[ITensors] [BUG] nnz methods duplicated with SparseArrays

[dgleich]

Description of bug

I believe that the nnz function for ITensors.jl should extend the one from SparseArrays. But this doesn't happen.

Minimal code demonstrating the bug or unexpected behavior

using ITensors, SparseArrays
A = sprand(10, 10, 0.5)
nnz(A) 

This gives

julia> nnz(A)
ERROR: UndefVarError: `nnz` not defined in `Main`
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name also exists in SparseArrays.
Hint: a global variable of this name also exists in NDTensors.
Hint: a global variable of this name also exists in ITensors.

Looking at the methods, it seems like this is probably an oversight:

julia> methods(ITensors.nnz)
# 5 methods for generic function "nnz" from NDTensors:
 [1] nnz(T::ITensor)
     @ ITensors ~/.julia/packages/ITensors/GkEpm/src/itensor.jl:855
 [2] nnz(::NDTensors.EmptyStorage)
     @ ~/.julia/packages/NDTensors/OehsJ/src/empty/empty.jl:69
 [3] nnz(bofs::Dictionaries.Dictionary{Block{N}, Int64} where N, inds)
     @ ~/.julia/packages/NDTensors/OehsJ/src/blocksparse/blockoffsets.jl:60
 [4] nnz(T::NDTensors.Tensor)
     @ ~/.julia/packages/NDTensors/OehsJ/src/tensor/tensor.jl:310
 [5] nnz(S::NDTensors.TensorStorage)
     @ ~/.julia/packages/NDTensors/OehsJ/src/tensorstorage/tensorstorage.jl:101

julia> methods(SparseArrays.nnz)
# 15 methods for generic function "nnz" from SparseArrays:
  [1] nnz(S::LinearAlgebra.LowerTriangular{<:Any, <:SparseArrays.AbstractSparseMatrixCSC})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:222
  [2] nnz(x::SubArray{Tv, 1, <:AbstractSparseVector{Tv, Ti}, Tuple{Base.Slice{Base.OneTo{Int64}}}, false} where {Tv, Ti})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsevector.jl:119
  [3] nnz(x::SubArray{Tv, 1, <:AbstractSparseVector{Tv, Ti}, <:Tuple{AbstractUnitRange}, false} where {Tv, Ti})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsevector.jl:120
  [4] nnz(x::SubArray{Tv, 1, <:SparseArrays.AbstractSparseMatrixCSC{Tv, Ti}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, false} where {Tv, Ti})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsevector.jl:115
  [5] nnz(S::SubArray{Tv, 2, <:SparseArrays.AbstractSparseMatrixCSC{Tv, Ti}, Tuple{Base.Slice{Base.OneTo{Int64}}, I}} where {Tv, Ti, I<:(AbstractVector{<:Integer})})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:223
  [6] nnz(lu::SparseArrays.UMFPACK.UmfpackLU)
     @ SparseArrays.UMFPACK /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/solvers/umfpack.jl:938
  [7] nnz(A::SparseArrays.CHOLMOD.Sparse{<:Union{Float32, Float64, ComplexF64, ComplexF32}, Int64})
     @ SparseArrays.CHOLMOD /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/solvers/cholmod.jl:601
  [8] nnz(A::SparseArrays.CHOLMOD.Sparse{<:Union{Float32, Float64, ComplexF64, ComplexF32}, Int32})
     @ SparseArrays.CHOLMOD /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/solvers/cholmod.jl:601
  [9] nnz(x::SparseArrays.AbstractCompressedVector)
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsevector.jl:114
 [10] nnz(S::SparseArrays.AbstractSparseMatrixCSC)
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:218
 [11] nnz(S::Base.ReshapedArray{<:Any, 1, <:SparseArrays.AbstractSparseMatrixCSC})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:219
 [12] nnz(S::LinearAlgebra.UpperTriangular{<:Any, <:SparseArrays.AbstractSparseMatrixCSC})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:221
 [13] nnz(F::SparseArrays.CHOLMOD.Factor)
     @ SparseArrays.CHOLMOD /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/solvers/cholmod.jl:1268
 [14] nnz(a::NDTensors.SparseArrayInterface.AbstractSparseArray)
     @ NDTensors.SparseArrayInterface ~/.julia/packages/NDTensors/OehsJ/src/lib/SparseArrayInterface/src/abstractsparsearray/SparseArrayInterfaceSparseArraysExt.jl:6
 [15] nnz(S::Union{LinearAlgebra.Adjoint{var"#s15", var"#s14"}, LinearAlgebra.Transpose{var"#s15", var"#s14"}} where {var"#s15", var"#s14"<:SparseArrays.AbstractSparseMatrixCSC})
     @ /Applications/Julia-1.11.app/Contents/Resources/julia/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:220

Version information

• Output from versioninfo():

julia> versioninfo()
Julia Version 1.11.0
Commit 501a4f25c2b (2024-10-07 11:40 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (x86_64-apple-darwin22.4.0)
  CPU: 16 × Intel(R) Xeon(R) W-2140B CPU @ 3.20GHz
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, skylake-avx512)
Threads: 1 default, 0 interactive, 1 GC (on 16 virtual cores)

• Output from using Pkg; Pkg.status("ITensors"):

julia> using Pkg; Pkg.status("ITensors")
⌅ [9136182c] ITensors v0.7.1

[mtfishman]

Thanks for pointing that out, that sounds right. We were changing over the style of our code to use explicit imports, probably this got messed up during that process.

[dgleich]

There's also permute which exists in SparseArrays too. But I'm not sure if you deliberately chose not extend that one as SparseArrays.permute does a row/column permutation whereas your permute reorders the indices.

[mtfishman]

There's also permute which exists in SparseArrays too. But I'm not sure if you deliberately chose not extend that one as SparseArrays.permute does a row/column permutation whereas your permute reorders the indices.

Thanks for the heads up about that. I feel less comfortable overloading SparseArrays.permute since as you identified ITensors.permute permutes/aligns the dimensions/indices, so they are pretty different concepts. Additionally, both are bad names for their respective operations, I don't understand why SparseArrays.permute(A, [4, 3, 2, 1], [1, 2, 3, 4]) even exists as an API since it should be the same as A[[4, 3, 2, 1], [1, 2, 3, 4]]. Additionally, ITensors.permute is a bad name since the input isn't a permutation, and we plan to rename it to something like align or aligndims, inspired by the existing/proposed APIs in NamedDims.jl, NamedPlus.jl, and PyTorch.

So in that case, I would recommend being explicit and qualifying the names with the modules, i.e. write ITensors.permute or SparseArrays.permute explicitly as needed (see https://docs.julialang.org/en/v1/manual/modules/#Handling-name-conflicts, https://github.com/ericphanson/ExplicitImports.jl).

[dgleich]

Thanks!!