Redesign GenericNamedGraph type

Project.toml

@@ -1,7 +1,7 @@
 name = "NamedGraphs"
 uuid = "678767b0-92e7-4007-89e4-4527a8725b19"
 authors = ["Matthew Fishman <mfishman@flatironinstitute.org> and contributors"]
-version = "0.5.1"
+version = "0.6.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"

README.md

@@ -49,7 +49,7 @@ julia> using NamedGraphs.GraphsExtensions: ⊔, disjoint_union, subgraph, rename
 
 julia> g = NamedGraph(grid((4,)), ["A", "B", "C", "D"])
 NamedGraphs.NamedGraph{String} with 4 vertices:
-4-element Dictionaries.Indices{String}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{String}
  "A"
  "B"
  "C"
@@ -82,7 +82,7 @@ julia> neighbors(g, "B")
 
 julia> subgraph(g, ["A", "B"])
 NamedGraphs.NamedGraph{String} with 2 vertices:
-2-element Dictionaries.Indices{String}
+2-element NamedGraphs.OrderedDictionaries.OrderedIndices{String}
  "A"
  "B"
 
@@ -109,7 +109,7 @@ julia> dims = (2, 2)
 
 julia> g = NamedGraph(grid(dims), Tuple.(CartesianIndices(dims)))
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Dictionaries.Indices{Tuple{Int64, Int64}}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -153,7 +153,7 @@ You can use vertex names to get [induced subgraphs](https://juliagraphs.org/Grap
 ```julia
 julia> subgraph(v -> v[1] == 1, g)
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
-2-element Dictionaries.Indices{Tuple{Int64, Int64}}
+2-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (1, 2)
 
@@ -163,7 +163,7 @@ and 1 edge(s):
 
 julia> subgraph(v -> v[2] == 2, g)
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
-2-element Dictionaries.Indices{Tuple{Int64, Int64}}
+2-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 2)
  (2, 2)
 
@@ -173,7 +173,7 @@ and 1 edge(s):
 
 julia> subgraph(g, [(1, 1), (2, 2)])
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
-2-element Dictionaries.Indices{Tuple{Int64, Int64}}
+2-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 2)
 
@@ -187,7 +187,7 @@ You can also take [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union
 ```julia
 julia> g₁ = g
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Dictionaries.Indices{Tuple{Int64, Int64}}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -202,7 +202,7 @@ and 4 edge(s):
 
 julia> g₂ = g
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Dictionaries.Indices{Tuple{Int64, Int64}}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -217,7 +217,7 @@ and 4 edge(s):
 
 julia> disjoint_union(g₁, g₂)
 NamedGraphs.NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
-8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
+8-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
  ((1, 2), 1)
@@ -240,7 +240,7 @@ and 8 edge(s):
 
 julia> g₁ ⊔ g₂ # Same as above
 NamedGraphs.NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
-8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
+8-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
  ((1, 2), 1)
@@ -280,7 +280,7 @@ The original graphs can be obtained from subgraphs:
 ```julia
 julia> rename_vertices(first, subgraph(v -> v[2] == 1, g₁ ⊔ g₂))
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Dictionaries.Indices{Tuple{Int64, Int64}}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -295,7 +295,7 @@ and 4 edge(s):
 
 julia> rename_vertices(first, subgraph(v -> v[2] == 2, g₁ ⊔ g₂))
 NamedGraphs.NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Dictionaries.Indices{Tuple{Int64, Int64}}
+4-element NamedGraphs.OrderedDictionaries.OrderedIndices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)

examples/mincut.jl

@@ -1,5 +1,4 @@
 using Graphs: path_graph
-using GraphsFlows: GraphsFlows
 using NamedGraphs: NamedGraph
 using NamedGraphs.GraphsExtensions: mincut_partitions
 
@@ -8,6 +7,8 @@ g = NamedGraph(path_graph(4), ["A", "B", "C", "D"])
 part1, part2 = mincut_partitions(g)
 @show part1, part2
 
+# Requires `GraphsFlows` to be loaded.
+using GraphsFlows: GraphsFlows
 part1, part2 = mincut_partitions(g, "A", "D")
 @show part1, part2
 

examples/multidimgraph_1d.jl

@@ -2,9 +2,9 @@ using Graphs: grid, has_edge, has_vertex, ne, nv
 using NamedGraphs: NamedGraph
 using NamedGraphs.GraphsExtensions: ⊔, subgraph
 
-parent_graph = grid((4,))
+position_graph = grid((4,))
 vs = ["A", "B", "C", "D"]
-g = NamedGraph(parent_graph, vs)
+g = NamedGraph(position_graph, vs)
 
 @show has_vertex(g, "A")
 @show !has_vertex(g, "E")

examples/multidimgraph_2d.jl

@@ -2,10 +2,10 @@ using Graphs: grid, has_edge, has_vertex, nv
 using NamedGraphs: NamedGraph
 using NamedGraphs.GraphsExtensions: ⊔, subgraph
 
-parent_graph = grid((2, 2))
+position_graph = grid((2, 2))
 vs = [("X", 1), ("X", 2), ("Y", 1), ("Y", 2)]
 
-g = NamedGraph(parent_graph, vs)
+g = NamedGraph(position_graph, vs)
 
 @show has_vertex(g, ("X", 1))
 @show has_edge(g, ("X", 1) => ("X", 2))
@@ -42,9 +42,9 @@ g_sub = subgraph(v -> v[2] == 2, g)
 @show !has_vertex(g_sub, ("Y", 1))
 @show has_vertex(g_sub, ("Y", 2))
 
-parent_graph = grid((2, 2))
-g1 = NamedGraph(parent_graph, Tuple.(CartesianIndices((2, 2))))
-g2 = NamedGraph(parent_graph, Tuple.(CartesianIndices((2, 2))))
+position_graph = grid((2, 2))
+g1 = NamedGraph(position_graph, Tuple.(CartesianIndices((2, 2))))
+g2 = NamedGraph(position_graph, Tuple.(CartesianIndices((2, 2))))
 
 g_disjoint_union = g1 ⊔ g2
 

ext/NamedGraphsGraphsFlowsExt/NamedGraphsGraphsFlowsExt.jl

@@ -6,14 +6,14 @@ using NamedGraphs:
   AbstractNamedGraph,
   DefaultNamedCapacity,
   _symmetrize,
-  dist_matrix_to_parent_dist_matrix,
-  parent_graph,
-  parent_vertices_to_vertices,
-  vertex_to_parent_vertex
+  dist_matrix_to_position_dist_matrix,
+  ordered_vertices,
+  position_graph,
+  vertex_positions
 using NamedGraphs.GraphsExtensions: GraphsExtensions, directed_graph
 using SimpleTraits: SimpleTraits, @traitfn
 
-@traitfn function NamedGraphs.dist_matrix_to_parent_dist_matrix(
+@traitfn function NamedGraphs.dist_matrix_to_position_dist_matrix(
   graph::AbstractNamedGraph::IsDirected, dist_matrix::DefaultNamedCapacity
 )
   return GraphsFlows.DefaultCapacity(graph)
@@ -26,15 +26,16 @@ end
   capacity_matrix=DefaultNamedCapacity(graph),
   algorithm::GraphsFlows.AbstractFlowAlgorithm=GraphsFlows.PushRelabelAlgorithm(),
 )
-  parent_part1, parent_part2, flow = GraphsFlows.mincut(
-    directed_graph(parent_graph(graph)),
-    vertex_to_parent_vertex(graph, source),
-    vertex_to_parent_vertex(graph, target),
-    dist_matrix_to_parent_dist_matrix(graph, capacity_matrix),
+  position_part1, position_part2, flow = GraphsFlows.mincut(
+    directed_graph(position_graph(graph)),
+    vertex_positions(graph)[source],
+    vertex_positions(graph)[target],
+    dist_matrix_to_position_dist_matrix(graph, capacity_matrix),
     algorithm,
   )
-  part1 = parent_vertices_to_vertices(graph, parent_part1)
-  part2 = parent_vertices_to_vertices(graph, parent_part2)
+  (part1, part2) = map((position_part1, position_part2)) do position_part
+    return map(v -> ordered_vertices(graph)[v], position_part)
+  end
   return (part1, part2, flow)
 end
 

src/NamedGraphs.jl

@@ -1,6 +1,8 @@
 module NamedGraphs
 include("lib/SimilarType/src/SimilarType.jl")
 include("lib/Keys/src/Keys.jl")
+include("lib/OrdinalIndexing/src/OrdinalIndexing.jl")
+include("lib/OrderedDictionaries/src/OrderedDictionaries.jl")
 include("lib/GraphGenerators/src/GraphGenerators.jl")
 include("lib/GraphsExtensions/src/GraphsExtensions.jl")
 include("utils.jl")