added adjacency_matrix for SCplx & minor fixes

src/ComputationalHomology.jl

@@ -1,7 +1,7 @@
 module ComputationalHomology
 
 using LinearAlgebra
-using SparseArrays
+import SparseArrays: SparseMatrixCSC, spzeros, sparse, findnz
 import SmithNormalForm: smith
 import Distances
 import Random
@@ -14,13 +14,14 @@ import Base.Iterators: pairs
 export AbstractCell,
        dim, faces, volume,
        AbstractSimplex,
+       values, vertecies,
        Simplex, Cube, Cell,
 
        AbstractChain,
        Chain, simplify,
 
        AbstractComplex,
-       boundary, coboundary, celltype, cells,
+       boundary, coboundary, celltype, cells, vertecies,
        SimplicialComplex, addsimplex!, addsimplices!,
        vietorisrips, witness, cech, čech,
 

src/cells.jl

@@ -36,7 +36,7 @@ abstract type AbstractSimplex <: AbstractCell end
 
 Get an array of `cell` values.
 """
-values(c::AbstractSimplex) = throw(MethodError(values,(typeof(c),))) #TODO: consider to move to AbstractSimplex
+values(c::AbstractSimplex) = throw(MethodError(values,(typeof(c),)))
 
 """
     vertecies(cell)

src/filtration.jl

@@ -126,7 +126,7 @@ function boundary(flt::Filtration; reduced=false)
     return bm
 end
 
-function SparseArrays.sparse(∂::Vector{<:AbstractSet})
+function sparse(∂::Vector{<:AbstractSet})
     m = length(∂)
     ret = spzeros(Int, m, m)
     for i in 1:m

src/simplicial.jl

@@ -48,7 +48,7 @@ union(u::Simplex, v::Simplex) = Simplex(collect(u.vs ∪ v.vs))
 
 function volume(S::AbstractMatrix)
     d, vc = size(S)
-    @assert d == vc-1 "Number of vertexes in simplex should be dim+1"
+    @assert d == vc-1 "Number of vertecies in simplex should be dim+1"
     v0 = S[:,1]
     return abs(det(S[:,2:end] .- v0))/prod(1:d)
 end
@@ -258,6 +258,23 @@ function Base.write(io::IO, cplx::SimplicialComplex)
     return
 end
 
+"""
+    adjacency_matrix(cplx, [T=Int])
+
+Construct an adjacency matrix of type `T` from a 1-skeleton (1D subcomplex) of the complex `cplx`.
+"""
+function adjacency_matrix(cplx::SimplicialComplex, ::Type{T}) where {T<:Integer}
+    C0 = map(hash, cells(cplx, 0))
+    N = length(C0)
+    adj = spzeros(T,N,N)
+    for c in cells(cplx, 1)
+        idxs = map(h->findfirst(isequal(h), C0), vertecies(c))
+        adj[idxs, idxs] .= one(T)
+    end
+    return adj
+end
+adjacency_matrix(cplx::SimplicialComplex) = adjacency_matrix(cplx, Int)
+
 #
 # Complex simplex iterator
 #

test/simplicial.jl

@@ -106,4 +106,8 @@
 
     ch = boundary(cplx2, 1, 0, Int)
     @test dim(ch) == -1
+
+    A = ComputationalHomology.adjacency_matrix(ComputationalHomology.sphere(1), UInt8)
+    @test collect(A) == fill(0x01,2,2)
+    @test eltype(A) == UInt8
 end