Internal documentation fixes

Project.toml

@@ -1,6 +1,6 @@
 name = "SimpleGraphs"
 uuid = "55797a34-41de-5266-9ec1-32ac4eb504d3"
-version = "0.8.2"
+version = "0.8.3"
 
 [deps]
 AbstractLattices = "398f06c4-4d28-53ec-89ca-5b2656b7603d"

extras/README.md

@@ -61,7 +61,7 @@ To save a table of trees to a file (to later recall with `load_trees_table`) use
 
 For example, here are the degree sequences of all distinct trees with 6 vertices:
 
-```julia
+```
 julia> include("distinct_trees.jl");
 
 julia> TT = build_trees_table(6);  # Information output omitted
@@ -81,7 +81,7 @@ julia> for T in TT[6]
 
 Aubrey de Grey created a unit distance graph with chromatic number 5. This graph can be seen using the function `deGrey` in the file `deGrey.jl`.
 
-```julia
+```
 julia> include("deGrey.jl")
 deGrey
 

extras/distinct_trees.jl

@@ -9,7 +9,7 @@ const DEFAULT_FILE_NAME = "tree_codes.jl"
 Create a new table of distinct trees on 1 and 2 vertices.
 """
 function init_trees_table()
-    TT = Dict{Int,Vector{SimpleGraph{Int}}}()
+    TT = Dict{Int,Vector{UG{Int}}}()
 
     TT[1] = [IntGraph(1)]
     T = IntGraph(2)
@@ -23,7 +23,7 @@ end
     check_in(G,S)
 See if the set `S` contains a graph isomorphic to `G`. Return `true` if so.
 """
-function check_in(G::SimpleGraph{Int}, S::Set{SimpleGraph{Int}})
+function check_in(G::UG{Int}, S::Set{UG{Int}})
     if isempty(S)
         return false
     end
@@ -40,9 +40,9 @@ end
 Given a table of distinct trees up to size `n`, extend that table to include 
 all distinct trees of size `n+1`.
 """
-function extend_trees_table!(TT::Dict{Int,Vector{SimpleGraph{Int}}})::Nothing
+function extend_trees_table!(TT::Dict{Int,Vector{UG{Int}}})::Nothing
     n = maximum(keys(TT))
-    outset = Set{SimpleGraph{Int}}()  # set of trees with n+1 vertices
+    outset = Set{UG{Int}}()  # set of trees with n+1 vertices
     for T ∈ TT[n]
         for w = 1:n
             X = deepcopy(T)
@@ -74,7 +74,7 @@ end
 Given a table of distinct trees, convert that into a table of Prufer codes.
 This is used by `save_trees_table` and not useful to be called directly. 
 """
-function create_codes_table(TT::Dict{Int64,Vector{SimpleGraph{Int}}})
+function create_codes_table(TT::Dict{Int64,Vector{UG{Int}}})
     codes = Dict{Int64,Vector{Vector{Int}}}()
     codes[2] = [Int[]]
     for n = 3:maximum(keys(TT))
@@ -89,7 +89,7 @@ Save a trees table into a file specified by `filename`.
 If the file name is omitted, use `codes.jl`.
 """
 function save_trees_table(
-    TT::Dict{Int64,Vector{SimpleGraph{Int}}},
+    TT::Dict{Int64,Vector{UG{Int}}},
     filename::String = DEFAULT_FILE_NAME,
 )
     outfile = open(filename, "w")

src/SimpleGraphs.jl

@@ -19,7 +19,7 @@ using RingLists
 import AbstractLattices: dist, ∨
 
 """
-`AbstractSimpleGraph` is a parent class for `SimpleGraph` and `SimpleDigraph`.
+`AbstractSimpleGraph` is a parent class for `UndirectedGraph` and `DirectedGraph`.
 """
 abstract type AbstractSimpleGraph end
 export AbstractSimpleGraph

src/bisect.jl

@@ -1,7 +1,7 @@
 export bisect, cross_edges
 
 """
-`bisect(G::SimpleGraph)` partitions the vertex set of `G` using the
+`bisect(G::UndirectedGraph)` partitions the vertex set of `G` using the
 eigenvector associated with the second smallest eigenvalue of the
 graph's Laplacian matrix (called `x` below).
 
@@ -96,7 +96,7 @@ end
 # import IterTools.product
 
 """
-`cross_edges(G::SimpleGraph,A,B)` returns the set of edges of `G` with
+`cross_edges(G::UndirectedGraph,A,B)` returns the set of edges of `G` with
 one end in `A` and one end in `B`. Here `A` and `B` are collections
 of vertices of `G`.
 """

src/d_simple_core.jl

@@ -7,9 +7,9 @@ export in_neighbors, out_neighbors, simplify, vertex_split
 export is_strongly_connected
 
 """
-`SimpleDigraph()` creates a new directed graph with vertices of `Any`
+`DirectedGraph()` creates a new directed graph with vertices of `Any`
 type. This can be restricted to vertics of type `T` with
-`SimpleDigraph{T}()`.
+`DirectedGraph{T}()`.
 """
 mutable struct DirectedGraph{T} <: AbstractSimpleGraph
     V::Set{T}              # vertex set of this graph
@@ -24,6 +24,10 @@ mutable struct DirectedGraph{T} <: AbstractSimpleGraph
     end
 end
 
+"""
+    DG
+Abbreviation for `DirectedGraph`.
+"""
 const DG = DirectedGraph
 export DG
 
@@ -280,7 +284,7 @@ end
 # directions (and loops)
 
 """
-`simplify(G::SimpleDigraph)` converts a directed graph into a `SimpleGraph`
+`simplify(G::DirectedGraph)` converts a directed graph into an `UndirectedGraph`
 by removing directions and loops.
 """
 function simplify(D::DirectedGraph{T}) where {T}

src/embedding/distxy.jl

@@ -93,7 +93,7 @@ end
 `demo_distxy(G,tol=1e-3)` presents an animation showing the evolving
 drawing found by `distxy!`.
 """
-function demo_distxy(G::SimpleGraph = BuckyBall(), tol = 1e-3)
+function demo_distxy(G::UndirectedGraph = BuckyBall(), tol = 1e-3)
     return demo_distxy(GraphEmbedding(G), tol)
 end
 

src/embedding/geogebra.jl

@@ -1,7 +1,7 @@
 export geogebra
 
 """
-`geogebra(G,file_name)` takes a `SimpleGraph` and writes out a
+`geogebra(G,file_name)` takes a `UndirectedGraph` and writes out a
 script to produce a drawing of this graph in GeoGebra.
 
 Here is the secret sauce to make this work.
@@ -34,7 +34,7 @@ named parameters as follows:
   default is `3`.
 """
 function geogebra(
-    G::SimpleGraph,
+    G::UndirectedGraph,
     file_name::String = "geogebra.txt";
     vertex_labels::Bool = false,
     vertex_color::String = "black",

src/embedding/getset.jl

@@ -21,7 +21,7 @@ function getxy(G::UndirectedGraph, v)
 end
 
 """
-`hasxy(G::SimpleGraph)` returns `true` if an embedding has been 
+`hasxy(G::UndirectedGraph)` returns `true` if an embedding has been 
 given to this graph.
 """
 hasxy(G::UndirectedGraph)::Bool = cache_check(G, :xy)
@@ -36,7 +36,7 @@ function get_line_color(G::UndirectedGraph)
 end
 
 """
-`set_line_color(G::SimpleGraph, hue=:black)` sets the color of the graph's 
+`set_line_color(G::UndirectedGraph, hue=:black)` sets the color of the graph's 
 edges and vertex boundaries.
 """
 function set_line_color(G::UndirectedGraph, hue = :black)
@@ -85,7 +85,7 @@ set_vertex_color(G::UndirectedGraph) = set_vertex_color(G, :white)
 
 
 """
-`set_vertex_color(G::SimpleGraph, d::Dict, palette)` where `d` is a dictionary 
+`set_vertex_color(G::UndirectedGraph, d::Dict, palette)` where `d` is a dictionary 
 mapping vertices to integers and `palette` is a list of colors. 
 
 Convert a mapping of vertices to integers into colors for the vertices.

src/embedding/graffle.jl

@@ -74,7 +74,7 @@ end
 
 
 """
-`graffle(G::SimpleGraph, filename="julia.graffle",rad=9)` creates
+`graffle(G::UndirectedGraph, filename="julia.graffle", rad=9)` creates
 an OmniGraffle document of this drawing.
 
 * `G` is the graph

src/embedding/spectral.jl

@@ -27,7 +27,7 @@ function _spectral(G::UndirectedGraph, xcol::Int = 2, ycol::Int = 3)
 end
 
 """
-    _normalized_spectral(G::SimpleGraph, xcol::Int = 2, ycol::Int = 3)
+    _normalized_spectral(G::UndirectedGraph, xcol::Int = 2, ycol::Int = 3)
 Same as `_spectral`, but use the normalized Laplacian matrix.
 """
 function _normalized_spectral(G::UndirectedGraph, xcol::Int = 2, ycol::Int = 3)

src/embedding/tutte.jl

@@ -1,12 +1,12 @@
 # export tutte
 
 """
-`tutte(G::SimpleGraph, outside)` gives `G` a Tutte embedding in which 
+`tutte(G::UndirectedGraph, outside)` gives `G` a Tutte embedding in which 
 the list of vertices in `outside` form the outer boundary. The graph 
 should be connected (ideally, 3-connected) and, if planar and `outside`
 defines a face, the embedding will be crossing free.
 
-`tutte(G::SimpleGraph)` assumes `G` has a rotation system in which case a 
+`tutte(G::UndirectedGraph)` assumes `G` has a rotation system in which case a 
 largest face will be selected to be `outside`.
 """
 function _tutte(G::UndirectedGraph{T}, outside::Vector{T}) where {T}

src/hyper/graph.jl

@@ -1,5 +1,5 @@
 """
-`SimpleGraph(H::HG)` demotes a hypergraph to
+`UndirectedGraph(H::HG)` demotes a hypergraph to
 a simple graph.
 """
 function UndirectedGraph(H::HG{T})::UndirectedGraph{T} where {T}
@@ -34,7 +34,7 @@ end
 `HG{T}()` creates a new hypergraph in which vertices have
 type `T`. **Warning**: Do not use `T=Any`.
 
-`HG(G::SimpleGraph)` converts a graph to
+`HG(G::UndirectedGraph)` converts a graph to
 the equivalent two-uniform hypergraph.
 """
 function HG(G::UndirectedGraph{T}) where {T}

src/indep_poly.jl

@@ -1,8 +1,7 @@
 export indep_poly
 
 """
-`indep_poly(G)` returns the independence polynomial of the
-`SimpleGraph` `G`.
+`indep_poly(G)` returns the independence polynomial of the `UndirectedGraph` `G`.
 """
 function indep_poly(G::UndirectedGraph, cache_flag::Bool = true)
     if cache_flag && cache_check(G, :indep_poly)

src/matching_poly.jl

@@ -2,7 +2,7 @@ export matching_poly
 
 """
 `matching_poly(G)` returns the matching polynomial of the
-`SimpleGraph` `G`.
+`UndirectedGraph` `G`.
 """
 function matching_poly(G::UndirectedGraph, cache_flag::Bool = true)
     if cache_flag && cache_check(G, :matching_poly)

src/platonic.jl

@@ -10,7 +10,7 @@ function add_edge_matrix!(G::UndirectedGraph, edges::Array{Int,2})
 end
 
 """
-`Tetrahedron()` creates the tetrahedron `SimpleGraph`.
+`Tetrahedron()` creates the tetrahedron graph.
 """
 function Tetrahedron()
     G = Wheel(4)
@@ -19,7 +19,7 @@ function Tetrahedron()
 end
 
 """
-`Dodecahedron()` creates the dodecahedron `SimpleGraph`.
+`Dodecahedron()` creates the dodecahedron graph.
 """
 function Dodecahedron()
     G = IntGraph()
@@ -63,7 +63,7 @@ function Dodecahedron()
 end
 
 """
-`Icosahedron()` creates the icosahedron `SimpleGraph`.
+`Icosahedron()` creates the icosahedron graph.
 """
 function Icosahedron()
     G = IntGraph()
@@ -107,7 +107,7 @@ function Icosahedron()
 end
 
 """
-`Octahedron()` creates the octaahedron `SimpleGraph`.
+`Octahedron()` creates the octaahedron graph.
 """
 function Octahedron()
     G = Complete([2, 2, 2])

src/prufer.jl

@@ -2,7 +2,7 @@ export prufer_code, is_tree, prufer_restore
 
 """
     is_tree(G)
-Determines if the `SimpleGraph` is a tree.
+Determines if the `UndirectedGraph` is a tree.
 """
 function is_tree(G::UndirectedGraph)
     return is_connected(G) && (NE(G) == NV(G) - 1)
@@ -11,7 +11,7 @@ end
 
 """
     lowest_leaf(G)
-Return the leaf of the `SimpleGraph` with the smallest label.
+Return the leaf of the `UndirectedGraph` with the smallest label.
 """
 function lowest_leaf(G::UndirectedGraph)
     leaves = [v for v ∈ G.V if deg(G, v) == 1]
@@ -20,7 +20,7 @@ end
 
 
 """
-    lowest_leaf_neighbor(G::SimpleGraph)
+    lowest_leaf_neighbor(G::UndirectedGraph)
 Return the unique neighbor of `lowest_leaf(G)`.
 """
 function lowest_leaf_neighbor(G::UndirectedGraph)
@@ -30,7 +30,7 @@ end
 
 """
     prufer_code(G)
-Return the Prufer code of the `SimpleGraph` which must be a tree.
+Return the Prufer code of the `UndirectedGraph` which must be a tree.
 The vertices must be `<`-comparable and preferrably are the integers 
 `{1,2,...,n}` (otherwise we cannot decode the sequence generated).
 """