Reintroduce nnz and nonzeros as discussed in JuliaLang#6769

Deprecate nfilled for SparseMatrixCSC.
Deprecate nonzeros for StridedArray and BitArray.
Deprecate nnz for StridedArray.
Update documentation for structural nonzeros.
Update NEWS

NEWS.md

@@ -320,7 +320,7 @@ Deprecated or removed
 
  * `factorize!` is deprecated in favor of `factorize`. ([#5526])
 
- * `nnz` is removed. Use `countnz` or `nfilled` instead ([#5538])
+ * `nnz` counts the number of structural nonzeros in a sparse matrix. Use `countnz` for the actual number of nonzeros. ([#6769])
 
  * `setfield` is renamed `setfield!` ([#5748])
 
@@ -383,7 +383,7 @@ Deprecated or removed
 [#4888]: https://github.com/JuliaLang/julia/pull/4888
 [#5475]: https://github.com/JuliaLang/julia/pull/5475
 [#5526]: https://github.com/JuliaLang/julia/pull/5526
-[#5538]: https://github.com/JuliaLang/julia/pull/5538
+[#6769]: https://github.com/JuliaLang/julia/pull/6769
 [#5726]: https://github.com/JuliaLang/julia/pull/5726
 [#5811]: https://github.com/JuliaLang/julia/pull/5811
 [#5462]: https://github.com/JuliaLang/julia/pull/5462

base/abstractarray.jl

@@ -19,7 +19,6 @@ isreal{T<:Real,n}(x::AbstractArray{T,n}) = true
 ndims{T,n}(::AbstractArray{T,n}) = n
 ndims{T,n}(::Type{AbstractArray{T,n}}) = n
 ndims{T<:AbstractArray}(::Type{T}) = ndims(super(T))
-nfilled(t::AbstractArray) = length(t)
 length(t::AbstractArray) = prod(size(t))::Int
 endof(a::AbstractArray) = length(a)
 first(a::AbstractArray) = a[1]

base/array.jl

@@ -1102,24 +1102,6 @@ function findnz{T}(A::StridedMatrix{T})
  return (I, J, NZs)
 end
 
-function nonzeros{T}(A::StridedArray{T})
- nnzA = countnz(A)
- V = similar(A, T, nnzA)
- count = 1
- if nnzA > 0
- for i=1:length(A)
- Ai = A[i]
- if Ai != 0
- V[count] = Ai
- count += 1
- end
- end
- end
- return V
-end
-
-nonzeros(x::Number) = x == 0 ? Array(typeof(x),0) : [x]
-
 function findmax(a)
  if isempty(a)
  error("array must be non-empty")

base/bitarray.jl

@@ -1385,8 +1385,6 @@ function findnz(B::BitMatrix)
  return I, J, trues(length(I))
 end
 
-nonzeros(B::BitArray) = trues(countnz(B))
-
 ## Reductions ##
 
 sum(A::BitArray, region) = reducedim(+, A, region, 0, Array(Int,reduced_dims(A,region)))

base/deprecated.jl

@@ -380,6 +380,17 @@ end
 export mmread
 
 # 0.3 deprecations
+
+function nfilled(X)
+ depwarn("nfilled has been renamed to nnz", :nfilled)
+ nnz(X)
+end
+export nfilled
+
+@deprecate nonzeros(A::StridedArray) A[find(A)]
+@deprecate nonzeros(B::BitArray) trues(countnz(B))
+@deprecate nnz(A::StridedArray) countnz(A)
+
 @deprecate dense full
 
 export Stat
@@ -448,12 +459,6 @@ Set{T<:Number}(xs::T...) = Set{T}(xs)
 
 # 0.3 discontinued functions
 
-function nnz(X)
- depwarn("nnz has been renamed to countnz and is no longer computed in constant time for sparse matrices. Instead, use nfilled() for the number of elements in a sparse matrix.", :nnz)
- countnz(X)
-end
-export nnz
-
 scale!{T<:Base.LinAlg.BlasReal}(X::Array{T}, s::Complex) = error("scale!: Cannot scale a real array by a complex value in-place. Use scale(X::Array{Real}, s::Complex) instead.")
 
 @deprecate which(f::Callable, args...) @which f(args...)

base/exports.jl

@@ -536,7 +536,7 @@ export
  minimum,
  minmax,
  ndims,
- nfilled,
+ nnz,
  nonzeros,
  nthperm!,
  nthperm,

base/linalg/cholmod.jl

@@ -14,7 +14,7 @@ export # types
 using Base.LinAlg.UMFPACK # for decrement, increment, etc.
 
 import Base: (*), convert, copy, ctranspose, eltype, findnz, getindex, hcat,
- isvalid, nfilled, show, size, sort!, transpose, vcat
+ isvalid, nnz, show, size, sort!, transpose, vcat
 
 import ..LinAlg: (\), A_mul_Bc, A_mul_Bt, Ac_ldiv_B, Ac_mul_B, At_ldiv_B, At_mul_B,
  cholfact, cholfact!, copy, det, diag,
@@ -778,7 +778,7 @@ for Ti in (:Int32,:Int64)
  (Ptr{c_CholmodSparse{Tv,$Ti}},Ptr{c_CholmodSparse{Tv,$Ti}},Cint,Ptr{Uint8}),
  &A.c,&B.c,true,cmn($Ti))
  end
- function nfilled{Tv<:CHMVTypes}(A::CholmodSparse{Tv,$Ti})
+ function nnz{Tv<:CHMVTypes}(A::CholmodSparse{Tv,$Ti})
  ccall((@chm_nm "nnz" $Ti
  ,:libcholmod), Int, (Ptr{c_CholmodSparse{Tv,$Ti}},Ptr{Uint8}),&A.c,cmn($Ti))
  end

base/linalg/sparse.jl

@@ -347,7 +347,7 @@ function sparse_diff1{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti})
  m,n = size(S)
  m > 1 || return SparseMatrixCSC{Tv,Ti}(0, n, ones(n+1), Ti[], Tv[])
  colptr = Array(Ti, n+1)
- numnz = 2 * nfilled(S) # upper bound; will shrink later
+ numnz = 2 * nnz(S) # upper bound; will shrink later
  rowval = Array(Ti, numnz)
  nzval = Array(Tv, numnz)
  numnz = 0
@@ -387,7 +387,7 @@ function sparse_diff2{Tv,Ti}(a::SparseMatrixCSC{Tv,Ti})
 
  m,n = size(a)
  colptr = Array(Ti, max(n,1))
- numnz = 2 * nfilled(a) # upper bound; will shrink later
+ numnz = 2 * nnz(a) # upper bound; will shrink later
  rowval = Array(Ti, numnz)
  nzval = Array(Tv, numnz)
 
@@ -516,8 +516,8 @@ end
 # kron
 
 function kron{Tv,Ti}(a::SparseMatrixCSC{Tv,Ti}, b::SparseMatrixCSC{Tv,Ti})
- numnzA = nfilled(a)
- numnzB = nfilled(b)
+ numnzA = nnz(a)
+ numnzB = nnz(b)
 
  numnz = numnzA * numnzB
 
@@ -593,7 +593,7 @@ inv(A::SparseMatrixCSC) = error("The inverse of a sparse matrix can often be den
 function scale!{Tv,Ti}(C::SparseMatrixCSC{Tv,Ti}, A::SparseMatrixCSC, b::Vector)
  m, n = size(A)
  (n==length(b) && size(A)==size(C)) || throw(DimensionMismatch(""))
- numnz = nfilled(A)
+ numnz = nnz(A)
  C.colptr = convert(Array{Ti}, A.colptr)
  C.rowval = convert(Array{Ti}, A.rowval)
  C.nzval = Array(Tv, numnz)
@@ -606,7 +606,7 @@ end
 function scale!{Tv,Ti}(C::SparseMatrixCSC{Tv,Ti}, b::Vector, A::SparseMatrixCSC)
  m, n = size(A)
  (n==length(b) && size(A)==size(C)) || throw(DimensionMismatch(""))
- numnz = nfilled(A)
+ numnz = nnz(A)
  C.colptr = convert(Array{Ti}, A.colptr)
  C.rowval = convert(Array{Ti}, A.rowval)
  C.nzval = Array(Tv, numnz)

base/sparse.jl

@@ -7,7 +7,7 @@ import Base.NonTupleType, Base.float
 
 export SparseMatrixCSC, 
  blkdiag, dense, diag, diagm, droptol!, dropzeros!, etree, full, 
- getindex, ishermitian, issparse, issym, istril, istriu, 
+ getindex, ishermitian, issparse, issym, istril, istriu, nnz,
  setindex!, sparse, sparsevec, spdiagm, speye, spones, 
  sprand, sprandbool, sprandn, spzeros, symperm, trace, tril, tril!, 
  triu, triu!

base/sparse/csparse.jl

@@ -128,7 +128,7 @@ function transpose!{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti}, T::SparseMatrixCSC{Tv,Ti})
  rowval_T = T.rowval
  nzval_T = T.nzval
 
- nnzS = nfilled(S)
+ nnzS = nnz(S)
  colptr_S = S.colptr
  rowval_S = S.rowval
  nzval_S = S.nzval
@@ -147,15 +147,15 @@ end
 
 function transpose{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti})
  (nT, mT) = size(S)
- nnzS = nfilled(S) 
+ nnzS = nnz(S) 
  rowval_S = S.rowval
 
  rowval_T = Array(Ti, nnzS)
  nzval_T = Array(Tv, nnzS)
 
  colptr_T = zeros(Ti, nT+1)
  colptr_T[1] = 1
- @inbounds for i=1:nfilled(S)
+ @inbounds for i=1:nnz(S)
  colptr_T[rowval_S[i]+1] += 1
  end
  colptr_T = cumsum(colptr_T)
@@ -172,7 +172,7 @@ function ctranspose!{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti}, T::SparseMatrixCSC{Tv,Ti}
  rowval_T = T.rowval
  nzval_T = T.nzval
 
- nnzS = nfilled(S)
+ nnzS = nnz(S)
  colptr_S = S.colptr
  rowval_S = S.rowval
  nzval_S = S.nzval
@@ -191,15 +191,15 @@ end
 
 function ctranspose{Tv,Ti}(S::SparseMatrixCSC{Tv,Ti}) 
  (nT, mT) = size(S)
- nnzS = nfilled(S)
+ nnzS = nnz(S)
  rowval_S = S.rowval
 
  rowval_T = Array(Ti, nnzS)
  nzval_T = Array(Tv, nnzS)
 
  colptr_T = zeros(Ti, nT+1)
  colptr_T[1] = 1
- @inbounds for i=1:nfilled(S)
+ @inbounds for i=1:nnz(S)
  colptr_T[rowval_S[i]+1] += 1
  end
  colptr_T = cumsum(colptr_T)
@@ -335,7 +335,7 @@ end
 # Section 2.7: Removing entries from a matrix
 # http:https://www.cise.ufl.edu/research/sparse/CSparse/
 function fkeep!{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, f, other)
- nzorig = nfilled(A)
+ nzorig = nnz(A)
  nz = 1
  for j = 1:A.n
  p = A.colptr[j] # record current position