Add Graphs.jl API support

Project.toml

@@ -9,6 +9,7 @@ Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Mangal = "b8b640a6-63d9-51e6-b784-5033db27bef2"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

src/SpeciesInteractionNetworks.jl

@@ -14,6 +14,7 @@ using StatsBase
 using TestItems
 import Tables
 import Mangal
+import Graphs
 
 # Various utilities for probabilities
 # include(joinpath(".", "misc", "probabilities.jl"))
@@ -45,6 +46,7 @@ include("interfaces/iteration.jl")
 include("interfaces/table.jl")
 include("interfaces/broadcast.jl")
 include("interfaces/linearalgebra.jl")
+include("interfaces/graphs.jl")
 
 export svd, rank, diag
 export complexity, tsvd, rdpg

src/interfaces/graphs.jl

@@ -0,0 +1,70 @@
+"""
+    Base.reverse(N::SpeciesInteractionNetwork{<:Partiteness, <:Interactions})
+
+Returns a copy of the network, in which the interactions have been flipped. In
+other words, an interaction A → B is now B → A. This maintains the nature of the
+interaction, and works for loops, self-edges etc.
+"""
+function Base.reverse(N::SpeciesInteractionNetwork{<:Partiteness, <:Interactions})
+    M = copy(N)
+    reverse!(M)
+end
+
+"""
+    Base.reverse!(N::SpeciesInteractionNetwork{<:Partiteness, <:Interactions})
+
+Modifies the network given as its argument so that the interactions are flipped.
+See [`reverse`](@ref) for more information.
+"""
+function Base.reverse!(N::SpeciesInteractionNetwork{<:Partiteness, <:Interactions})
+    for interaction in interactions(N)
+        N[interaction[2], interaction[1]], N[interaction[1], interaction[2]] = N[interaction[1], interaction[2]], N[interaction[2], interaction[1]]
+    end
+    return N
+end
+
+@testitem "We can reverse a network" begin
+    edges = Binary(Bool[0 1 0 0; 0 0 1 0; 1 0 0 0; 0 1 1 1])
+    nodes = Unipartite(edges)
+    N = SpeciesInteractionNetwork(nodes, edges)
+    R = reverse(N)
+    for interaction in interactions(R)
+        @test N[interaction[2], interaction[1]] == interaction[3]
+    end
+end
+
+Graphs.has_vertex(N::T, v) where {T <: SpeciesInteractionNetwork} = v in species(N)
+
+@testitem "We can check the existence of a vertex" begin
+    import SpeciesInteractionNetworks.Graphs
+    edges = Binary(Bool[0 1 0 0; 0 0 1 0; 1 0 0 0; 0 1 1 1])
+    nodes = Unipartite(edges)
+    N = SpeciesInteractionNetwork(nodes, edges)
+    @test Graphs.has_vertex(N, :node_1)
+    @test !Graphs.has_vertex(N, :node_1000)
+end
+
+function Graphs.has_edge(N::T, s, d) where {T <: SpeciesInteractionNetwork}
+    if !(Graphs.has_vertex(N, s) && Graphs.has_vertex(N, d))
+        return false
+    else
+        return !iszero(N[s,d])        
+    end
+end
+
+@testitem "We can check the existence of an edge" begin
+    import SpeciesInteractionNetworks.Graphs
+    edges = Binary(Bool[0 1 0 0; 0 0 1 0; 1 0 0 0; 0 1 1 1])
+    nodes = Unipartite(edges)
+    N = SpeciesInteractionNetwork(nodes, edges)
+    @test Graphs.has_edge(N, :node_1, :node_2)
+    @test !Graphs.has_edge(N, :node_2, :node_1)
+    @test !Graphs.has_edge(N, :node_2000, :node_1)
+    @test !Graphs.has_edge(N, :node_2, :node_1000)
+    @test !Graphs.has_edge(N, :node_20000, :node_1000)
+end
+
+Graphs.inneighbors(N::T, v) where {T <: SpeciesInteractionNetwork} = predecessors(N, v)
+Graphs.outneighbors(N::T, v) where {T <: SpeciesInteractionNetwork} = successors(N, v)
+
+Graphs.edgetype(N::T) where {T <: SpeciesInteractionNetwork} = eltype(N)