Update the compatibility with Graphs API (#15)

* update the compatibility with Graphs API

* 2prev

* fix docs

* formatting

Author: bvdmitri

docs/src/api.md

@@ -52,13 +52,18 @@ Functions that compute properties of the graph:
 ```@docs
 nv
 ne
+vertices
+has_vertex
 has_edge
 edges
 neighbors
 all_neighbors
+inneighbors
+outneighbors
 degree
 indegree
 outdegree
 density
 is_bipartite
+is_directed
 ``` 

src/BipartiteFactorGraphs.jl

@@ -2,7 +2,24 @@ module BipartiteFactorGraphs
 
 using Graphs
 import Graphs:
-    add_edge!, has_edge, edges, neighbors, nv, ne, all_neighbors, degree, indegree, outdegree, density, is_bipartite
+    AbstractGraph,
+    vertices,
+    has_vertex,
+    add_edge!,
+    has_edge,
+    edges,
+    neighbors,
+    nv,
+    ne,
+    all_neighbors,
+    inneighbors,
+    outneighbors,
+    degree,
+    indegree,
+    outdegree,
+    density,
+    is_bipartite,
+    is_directed
 
 export BipartiteFactorGraph,
     add_variable!,
@@ -19,18 +36,23 @@ export BipartiteFactorGraph,
     num_variables,
     num_factors,
     # Reexport used Graphs functions
+    vertices,
+    has_vertex,
     add_edge!,
     has_edge,
     edges,
     neighbors,
     nv,
     ne,
     all_neighbors,
+    inneighbors,
+    outneighbors,
     degree,
     indegree,
     outdegree,
     density,
-    is_bipartite
+    is_bipartite,
+    is_directed
 
 struct UnorderedPair{T}
     a::T
@@ -97,7 +119,7 @@ struct BipartiteFactorGraph{
     DVars <: AbstractDict{Int, TVar},
     DFacs <: AbstractDict{Int, TFac},
     DE <: AbstractDict{UnorderedPair{Int}, E}
-}
+} <: AbstractGraph{Int}
     graph::SimpleGraph{Int}
     variable_data::DVars
     factor_data::DFacs
@@ -289,6 +311,26 @@ Get the number of factor nodes in the graph.
 """
 num_factors(g::BipartiteFactorGraph) = length(g.factor_data)
 
+"""
+    vertices(g::BipartiteFactorGraph)
+
+Get all vertices in the graph. Note, that it returns vertices that represent both variable and factor nodes.
+Use [`variables`](@ref) and [`factors`](@ref) to get only variable or factor nodes.
+"""
+function Graphs.vertices(g::BipartiteFactorGraph)
+    return Graphs.vertices(g.graph)
+end
+
+"""
+    has_vertex(g::BipartiteFactorGraph, v::Int)
+
+Check if vertex `v` is in the graph. Note, that it returns true for both variable and factor nodes.
+Use [`is_variable`](@ref) and [`is_factor`](@ref) to check existence of a node with a specific type.
+"""
+function Graphs.has_vertex(g::BipartiteFactorGraph, v::Int)
+    return Graphs.has_vertex(g.graph, v)
+end
+
 """
     has_edge(g::BipartiteFactorGraph, var::Int, fac::Int)
 
@@ -340,6 +382,24 @@ function all_neighbors(g::BipartiteFactorGraph, v::Int)
     return Graphs.neighbors(g.graph, v)
 end
 
+"""
+    inneighbors(g::BipartiteFactorGraph, v::Int)
+
+Return a list of all in-neighbors of vertex `v` in graph `g`.
+"""
+function inneighbors(g::BipartiteFactorGraph, v::Int)
+    return Graphs.inneighbors(g.graph, v)
+end
+
+"""
+    outneighbors(g::BipartiteFactorGraph, v::Int)
+
+Return a list of all out-neighbors of vertex `v` in graph `g`.
+"""
+function outneighbors(g::BipartiteFactorGraph, v::Int)
+    return Graphs.outneighbors(g.graph, v)
+end
+
 """
     degree(g::BipartiteFactorGraph[, v])
 
@@ -405,4 +465,13 @@ function is_bipartite(g::BipartiteFactorGraph)
     return Graphs.is_bipartite(g.graph)
 end
 
+"""
+    is_directed(g::BipartiteFactorGraph)
+
+Check if the graph is directed. For BipartiteFactorGraph this is always false since the graph is undirected.
+"""
+function is_directed(g::BipartiteFactorGraph)
+    return false
+end
+
 end # module

test/graph_api_tests.jl

@@ -4,10 +4,15 @@
 
     g = BipartiteFactorGraph(Float64, String, Bool)
 
+    @test !is_directed(g)
+
     # Test empty graph properties
     @test Graphs.nv(g) == 0
     @test Graphs.ne(g) == 0
     @test Graphs.density(g) == 0.0
+    @test Graphs.eltype(g) == Int
+
+    @test isempty(vertices(g))
 
     # Add some nodes and edges
     v1 = add_variable!(g, 1.0)
@@ -17,15 +22,68 @@
     f1 = add_factor!(g, "factor1")
     f2 = add_factor!(g, "factor2")
 
+    @test !isempty(vertices(g))
+    @test length(vertices(g)) == 5
     @test length(edges(g)) == 0
 
+    @test v1 in vertices(g)
+    @test f1 in vertices(g)
+    @test v2 in vertices(g)
+    @test f2 in vertices(g)
+    @test v3 in vertices(g)
+
+    @test v1 in variables(g)
+    @test v2 in variables(g)
+    @test v3 in variables(g)
+
+    @test f1 in factors(g)
+    @test f2 in factors(g)
+
+    @test !(v1 in factors(g))
+    @test !(v2 in factors(g))
+    @test !(v3 in factors(g))
+
+    @test !(f1 in variables(g))
+    @test !(f2 in variables(g))
+
+    @test has_vertex(g, v1)
+    @test has_vertex(g, v2)
+    @test has_vertex(g, v3)
+    @test has_vertex(g, f1)
+    @test has_vertex(g, f2)
+    @test !has_vertex(g, -1)
+
+    @test !has_edge(g, v1, f1)
+    @test !has_edge(g, v2, f1)
+    @test !has_edge(g, v2, f2)
+    @test !has_edge(g, v3, f2)
+    @test !has_edge(g, v1, f2)
+
     add_edge!(g, v1, f1, true)
     add_edge!(g, v2, f1, true)
     add_edge!(g, v2, f2, false)
     add_edge!(g, v3, f2, true)
 
     @test length(edges(g)) == 4
 
+    @test has_edge(g, v1, f1)
+    @test has_edge(g, v2, f1)
+    @test has_edge(g, v2, f2)
+    @test has_edge(g, v3, f2)
+    @test !has_edge(g, v1, f2)
+
+    @test inneighbors(g, v1) == [f1]
+    @test inneighbors(g, v2) == [f1, f2]
+    @test inneighbors(g, v3) == [f2]
+    @test inneighbors(g, f1) == [v1, v2]
+    @test inneighbors(g, f2) == [v2, v3]
+
+    @test outneighbors(g, v1) == [f1]
+    @test outneighbors(g, v2) == [f1, f2]
+    @test outneighbors(g, v3) == [f2]
+    @test outneighbors(g, f1) == [v1, v2]
+    @test outneighbors(g, f2) == [v2, v3]
+
     # Test graph properties
     @test Graphs.nv(g) == 5  # 3 variables + 2 factors
     @test Graphs.ne(g) == 4  # 4 edges