
     indegree, outdegree, degree, has_self_loops, num_self_loops,
 
-    add_vertices!, adjacency_matrix, weights, connected_components, cartesian_product,
+    add_vertices!, adjacency_matrix, laplacian_matrix, weights,
+    connected_components, cartesian_product,
 
     AbstractGraphFormat, loadgraph, loadgraphs, savegraph,
     pagerank, induced_subgraph
@@ -33,7 +34,8 @@ export
     get_weight,
     WGraph,
     WDiGraph,
-    SWGFormat
+    SWGFormat,
+    degree_matrix
 
 include("simpleweightededge.jl")
 

src/overrides.jl

@@ -10,14 +10,35 @@ function add_vertices!(g::AbstractSimpleWeightedGraph, n::Integer)
     return true
 end
 
-function adjacency_matrix(g::AbstractSimpleWeightedGraph, T::DataType=Int; dir::Symbol=:out)
+function degree_matrix(g::AbstractSimpleWeightedGraph, T::DataType=weighttype(g); dir::Symbol=:out)
+    if is_directed(g)
+        if dir == :out
+            d = vec(sum(g.weights, dims=1))
+        elseif dir == :in
+            d = vec(sum(g.weights, dims=2))
+        elseif dir == :both
+            d = vec(sum(g.weights, dims=1)) + vec(sum(g.weights, dims=2))
+        else
+            throw(DomainError(dir, "invalid argument, only accept :in, :out and :both"))
+        end
+    else
+        d = vec(sum(g.weights, dims=1))
+    end
+    return SparseMatrixCSC(T.(diagm(0=>d)))
+end
+
+function adjacency_matrix(g::AbstractSimpleWeightedGraph, T::DataType=weighttype(g); dir::Symbol=:out)
     if dir == :out
-        return SparseMatrixCSC(T.(LinearAlgebra.fillstored!(copy(g.weights), 1))')
+        return SparseMatrixCSC(T.(copy(g.weights))')
     else
-        return T.(LinearAlgebra.fillstored!(copy(g.weights), 1))
+        return T.(copy(g.weights))
     end
 end
 
+function laplacian_matrix(g::AbstractSimpleWeightedGraph, T::DataType=weighttype(g); dir::Symbol=:out)
+    degree_matrix(g, T; dir=dir) - adjacency_matrix(g, T; dir=dir)
+end
+
 function pagerank(g::SimpleWeightedDiGraph, α=0.85, n=100::Integer, ϵ=1.0e-6)
     A = weights(g)
     S = vec(sum(A, dims=1))
@@ -123,4 +144,3 @@ function induced_subgraph(g::T, vlist::AbstractVector{U}) where T <: AbstractSim
     newg.weights = new_weights
     return newg, Vector{E}(vlist)
 end
-

test/overrides.jl

@@ -1,30 +1,66 @@
 @testset "Overrides" begin
     g3 = SimpleWeightedGraph(PathGraph(5))
+    g3_d = [1. 0. 0. 0. 0.;
+            0. 2. 0. 0. 0.;
+            0. 0. 2. 0. 0.;
+            0. 0. 0. 2. 0.;
+            0. 0. 0. 0. 1.]
+    g3_l = [1. -1. 0. 0. 0.;
+           -1. 2. -1. 0. 0.;
+            0. -1. 2. -1. 0.;
+            0. 0. -1. 2. -1.;
+            0. 0. 0. -1. 1.]
     g5 = SimpleWeightedDiGraph(4)
+    g5_din = [0. 0. 0. 0.;
+              0. 2. 0. 0.;
+              0. 0. 3. 0.;
+              0. 0. 0. 5.]
+    g5_dout = [3. 0. 0. 0.;
+               0. 2. 0. 0.;
+               0. 0. 5. 0.;
+               0. 0. 0. 0.]
+    g5_dboth = [3. 0. 0. 0.;
+                0. 4. 0. 0.;
+                0. 0. 8. 0.;
+                0. 0. 0. 5.]
+    g5_l = [3. -2. -1. 0.;
+            0. 2. -2. 0.;
+            0. 0. 5. -5.;
+            0. 0. 0. 0.]
 
     for g in testgraphs(g3)
         @test @inferred(adjacency_matrix(g, Bool)) == adjacency_matrix(g, Bool; dir=:out)
         @test @inferred(adjacency_matrix(g))[3, 2] == 1
+        @test degree_matrix(g, Float64, dir=:out) == g3_d
+        @test degree_matrix(g, Float64, dir=:out) == degree_matrix(g, Float64, dir=:in)
         @test adjacency_matrix(g)[2, 4] == 0
         @test adjacency_matrix(g; dir=:out) == adjacency_matrix(g; dir=:in)'
+        @test issymmetric(laplacian_matrix(g))
+        @test laplacian_matrix(g, Float64) ≈ g3_l
         @test g[1:3] == SimpleWeightedGraph{eltype(g), weighttype(g)}(PathGraph(3))
         gx = copy(g)
         add_edge!(gx, 2, 3, 99)
         gi = gx[2:4]
         @test weights(gi)[1, 2] == 99
-        
+
         h = @inferred(cartesian_product(g, g))
         @test nv(h) == 25
         @test ne(h) == 40
         gz = g3[1:4]
         add_edge!(gz, 3, 4, 87)
-        @test weights(cartesian_product(g3,gz))[11,12]==weights(gz)[3,4]  
+        @test weights(cartesian_product(g3,gz))[11,12]==weights(gz)[3,4]
     end
 
     add_edge!(g5, 1, 2, 2); add_edge!(g5, 2, 3, 2); add_edge!(g5, 1, 3, 1); add_edge!(g5, 3, 4, 5)
     for g in testdigraphs(g5)
-        @test @inferred(adjacency_matrix(g, Bool)) == adjacency_matrix(g, Bool; dir=:out)
+        @test degree_matrix(g, Float64, dir=:out) == g5_dout
+        @test degree_matrix(g, Float64, dir=:in) == g5_din
+        @test degree_matrix(g, Float64, dir=:both) == g5_dboth
+        @test_throws DomainError degree_matrix(g, dir=:other)
+        @test @inferred(adjacency_matrix(g, Int64)) == adjacency_matrix(g, Int64; dir=:out)
         @test adjacency_matrix(g; dir=:out) == adjacency_matrix(g; dir=:in)'
+        @test !issymmetric(laplacian_matrix(g))
+        @test laplacian_matrix(g, Float64) ≈ g5_l
         @test @inferred(pagerank(g))[3] ≈ 0.2266 atol=0.001
         @test length(@inferred(pagerank(g))) == nv(g)
         @test_throws ErrorException pagerank(g, 2)
@@ -35,4 +71,3 @@
         @test weights(g[2:3])[1, 2] == 2
     end
 end
-

test/runtests.jl

@@ -1,5 +1,6 @@
 using LightGraphs
 using SimpleWeightedGraphs
+using LinearAlgebra
 using Test
 
 testdir = dirname(@__FILE__)

test/simpleweightededge.jl

@@ -20,12 +20,14 @@ import SimpleWeightedGraphs.SimpleWeightedEdge
 
         @test src(ep1) == src(ep2) == src(ep3) == src(ep) == s
         @test dst(ep1) == dst(ep2) == dst(ep3) == dst(ep) == s + one(T)
+        @test weight(ep1) == one(T)
 
         @test eltype(t) == typeof(s)
         @test SimpleWeightedEdge(t) == e3
         @test SimpleWeightedEdge(t1) == SimpleWeightedEdge(t2)
         @test SimpleWeightedEdge(t1) == SimpleWeightedEdge{UInt8, Float64}(t1) == SimpleWeightedEdge{Int16, Float64}(t1)
         @test SimpleWeightedEdge{Int64, Float64}(ep1) == e3
+        @test Tuple(ep1) == t2
 
         @test reverse(ep1) == re
         @test sprint(show, ep1) == "Edge 1 => 2 with weight 1"