Migrate from LightGraphs to Graphs.jl

Author: simonschoelly

Project.toml

@@ -1,15 +1,15 @@
 name = "GraphPlot"
 uuid = "a2cc645c-3eea-5389-862e-a155d0052231"
 authors = ["JuliaGraphs"]
-version = "0.4.4"
+version = "0.5.0"
 
 [deps]
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Compose = "a81c6b42-2e10-5240-aca2-a61377ecd94b"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -19,7 +19,7 @@ ArnoldiMethod = "0.0.4, 0.1"
 ColorTypes = "0.9, 0.10"
 Colors = "0.11, 0.12"
 Compose = "0.8, 0.9"
-LightGraphs = "1.1"
+Graphs = "1.4"
 VisualRegressionTests = "0.3, 1"
 julia = "1.3"
 

README.md

@@ -25,15 +25,15 @@ using GraphPlot
 # Usage
 ## karate network
 ```julia
-using LightGraphs: smallgraph
+using Graphs: smallgraph
 g = smallgraph(:karate)
 gplot(g)
 
 ```
 
 ## Add node label
 ```julia
-using LightGraphs
+using Graphs
 nodelabel = 1:nv(g)
 gplot(g, nodelabel=nodelabel)
 
@@ -47,7 +47,7 @@ gplot(g, nodelabel=nodelabel, nodelabeldist=1.5, nodelabelangleoffset=π/4)
 ## Control the node size
 ```julia
 # nodes size proportional to their degree
-nodesize = [LightGraphs.outdegree(g, v) for v in LightGraphs.vertices(g)]
+nodesize = [Graphs.outdegree(g, v) for v in Graphs.vertices(g)]
 gplot(g, nodesize=nodesize)
 ```
 
@@ -76,13 +76,13 @@ gplot(g, nodelabelsize=nodelabelsize, nodesize=nodesize, nodelabel=nodelabel)
 
 ## Draw edge labels
 ```julia
-edgelabel = 1:LightGraphs.ne(g)
+edgelabel = 1:Graphs.ne(g)
 gplot(g, edgelabel=edgelabel, nodelabel=nodelabel)
 ```
 
 ## Adjust edge labels
 ```julia
-edgelabel = 1:LightGraphs.ne(g)
+edgelabel = 1:Graphs.ne(g)
 gplot(g, edgelabel=edgelabel, nodelabel=nodelabel, edgelabeldistx=0.5, edgelabeldisty=0.5)
 ```
 
@@ -142,9 +142,9 @@ draw(PNG("karate.png", 16cm, 16cm), gplot(g))
 # save to svg
 draw(SVG("karate.svg", 16cm, 16cm), gplot(g))
 ```
-# LightGraphs integration
+# Graphs.jl integration
 ```julia
-using LightGraphs
+using Graphs
 h = watts_strogatz(50, 6, 0.3)
 gplot(h)
 ```

examples/graphplot.ipynb

@@ -49,7 +49,7 @@
    "outputs": [],
    "source": [
     "# load needed package firstly\n",
-    "using LightGraphs\n",
+    "using Graphs\n",
     "using GraphPlot"
    ]
   },
@@ -12127,7 +12127,7 @@
     }
    },
    "source": [
-    "# Native LightGraphs integration"
+    "# Native Graphs.jl integration"
    ]
   },
   {

src/GraphPlot.jl

@@ -1,7 +1,7 @@
 module GraphPlot
 
 using Compose  # for plotting features
-using LightGraphs
+using Graphs
 
 const gadflyjs = joinpath(dirname(Base.source_path()), "gadfly.js")
 

src/collapse_plot.jl

@@ -64,11 +64,11 @@ function community_layout(g::AbstractGraph, membership::Vector{Int})
 end
 
 function collapse_layout(g::AbstractGraph, membership::Vector{Int})
-    lightg = LightGraphs.SimpleGraph(nv(g))
+    sg = Graphs.SimpleGraph(nv(g))
     for e in edges(g)
         u = src(e)
         v = dst(e)
-        LightGraphs.add_edge!(lightg, u, v)
+        Graphs.add_edge!(sg, u, v)
     end
     N = length(membership)
     lx = zeros(N)
@@ -84,7 +84,7 @@ function collapse_layout(g::AbstractGraph, membership::Vector{Int})
     h, w = collapse_graph(g, membership)
     clx, cly = spring_layout(h)
     for (lbl, nodes) in comms
-        subg = lightg[nodes]
+        subg = sg[nodes]
         sublx, subly = spring_layout(subg)
         θ = range(0, stop=2pi, length=(length(nodes) + 1))[1:end-1]
         for (idx, node) in enumerate(nodes)

src/deprecations.jl

@@ -1,49 +1,49 @@
 using Base: depwarn
 
 
-function _nv(g) 
-    depwarn("`GraphPlot._nv(g)` is deprectated. Use `LightGraphs.nv(g)` instead.", :_nv)  
-    return LightGraphs.nv(g)
+function _nv(g)
+    depwarn("`GraphPlot._nv(g)` is deprectated. Use `Graphs.nv(g)` instead.", :_nv)
+    return Graphs.nv(g)
 end
 
-function _ne(g) 
-    depwarn("`GraphPlot._ne(g)` is deprectated. Use `LightGraphs.ne(g)` instead.", :_ne)  
-    return LightGraphs.ne(g)
+function _ne(g)
+    depwarn("`GraphPlot._ne(g)` is deprectated. Use `Graphs.ne(g)` instead.", :_ne)
+    return Graphs.ne(g)
 end
 
-function _vertices(g) 
-    depwarn("`GraphPlot._vertices(g)` is deprectated. Use `LightGraphs.vertices(g)` instead.", :_vertices)  
-    return LightGraphs.vertices(g)
+function _vertices(g)
+    depwarn("`GraphPlot._vertices(g)` is deprectated. Use `Graphs.vertices(g)` instead.", :_vertices)
+    return Graphs.vertices(g)
 end
 
-function _edges(g) 
-    depwarn("`GraphPlot._edges(g)` is deprectated. Use `LightGraphs.edges(g)` instead.", :_edges)  
-    return LightGraphs.edges(g)
+function _edges(g)
+    depwarn("`GraphPlot._edges(g)` is deprectated. Use `Graphs.edges(g)` instead.", :_edges)
+    return Graphs.edges(g)
 end
 
-function _src_index(e, g) 
-    depwarn("`GraphPlot._src_index(g)` is deprectated. Use `LightGraphs.src(e)` instead.", :_src_index)  
-    return LightGraphs.src(e)
+function _src_index(e, g)
+    depwarn("`GraphPlot._src_index(g)` is deprectated. Use `Graphs.src(e)` instead.", :_src_index)
+    return Graphs.src(e)
 end
 
-function _dst_index(e, g) 
-    depwarn("`GraphPlot._dst_index(g)` is deprectated. Use `LightGraphs.dst(e)` instead.", :_dst_index)  
-    return LightGraphs.dst(e)
+function _dst_index(e, g)
+    depwarn("`GraphPlot._dst_index(g)` is deprectated. Use `Graphs.dst(e)` instead.", :_dst_index)
+    return Graphs.dst(e)
 end
 
-function _adjacency_matrix(g) 
-    depwarn("`GraphPlot._adjacency_matrix(g)` is deprectated. Use `LightGraphs.adjacency_matrix(g)` instead.", :_adjacency_matrix)  
-    return LightGraphs.adjacency_matrix(g)
+function _adjacency_matrix(g)
+    depwarn("`GraphPlot._adjacency_matrix(g)` is deprectated. Use `Graphs.adjacency_matrix(g)` instead.", :_adjacency_matrix)
+    return Graphs.adjacency_matrix(g)
 end
 
-function _is_directed(g) 
-    depwarn("`GraphPlot._is_directed(g)` is deprectated. Use `LightGraphs.is_directed(g)` instead.", :_is_directed)  
-    return LightGraphs.is_directed(g)
+function _is_directed(g)
+    depwarn("`GraphPlot._is_directed(g)` is deprectated. Use `Graphs.is_directed(g)` instead.", :_is_directed)
+    return Graphs.is_directed(g)
 end
 
-function _laplacian_matrix(g) 
-    depwarn("`GraphPlot._laplacian_matrix(g)` is deprectated. Use `LightGraphs.laplacian_matrix(g)` instead.", :_laplacian_matrix)  
-    return LightGraphs.laplacian_matrix(g)
+function _laplacian_matrix(g)
+    depwarn("`GraphPlot._laplacian_matrix(g)` is deprectated. Use `Graphs.laplacian_matrix(g)` instead.", :_laplacian_matrix)
+    return Graphs.laplacian_matrix(g)
 end
 
 

src/layout.jl

@@ -280,7 +280,7 @@ function _spectral(A::SparseMatrixCSC)
     data = vec(sum(A, dims=1))
     D = sparse(Base.OneTo(length(data)), Base.OneTo(length(data)), data)
     L = D - A
-    eigenvalues, eigenvectors = LightGraphs.LinAlg.eigs(L, nev=3, which=SR())
+    eigenvalues, eigenvectors = Graphs.LinAlg.eigs(L, nev=3, which=SR())
     index = sortperm(real(eigenvalues))[2:3]
     return real(eigenvectors[:, index[1]]), real(eigenvectors[:, index[2]])
 end

test/runtests.jl

@@ -3,7 +3,7 @@
 (Sys.islinux() || Sys.iswindows()) && import ImageMagick
 
 using GraphPlot
-using LightGraphs
+using Graphs
 using Cairo
 using Colors
 using Compose
@@ -19,7 +19,7 @@ datadir = joinpath(@__DIR__, "data")
 
 
 
-# TODO smallgraph(:karate) has already been added to LightGraphs
+# TODO smallgraph(:karate) has already been added to Graphs
 # but as there hasn't been any new version tagged, we relay on this instead
 karate_edges = Edge.([
   1 => 2,   1 => 3,   1 => 4,   1 => 5,   1 => 6,   1 => 7,
@@ -39,7 +39,7 @@ karate_edges = Edge.([
 # graphs to test
 #g = smallgraph(:karate)
 g = SimpleGraph(karate_edges)
-h = LightGraphs.WheelGraph(10)
+h = Graphs.WheelGraph(10)
 
 test_layout(g::AbstractGraph; kws...) = spring_layout(g, 2017, kws...)