Expand functionality and tests (#69)

Author: mtfishman

Project.toml

@@ -1,7 +1,7 @@
 name = "NamedGraphs"
 uuid = "678767b0-92e7-4007-89e4-4527a8725b19"
 authors = ["Matthew Fishman <[email protected]> and contributors"]
-version = "0.4.2"
+version = "0.5.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

README.md

@@ -48,7 +48,7 @@ julia> using NamedGraphs: NamedGraph
 julia> using NamedGraphs.GraphsExtensions: ⊔, disjoint_union, subgraph, rename_vertices
 
 julia> g = NamedGraph(grid((4,)), ["A", "B", "C", "D"])
-NamedGraph{String} with 4 vertices:
+NamedGraphs.NamedGraph{String} with 4 vertices:
 4-element Dictionaries.Indices{String}
  "A"
  "B"
@@ -81,7 +81,7 @@ julia> neighbors(g, "B")
  "C"
 
 julia> subgraph(g, ["A", "B"])
-NamedGraph{String} with 2 vertices:
+NamedGraphs.NamedGraph{String} with 2 vertices:
 2-element Dictionaries.Indices{String}
  "A"
  "B"
@@ -108,7 +108,7 @@ julia> dims = (2, 2)
 (2, 2)
 
 julia> g = NamedGraph(grid(dims), Tuple.(CartesianIndices(dims)))
-NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
 4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
@@ -152,7 +152,7 @@ You can use vertex names to get [induced subgraphs](https://juliagraphs.org/Grap
 
 ```julia
 julia> subgraph(v -> v[1] == 1, g)
-NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
 2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (1, 2)
@@ -162,7 +162,7 @@ and 1 edge(s):
 
 
 julia> subgraph(v -> v[2] == 2, g)
-NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
 2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 2)
  (2, 2)
@@ -172,7 +172,7 @@ and 1 edge(s):
 
 
 julia> subgraph(g, [(1, 1), (2, 2)])
-NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
 2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 2)
@@ -186,7 +186,7 @@ You can also take [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union
 
 ```julia
 julia> g₁ = g
-NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
 4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
@@ -201,7 +201,7 @@ and 4 edge(s):
 
 
 julia> g₂ = g
-NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
 4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
@@ -216,7 +216,7 @@ and 4 edge(s):
 
 
 julia> disjoint_union(g₁, g₂)
-NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
+NamedGraphs.NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
 8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
@@ -239,7 +239,7 @@ and 8 edge(s):
 
 
 julia> g₁ ⊔ g₂ # Same as above
-NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
+NamedGraphs.NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
 8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
@@ -279,7 +279,7 @@ The original graphs can be obtained from subgraphs:
 
 ```julia
 julia> rename_vertices(first, subgraph(v -> v[2] == 1, g₁ ⊔ g₂))
-NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
 4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
@@ -294,7 +294,7 @@ and 4 edge(s):
 
 
 julia> rename_vertices(first, subgraph(v -> v[2] == 2, g₁ ⊔ g₂))
-NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
+NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
 4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)

src/NamedGraphs.jl

@@ -1,4 +1,5 @@
 module NamedGraphs
+include("lib/SimilarType/src/SimilarType.jl")
 include("lib/Keys/src/Keys.jl")
 include("lib/GraphGenerators/src/GraphGenerators.jl")
 include("lib/GraphsExtensions/src/GraphsExtensions.jl")
@@ -16,7 +17,7 @@ include("namedgraph.jl")
 include("lib/NamedGraphGenerators/src/NamedGraphGenerators.jl")
 include("lib/PartitionedGraphs/src/PartitionedGraphs.jl")
 
-export NamedGraph, NamedDiGraph, NamedEdge
+export AbstractNamedGraphs, NamedDiGraph, NamedEdge, NamedGraph
 
 using PackageExtensionCompat: @require_extensions
 function __init__()

src/decorate.jl

@@ -3,7 +3,7 @@ using Graphs.SimpleGraphs: SimpleGraph
 using .GraphsExtensions: GraphsExtensions, add_edges!
 
 function GraphsExtensions.decorate_graph_edges(
-  g::AbstractNamedGraph; edge_map::Function=Returns(SimpleGraph(1))
+  g::AbstractNamedGraph; edge_map::Function=Returns(NamedGraph(1))
 )
   g_dec = copy(g)
   es = edges(g_dec)
@@ -19,7 +19,7 @@ function GraphsExtensions.decorate_graph_edges(
 end
 
 function GraphsExtensions.decorate_graph_vertices(
-  g::AbstractNamedGraph; vertex_map::Function=Returns(SimpleGraph(1))
+  g::AbstractNamedGraph; vertex_map::Function=Returns(NamedGraph(1))
 )
   g_dec = copy(g)
   vs = vertices(g_dec)

src/lib/GraphGenerators/src/GraphGenerators.jl

@@ -1,6 +1,7 @@
 module GraphGenerators
 using Dictionaries: Dictionary
-using Graphs: SimpleGraph, add_edge!
+using Graphs: add_edge!, dst, edges, nv, src
+using Graphs.SimpleGraphs: SimpleDiGraph, SimpleGraph, binary_tree
 
 function comb_tree(dims::Tuple)
   @assert length(dims) == 2
@@ -28,4 +29,16 @@ function comb_tree(tooth_lengths::Vector{<:Integer})
   end
   return graph
 end
+
+# TODO: More efficient implementation based
+# on the implementation of `binary_tree`.
+function binary_arborescence(k::Integer)
+  graph = binary_tree(k)
+  digraph = SimpleDiGraph(nv(graph))
+  for e in edges(graph)
+    @assert dst(e) > src(e)
+    add_edge!(digraph, e)
+  end
+  return digraph
+end
 end

src/lib/GraphsExtensions/.JuliaFormatter.toml

@@ -0,0 +1,2 @@
+style = "blue"
+indent = 2

src/lib/GraphsExtensions/Project.toml

@@ -0,0 +1,6 @@
+[deps]
+AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+NamedGraphs = "678767b0-92e7-4007-89e4-4527a8725b19"
+SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+SplitApplyCombine = "03a91e81-4c3e-53e1-a0a4-9c0c8f19dd66"

src/lib/GraphsExtensions/src/GraphsExtensions.jl

@@ -1,5 +1,6 @@
 module GraphsExtensions
 include("abstractgraph.jl")
+include("abstracttrees.jl")
 include("boundary.jl")
 include("shortestpaths.jl")
 include("symrcm.jl")