Add convenience functions and reexport Graph.jl API

README.md

@@ -15,7 +15,7 @@ pkg> add NautyGraphs
 ## Basic Usage
 NautyGraphs.jl defines the `NautyGraph` or `NautyDiGraph` graph formats, which can be constructed and modified in the same way as regular `Graphs` from Graphs.jl:
 ```julia
-using NautyGraphs, Graphs
+using NautyGraphs
 
 A = [0 1 0 0;
      1 0 1 1;

docs/make.jl

@@ -1,8 +1,6 @@
-using Pkg; Pkg.add("Graphs")
-
 using Documenter, NautyGraphs
 
-DocMeta.setdocmeta!(NautyGraphs, :DocTestSetup, :(using NautyGraphs, Graphs); recursive=true)
+DocMeta.setdocmeta!(NautyGraphs, :DocTestSetup, :(using NautyGraphs); recursive=true)
 
 makedocs(sitename="NautyGraphs.jl";
     pages = [

docs/src/graph_creation.md

@@ -7,7 +7,7 @@ are intrinsically compatible with _nauty_, performing isomorphism checks or grap
 `NautyGraphs` and `NautyDiGraphs` can be created in the same way as graphs from `Graphs.jl`.  As an example, here are three different ways to define the same graph:
 
 ```jldoctest default
-using NautyGraphs, Graphs
+using NautyGraphs
 
 A = [0 1 0 0;
      1 0 1 1;

docs/src/index.md

@@ -10,7 +10,7 @@ pkg> add NautyGraphs
 ## Basic Usage
 NautyGraphs.jl defines the `NautyGraph` or `NautyDiGraph` graph formats, which can be constructed and modified in the same way as regular `Graphs` from Graphs.jl:
 ```jldoctest intro; output=false
-using NautyGraphs, Graphs
+using NautyGraphs
 
 A = [0 1 0 0;
      1 0 1 1;

docs/src/isomorphism.md

@@ -8,7 +8,7 @@ The _nauty_ library actually does not solve the graph isomorphsim problem direct
 
 To see what this looks like in practice, let's first construct two unequal, but isomorphic graphs:
 ```jldoctest isomorph
-using NautyGraphs, Graphs
+using NautyGraphs
 g1 = NautyGraph([Edge(1, 2), Edge(2, 3), Edge(2, 4), Edge(3, 4)])
 g2 = g1[[3, 2, 4, 1]] # permute the vertices of g1
 

src/NautyGraphs.jl

@@ -24,6 +24,22 @@ function __init__()
     return
 end
 
+export
+    add_edge!,
+    rem_edge!,
+    add_vertex!,
+    add_vertices!,
+    rem_vertex!,
+    rem_vertices!,
+    nv, ne, 
+    vertices, edges,
+    has_vertex, has_edge,
+    inneighbors, outneighbors,
+    neighbors,
+    is_directed,
+    edgetype,
+    Edge
+
 export
     AbstractNautyGraph,
     NautyGraph,
@@ -34,8 +50,9 @@ export
     iscanon,
     nauty,
     canonize!,
+    canonize,
     canonical_permutation,
+    canonical_id,
     is_isomorphic,
-    ≃,
-    canonical_id
+    ≃
 end

src/nauty.jl

@@ -140,6 +140,20 @@ function canonize!(g::DenseNautyGraph)
     _copycanon!(g, canong, canonperm)
     return canonperm
 end
+
+"""
+    canonize(g::AbstractNautyGraph)
+
+Canonize a copy of `g` and return the copy and canonical permutation.
+"""
+function canonize(::AbstractNautyGraph) end
+
+function canonize(g::DenseNautyGraph)
+    h = copy(g)
+    perm = canonize!(h)
+    return h, perm
+end
+
 function _copycanon!(g, canong, canonperm)
     copy!(g.graphset, canong)
     permute!(g.labels, canonperm)