Improve namespacing (#64)

ITensor · Apr 16, 2024 · 254e4cd · 254e4cd · mtfishman · Apr 16, 2024
1 parent d561823
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diff --git a/Project.toml b/Project.toml
@@ -1,36 +1,52 @@
 name = "NamedGraphs"
 uuid = "678767b0-92e7-4007-89e4-4527a8725b19"
 authors = ["Matthew Fishman <[email protected]> and contributors"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-GraphsFlows = "06909019-6f44-4949-96fc-b9d9aaa02889"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+PackageExtensionCompat = "65ce6f38-6b18-4e1d-a461-8949797d7930"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SplitApplyCombine = "03a91e81-4c3e-53e1-a0a4-9c0c8f19dd66"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
+
+[weakdeps]
+GraphsFlows = "06909019-6f44-4949-96fc-b9d9aaa02889"
+KaHyPar = "2a6221f6-aa48-11e9-3542-2d9e0ef01880"
+Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"
 SymRCM = "286e6d88-80af-4590-acc9-0001b223b9bd"
 
+[extensions]
+NamedGraphsGraphsFlowsExt = "GraphsFlows"
+NamedGraphsKaHyParExt = "KaHyPar"
+NamedGraphsMetisExt = "Metis"
+NamedGraphsSymRCMExt = "SymRCM"
+
 [compat]
 AbstractTrees = "0.3, 0.4"
 Dictionaries = "0.4"
 Graphs = "1.8"
 GraphsFlows = "0.1.1"
+KaHyPar = "0.3.1"
 LinearAlgebra = "1.7"
+Metis = "1.4"
+PackageExtensionCompat = "1"
 SimpleTraits = "0.9"
 SparseArrays = "1.7"
 SplitApplyCombine = "1.2.2"
-SymRCM = "0.2.1"
 Suppressor = "0.2"
-Requires = "1.3"
+SymRCM = "0.2.1"
 julia = "1.7"
 
 [extras]
+GraphsFlows = "06909019-6f44-4949-96fc-b9d9aaa02889"
+KaHyPar = "2a6221f6-aa48-11e9-3542-2d9e0ef01880"
+Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"
+SymRCM = "286e6d88-80af-4590-acc9-0001b223b9bd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]

diff --git a/README.md b/README.md
@@ -41,13 +41,15 @@ Graphs.jl operations, and two implementations: `NamedGraph` and `NamedDiGraph`.
 `NamedGraph` simply takes a set of names for the vertices of the graph. For example:
 
 ```julia
-julia> using Graphs
+julia> using Graphs: grid, has_edge, has_vertex, neighbors
 
-julia> using NamedGraphs
+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:
-4-element Indices{String}
+4-element Dictionaries.Indices{String}
  "A"
  "B"
  "C"
@@ -80,7 +82,7 @@ julia> neighbors(g, "B")
 
 julia> subgraph(g, ["A", "B"])
 NamedGraph{String} with 2 vertices:
-2-element Indices{String}
+2-element Dictionaries.Indices{String}
  "A"
  "B"
 
@@ -107,7 +109,7 @@ julia> dims = (2, 2)
 
 julia> g = NamedGraph(grid(dims), Tuple.(CartesianIndices(dims)))
 NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Indices{Tuple{Int64, Int64}}
+4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -151,7 +153,7 @@ 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:
-2-element Indices{Tuple{Int64, Int64}}
+2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (1, 2)
 
@@ -161,7 +163,7 @@ and 1 edge(s):
 
 julia> subgraph(v -> v[2] == 2, g)
 NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
-2-element Indices{Tuple{Int64, Int64}}
+2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 2)
  (2, 2)
 
@@ -171,7 +173,7 @@ and 1 edge(s):
 
 julia> subgraph(g, [(1, 1), (2, 2)])
 NamedGraph{Tuple{Int64, Int64}} with 2 vertices:
-2-element Indices{Tuple{Int64, Int64}}
+2-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 2)
 
@@ -185,7 +187,7 @@ You can also take [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union
 ```julia
 julia> g₁ = g
 NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Indices{Tuple{Int64, Int64}}
+4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -200,7 +202,7 @@ and 4 edge(s):
 
 julia> g₂ = g
 NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Indices{Tuple{Int64, Int64}}
+4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -215,7 +217,7 @@ and 4 edge(s):
 
 julia> disjoint_union(g₁, g₂)
 NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
-8-element Indices{Tuple{Tuple{Int64, Int64}, Int64}}
+8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
  ((1, 2), 1)
@@ -238,7 +240,7 @@ and 8 edge(s):
 
 julia> g₁ ⊔ g₂ # Same as above
 NamedGraph{Tuple{Tuple{Int64, Int64}, Int64}} with 8 vertices:
-8-element Indices{Tuple{Tuple{Int64, Int64}, Int64}}
+8-element Dictionaries.Indices{Tuple{Tuple{Int64, Int64}, Int64}}
  ((1, 1), 1)
  ((2, 1), 1)
  ((1, 2), 1)
@@ -278,7 +280,7 @@ 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:
-4-element Indices{Tuple{Int64, Int64}}
+4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -293,7 +295,7 @@ and 4 edge(s):
 
 julia> rename_vertices(first, subgraph(v -> v[2] == 2, g₁ ⊔ g₂))
 NamedGraph{Tuple{Int64, Int64}} with 4 vertices:
-4-element Indices{Tuple{Int64, Int64}}
+4-element Dictionaries.Indices{Tuple{Int64, Int64}}
  (1, 1)
  (2, 1)
  (1, 2)
@@ -315,8 +317,9 @@ and 4 edge(s):
 This file was generated with [Weave.jl](https://github.com/JunoLab/Weave.jl) with the following commands:
 
 ```julia
-using NamedGraphs, Weave
-weave(
+using NamedGraphs: NamedGraphs
+using Weave: Weave
+Weave.weave(
   joinpath(pkgdir(NamedGraphs), "examples", "README.jl");
   doctype="github",
   out_path=pkgdir(NamedGraphs),

diff --git a/examples/README.jl b/examples/README.jl
@@ -25,8 +25,9 @@
 #' `NamedGraph` simply takes a set of names for the vertices of the graph. For example:
 #+ term=true
 
-using Graphs
-using NamedGraphs
+using Graphs: grid, has_edge, has_vertex, neighbors
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: ⊔, disjoint_union, subgraph, rename_vertices
 g = NamedGraph(grid((4,)), ["A", "B", "C", "D"])
 
 #'Common operations are defined as you would expect:
@@ -94,8 +95,9 @@ rename_vertices(first, subgraph(v -> v[2] == 2, g₁ ⊔ g₂))
 #' This file was generated with [Weave.jl](https://github.com/JunoLab/Weave.jl) with the following commands:
 #+ eval=false
 
-using NamedGraphs, Weave
-weave(
+using NamedGraphs: NamedGraphs
+using Weave: Weave
+Weave.weave(
   joinpath(pkgdir(NamedGraphs), "examples", "README.jl");
   doctype="github",
   out_path=pkgdir(NamedGraphs),

diff --git a/examples/boundary.jl b/examples/boundary.jl
@@ -1,5 +1,6 @@
-using NamedGraphs
-using Graphs
+using NamedGraphs.GraphsExtensions:
+  boundary_edges, boundary_vertices, inner_boundary_vertices, outer_boundary_vertices
+using NamedGraphs.NamedGraphGenerators: named_grid
 
 g = named_grid((5, 5))
 subgraph_vertices = [(2, 2), (2, 3), (2, 4), (3, 2), (3, 3), (3, 4), (4, 2), (4, 3), (4, 4)]

diff --git a/examples/disjoint_union.jl b/examples/disjoint_union.jl
@@ -1,5 +1,6 @@
-using Graphs
-using NamedGraphs
+using Graphs: grid
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: ⊔, subgraph
 
 g1 = NamedGraph(grid((2, 2)), Tuple.(CartesianIndices((2, 2))))
 g2 = NamedGraph(grid((2, 2)), Tuple.(CartesianIndices((2, 2))))

diff --git a/examples/mincut.jl b/examples/mincut.jl
@@ -1,5 +1,7 @@
-using NamedGraphs
-using GraphsFlows
+using Graphs: path_graph
+using GraphsFlows: GraphsFlows
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: mincut_partitions
 
 g = NamedGraph(path_graph(4), ["A", "B", "C", "D"])
 

diff --git a/examples/multidimgraph_1d.jl b/examples/multidimgraph_1d.jl
@@ -1,5 +1,6 @@
-using Graphs
-using NamedGraphs
+using Graphs: grid, has_edge, has_vertex, ne, nv
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: ⊔, subgraph
 
 parent_graph = grid((4,))
 vs = ["A", "B", "C", "D"]

diff --git a/examples/multidimgraph_2d.jl b/examples/multidimgraph_2d.jl
@@ -1,5 +1,6 @@
-using Graphs
-using NamedGraphs
+using Graphs: grid, has_edge, has_vertex, nv
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: ⊔, subgraph
 
 parent_graph = grid((2, 2))
 vs = [("X", 1), ("X", 2), ("Y", 1), ("Y", 2)]
@@ -11,14 +12,14 @@ g = NamedGraph(parent_graph, vs)
 @show !has_edge(g, ("X", 2) => ("Y", 1))
 @show has_edge(g, ("X", 2) => ("Y", 2))
 
-g_sub = g[[("X", 1)]]
+g_sub = subgraph(g, [("X", 1)])
 
 @show has_vertex(g_sub, ("X", 1))
 @show !has_vertex(g_sub, ("X", 2))
 @show !has_vertex(g_sub, ("Y", 1))
 @show !has_vertex(g_sub, ("Y", 2))
 
-g_sub = g[[("X", 1), ("X", 2)]]
+g_sub = subgraph(g, [("X", 1), ("X", 2)])
 
 @show has_vertex(g_sub, ("X", 1))
 @show has_vertex(g_sub, ("X", 2))

diff --git a/examples/namedgraph.jl b/examples/namedgraph.jl
@@ -1,5 +1,6 @@
-using Graphs
-using NamedGraphs
+using Graphs: add_edge!, grid, has_edge, has_vertex, neighbors
+using NamedGraphs: NamedGraph
+using NamedGraphs.GraphsExtensions: subgraph
 
 g = NamedGraph(grid((4,)), ["A", "B", "C", "D"])
 

diff --git a/examples/partitioning.jl b/examples/partitioning.jl
diff --git a/ext/NamedGraphsGraphsFlowsExt/NamedGraphsGraphsFlowsExt.jl b/ext/NamedGraphsGraphsFlowsExt/NamedGraphsGraphsFlowsExt.jl
@@ -0,0 +1,63 @@
+module NamedGraphsGraphsFlowsExt
+using Graphs: AbstractGraph, IsDirected
+using GraphsFlows: GraphsFlows
+using NamedGraphs:
+  NamedGraphs,
+  AbstractNamedGraph,
+  DefaultNamedCapacity,
+  _symmetrize,
+  dist_matrix_to_parent_dist_matrix,
+  parent_graph,
+  parent_vertices_to_vertices,
+  vertex_to_parent_vertex
+using NamedGraphs.GraphsExtensions: GraphsExtensions, directed_graph
+using SimpleTraits: SimpleTraits, @traitfn
+
+@traitfn function NamedGraphs.dist_matrix_to_parent_dist_matrix(
+  graph::AbstractNamedGraph::IsDirected, dist_matrix::DefaultNamedCapacity
+)
+  return GraphsFlows.DefaultCapacity(graph)
+end
+
+@traitfn function GraphsFlows.mincut(
+  graph::AbstractNamedGraph::IsDirected,
+  source,
+  target,
+  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),
+    algorithm,
+  )
+  part1 = parent_vertices_to_vertices(graph, parent_part1)
+  part2 = parent_vertices_to_vertices(graph, parent_part2)
+  return (part1, part2, flow)
+end
+
+@traitfn function GraphsFlows.mincut(
+  graph::AbstractNamedGraph::(!IsDirected),
+  source,
+  target,
+  capacity_matrix=DefaultNamedCapacity(graph),
+  algorithm::GraphsFlows.AbstractFlowAlgorithm=GraphsFlows.PushRelabelAlgorithm(),
+)
+  return GraphsFlows.mincut(
+    directed_graph(graph), source, target, _symmetrize(capacity_matrix), algorithm
+  )
+end
+
+function GraphsExtensions.mincut_partitions(
+  graph::AbstractGraph,
+  source,
+  target,
+  capacity_matrix=DefaultNamedCapacity(graph),
+  algorithm::GraphsFlows.AbstractFlowAlgorithm=GraphsFlows.PushRelabelAlgorithm(),
+)
+  part1, part2, flow = GraphsFlows.mincut(graph, source, target, capacity_matrix, algorithm)
+  return part1, part2
+end
+end