Remove NamedDimGraph, refactor and simplify

Project.toml

@@ -1,19 +1,19 @@
 name = "NamedGraphs"
 uuid = "678767b0-92e7-4007-89e4-4527a8725b19"
 authors = ["Matthew Fishman <[email protected]> and contributors"]
-version = "0.0.1"
+version = "0.1.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-MultiDimDictionaries = "87ff4268-a46e-478f-b30a-76b83dd64e3c"
+SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 
 [compat]
 AbstractTrees = "0.3, 0.4"
 Dictionaries = "0.3"
 Graphs = "1"
-MultiDimDictionaries = "0.0.1"
+SimpleTraits = "0.9"
 julia = "1.7"
 
 [extras]

examples/README.jl

@@ -18,7 +18,7 @@
 #' This packages introduces graph types with named edges, which are built on top of the `Graph`/`SimpleGraph` type in the [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) package that only have contiguous integer edges (i.e. linear indexing).
 
 #' There is a supertype `AbstractNamedGraph` that defines an interface and fallback implementations of standard
-#' Graphs.jl operations, and two implementations: `NamedGraph` and `NamedDimGraph`.
+#' Graphs.jl operations, and two implementations: `NamedGraph` and `NamedDiGraph`.
 
 #' ## `NamedGraph`
 
@@ -28,6 +28,7 @@
 using Graphs
 using NamedGraphs
 g = NamedGraph(grid((4,)), ["A", "B", "C", "D"])
+g = NamedGraph(grid((4,)); vertices=["A", "B", "C", "D"]) # Same as above
 
 #'Common operations are defined as you would expect:
 #+ term=true
@@ -42,84 +43,65 @@ g[["A", "B"]]
 
 #' Graph operations are implemented by mapping back and forth between the generalized named vertices and the linear index vertices of the `SimpleGraph`.
 
-#' ## `NamedDimGraph`
-
-#' `NamedDimGraph` is very similar to a `NamedGraph` but a bit more sophisticated. It has generalized
-#' multi-dimensional array indexing, mixed with named dimensions like [NamedDims.jl](https://github.com/invenia/NamedDims.jl).
-
-#' This allows for more sophisticated behavior, such as slicing dimensions and [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union) (generalizations of array concatenations).
-
-#' We start out by making a multi-dimensional graph where we specify the dimensions, which
-#' assigns vertex labels based on cartesian coordinates:
+#' It is natural to use tuples of integers as the names for the vertices of graphs with grid connectivities.
+#' For this, we use the convention that if a tuple is input, it is interpreted as the grid size and
+#' the vertex names label cartesian coordinates:
 #+ term=true
 
-g = NamedDimGraph(grid((2, 2)); dims=(2, 2))
+g = NamedGraph(grid((2, 2)); vertices=(2, 2))
 
 #' Internally the vertices are all stored as tuples with a label in each dimension.
 
-#' Vertices can be referred to by their tuples or splatted indices in each dimension:
+#' Vertices can be referred to by their tuples:
 #+ term=true
 
 has_vertex(g, (1, 1))
-has_vertex(g, 1, 1)
 has_edge(g, (1, 1) => (2, 1))
 has_edge(g, (1, 1) => (2, 2))
 neighbors(g, (2, 2))
 
-#' This allows the graph to be treated partially as a set of named vertices and
-#' partially with multi-dimensional array indexing syntax. For example
-#' you can slice a dimension to get the [induced subgraph](https://juliagraphs.org/Graphs.jl/dev/core_functions/operators/#Graphs.induced_subgraph-Union{Tuple{T},%20Tuple{U},%20Tuple{T,%20AbstractVector{U}}}%20where%20{U%3C:Integer,%20T%3C:AbstractGraph}):
+#' You can use vertex names to get [induced subgraphs](https://juliagraphs.org/Graphs.jl/dev/core_functions/operators/#Graphs.induced_subgraph-Union{Tuple{T},%20Tuple{U},%20Tuple{T,%20AbstractVector{U}}}%20where%20{U%3C:Integer,%20T%3C:AbstractGraph}):
 #+ term=true
 
-g[1, :]
-g[:, 2]
+subgraph(v -> v[1] == 1, g)
+subgraph(v -> v[2] == 2, g)
 g[[(1, 1), (2, 2)]]
 
-#' Note that slicing drops the dimensions of single indices, just like Julia Array slicing:
-
-#+ echo=false
-
-using Random
-Random.seed!(1234);
+#' Note that this is similar to multidimensional array slicing, and we may support syntax like `subgraph(v, 1, :)` in the future.
 
+#' You can also take [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union) or concatenations of graphs:
 #+ term=true
 
-x = randn(2, 2)
-x[1, :]
-
-#' Graphs can also take [disjoint unions](https://en.wikipedia.org/wiki/Disjoint_union) or concatenations of graphs:
-#+ term=true
-
-disjoint_union(g, g)
-g ⊔ g
+g₁ = g
+g₂ = g
+disjoint_union(g₁, g₂)
+g₁ ⊔ g₂ # Same as above
 
 #' The symbol `⊔` is just an alias for `disjoint_union` and can be written in the terminal
 #' or in your favorite [ide with the appropriate Julia extension](https://julialang.org/) with `\sqcup<tab>`
 
-#' Note that by default this introduces new dimension names (which by default are contiguous integers
-#' starting from 1) in the first dimension of the graph, so we can get back
-#' the original graphs by slicing and setting the first dimension:
-#+ term=true
+#' By default, this maps the vertices `v₁ ∈ vertices(g₁)` to `(v₁, 1)` and the vertices `v₂ ∈ vertices(g₂)`
+#' to `(v₂, 1)`, so the resulting vertices of the unioned graph will always be unique.
+#' The resulting graph will have no edges between vertices `(v₁, 1)` and `(v₂, 1)`, these would have to
+#' be added manually.
 
-(g ⊔ g)[1, :]
-(g ⊔ g)[2, :]
-
-#' or slice across the graphs that we disjoint unioned:
-#+ term=true
-
-(g ⊔ g)[:, 1, :]
-
-#' Additionally, we can use standard array concatenation syntax, such as:
+#' The original graphs can be obtained from subgraphs:
 #+ term=true
 
-[g; g]
-
-#' which is equivalent to `vcat(g, g)` or:
-#+ term=true
-
-[g;; g]
-
-#' which is the same as `hcat(g, g)`.
+rename_vertices(v -> v[1], subgraph(v -> v[2] == 1, g₁ ⊔ g₂))
+rename_vertices(v -> v[1], subgraph(v -> v[2] == 2, g₁ ⊔ g₂))
+
+## #' Additionally, we can use standard array concatenation syntax, such as:
+## #+ term=true
+## 
+## [g; g]
+## 
+## #' which is equivalent to `vcat(g, g)` or:
+## #+ term=true
+## 
+## [g;; g]
+## 
+## #' which is the same as `hcat(g, g)`.
 
 #' ## Generating this README
 

examples/disjoint_union.jl

@@ -1,12 +1,12 @@
 using Graphs
 using NamedGraphs
 
-g1 = NamedDimGraph(grid((2, 2)); dims=(2, 2))
-g2 = NamedDimGraph(grid((2, 2)); dims=(2, 2))
-g = ⊔(g1, g2; new_dim_names=("X", "Y"))
+g1 = NamedGraph(grid((2, 2)); vertices=(2, 2))
+g2 = NamedGraph(grid((2, 2)); vertices=(2, 2))
+g = ⊔("X" => g1, "Y" => g2)
 
 @show g1
 @show g2
 @show g
-@show g["X", :]
-@show g["Y", :]
+@show subgraph(v -> v[1] == "X", g)
+@show subgraph(v -> v[1] == "Y", g)

examples/multidimgraph_1d.jl

@@ -2,8 +2,8 @@ using Graphs
 using NamedGraphs
 
 parent_graph = grid((4,))
-vertices = ["A", "B", "C", "D"]
-g = NamedDimGraph(parent_graph, vertices)
+vs = ["A", "B", "C", "D"]
+g = NamedGraph(parent_graph, vs)
 
 @show has_vertex(g, "A")
 @show !has_vertex(g, "E")
@@ -26,26 +26,28 @@ g_sub = g[["A", "B"]]
 
 @show has_edge(g_sub, "A" => "B")
 
-g_sub = g[:]
+g_sub = subgraph(Returns(true), g)
 
 @show has_vertex(g_sub, "A")
 @show has_vertex(g_sub, "B")
 @show has_vertex(g_sub, "C")
 @show has_vertex(g_sub, "D")
 
-# Error: vertex names are the same
-# g_vcat = [g; g]
-
-g_hcat = [g;; g]
-
-@show nv(g_hcat) == 8
-@show ne(g_hcat) == 6
-
-@show has_vertex(g_hcat, "A", 1)
-
 g_union = g ⊔ g
 
 @show nv(g_union) == 8
 @show ne(g_union) == 6
 
-@show has_vertex(g_union, 1, "A")
+@show has_vertex(g_union, ("A", 1))
+@show has_vertex(g_union, ("A", 2))
+
+# Error: vertex names are the same
+# g_vcat = [g; g]
+
+# TODO: Implement
+## g_hcat = [g;; g]
+## 
+## @show nv(g_hcat) == 8
+## @show ne(g_hcat) == 6
+## 
+## @show has_vertex(g_hcat, ("A", 1))

examples/multidimgraph_2d.jl

@@ -2,55 +2,57 @@ using Graphs
 using NamedGraphs
 
 parent_graph = grid((2, 2))
-vertices = [("X", 1), ("X", 2), ("Y", 1), ("Y", 2)]
+vs = [("X", 1), ("X", 2), ("Y", 1), ("Y", 2)]
 
-g = NamedDimGraph(parent_graph, vertices)
+g = NamedGraph(parent_graph, vs)
 
-@show has_vertex(g, "X", 1)
+@show has_vertex(g, ("X", 1))
 @show has_edge(g, ("X", 1) => ("X", 2))
 @show !has_edge(g, ("X", 2) => ("Y", 1))
 @show has_edge(g, ("X", 2) => ("Y", 2))
 
 g_sub = 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)
+@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)]]
 
-@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)
+@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", :]
+# g_sub = g["X", :]
+g_sub = subgraph(v -> v[1] == "X", g)
 
-@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)
+@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[:, 2]
+# g_sub = g[:, 2]
+g_sub = subgraph(v -> v[2] == 2, g)
 
-@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)
+@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))
 
 parent_graph = grid((2, 2))
-g1 = NamedDimGraph(parent_graph; dims=(2, 2))
-g2 = NamedDimGraph(parent_graph; dims=(2, 2))
-
-g_vcat = [g1; g2]
-
-@show nv(g_vcat) == 8
-
-g_hcat = [g1;; g2]
-
-@show nv(g_hcat) == 8
+g1 = NamedGraph(parent_graph; vertices=(2, 2))
+g2 = NamedGraph(parent_graph; vertices=(2, 2))
 
 g_disjoint_union = g1 ⊔ g2
 
 @show nv(g_disjoint_union) == 8
+
+## g_vcat = [g1; g2]
+## 
+## @show nv(g_vcat) == 8
+## 
+## g_hcat = [g1;; g2]
+## 
+## @show nv(g_hcat) == 8

examples/namedgraph.jl

@@ -22,3 +22,4 @@ g_sub = g[["A", "B"]]
 @show has_vertex(g_sub, "B")
 @show !has_vertex(g_sub, "C")
 @show !has_vertex(g_sub, "D")
+@show has_edge(g_sub, "A" => "B")