Fix issues reported by JET

.gitignore

@@ -4,4 +4,5 @@ LocalPreferences.toml
 */.*swp
 scratch/
 *.cov
-.vscode
+.vscode
+test/.CondaPkg/

src/QuantumClifford.jl

@@ -26,7 +26,7 @@ export
     nqubits,
     stabilizerview, destabilizerview, logicalxview, logicalzview, phases,
     fastcolumn, fastrow,
-    bitview, quantumstate, tab,
+    bitview, quantumstate, tab, rank,
     BadDataStructure,
     affectedqubits, #TODO move to QuantumInterface?
     # GF2
@@ -173,7 +173,7 @@ Tableau(xzs::AbstractMatrix{Bool}) = Tableau(zeros(UInt8, size(xzs,1)), xzs[:,1:
 
 Tableau(t::Tableau) = t
 
-function _T_str(a) # TODO this can be optimized by not creating intermediary PauliOperator objects
+function _T_str(a::Union{String,SubString{String}}) # TODO this can be optimized by not creating intermediary PauliOperator objects
     paulis = [_P_str(strip(s.match)) for s in eachmatch(r"[+-]?\h*[i]?\h*[XYZI_]+", a)]
     Tableau(paulis)
 end
@@ -229,18 +229,18 @@ end
 
 Base.firstindex(tab::Tableau) = 1
 
-Base.lastindex(tab::Tableau) = length(tab.phases)
+Base.lastindex(tab::Tableau) = length(tab.phases)::Int
 Base.lastindex(tab::Tableau, i) = size(tab)[i]
 
-Base.eachindex(tab::Tableau) = Base.OneTo(lastindex(tab.phases))
+Base.eachindex(tab::Tableau) = Base.OneTo(lastindex(tab.phases)::Int)
 
 Base.axes(tab::Tableau) = (Base.OneTo(lastindex(tab)), Base.OneTo(nqubits(tab)))
 Base.axes(tab::Tableau,i) = axes(tab)[i]
 
-Base.size(tab::Tableau) = (length(tab.phases),nqubits(tab))
+Base.size(tab::Tableau) = (length(tab.phases)::Int, nqubits(tab))
 Base.size(tab::Tableau,i) = size(tab)[i]
 
-Base.length(tab::Tableau) = length(tab.phases)
+Base.length(tab::Tableau) = length(tab.phases)::Int
 
 Base.:(==)(l::Tableau, r::Tableau) = r.nqubits==l.nqubits && r.phases==l.phases && r.xzs==l.xzs
 
@@ -378,7 +378,7 @@ macro S_str(a)
     quote Stabilizer(_T_str($a)) end
 end
 Base.getindex(stab::Stabilizer, i::Int) = tab(stab)[i]
-Base.getindex(stab::Stabilizer, i) = Stabilizer(tab(stab)[i])
+Base.getindex(stab::Stabilizer, i) = Stabilizer(tab(stab)[i]::Tableau)
 @inline Base.getindex(stab::Stabilizer, r::Int, c) = tab(stab)[r,c]
 Base.getindex(stab::Stabilizer, r, c) = Stabilizer(tab(stab)[r,c])
 Base.view(stab::Stabilizer, r) = Stabilizer(view(tab(stab),r))
@@ -497,11 +497,11 @@ function MixedStabilizer(s::Stabilizer{T}) where {T}
     MixedStabilizer(spadded,zr)
 end
 
-MixedStabilizer(s::Stabilizer,rank::Int) = MixedStabilizer(tab(s),rank)
+MixedStabilizer(s::Stabilizer,rank::Int) = MixedStabilizer(tab(s), rank)
 
-Base.length(d::MixedStabilizer) = length(d.tab)
+Base.length(d::MixedStabilizer) = length(tab(d))
 
-Base.copy(ms::MixedStabilizer) = MixedStabilizer(copy(ms.tab),ms.rank)
+Base.copy(ms::MixedStabilizer) = MixedStabilizer(copy(tab(ms)), rank(ms))
 
 ##############################
 # Mixed Destabilizer states
@@ -580,15 +580,15 @@ function MixedDestabilizer(stab::Stabilizer{T}; undoperm=true, reportperm=false)
 end
 
 function MixedDestabilizer(d::Destabilizer, r::Int)
-    l,n = size(d.tab)
+    l,n = size(tab(d))
     if l==2n
         MixedDestabilizer(tab(d), r)
     else
         throw(DomainError("Only full-rank `Destabilizer` can be converted to `MixedDestabilizer` with specific rank. Try not specifying `r`."))
     end
 end
 function MixedDestabilizer(d::Destabilizer)
-    l,n = size(d.tab)
+    l,n = size(tab(d))
     if l==2n
         MixedDestabilizer(d, nqubits(d))
     else
@@ -599,9 +599,9 @@ end
 MixedDestabilizer(d::MixedStabilizer) = MixedDestabilizer(stabilizerview(d))
 MixedDestabilizer(d::MixedDestabilizer) = d
 
-Base.length(d::MixedDestabilizer) = length(d.tab)÷2
+Base.length(d::MixedDestabilizer) = length(tab(d))÷2
 
-Base.copy(d::MixedDestabilizer) = MixedDestabilizer(copy(d.tab),d.rank)
+Base.copy(d::MixedDestabilizer) = MixedDestabilizer(copy(tab(d)),rank(d))
 
 ##############################
 # Subtableau views
@@ -610,17 +610,17 @@ Base.copy(d::MixedDestabilizer) = MixedDestabilizer(copy(d.tab),d.rank)
 """A view of the subtableau corresponding to the stabilizer. See also [`tab`](@ref), [`destabilizerview`](@ref), [`logicalxview`](@ref), [`logicalzview`](@ref)"""
 @inline stabilizerview(s::Stabilizer) = s
 @inline stabilizerview(s::Destabilizer) = Stabilizer(@view tab(s)[end÷2+1:end])
-@inline stabilizerview(s::MixedStabilizer) = Stabilizer(@view tab(s)[1:s.rank])
-@inline stabilizerview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[end÷2+1:end÷2+s.rank])
+@inline stabilizerview(s::MixedStabilizer) = Stabilizer(@view tab(s)[1:rank(s)])
+@inline stabilizerview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[end÷2+1:end÷2+rank(s)])
 
 """A view of the subtableau corresponding to the destabilizer. See also [`tab`](@ref), [`stabilizerview`](@ref), [`logicalxview`](@ref), [`logicalzview`](@ref)"""
 @inline destabilizerview(s::Destabilizer) = Stabilizer(@view tab(s)[1:end÷2])
-@inline destabilizerview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[1:s.rank])
+@inline destabilizerview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[1:rank(s)])
 
 """A view of the subtableau corresponding to the logical X operators. See also [`tab`](@ref), [`stabilizerview`](@ref), [`destabilizerview`](@ref), [`logicalzview`](@ref)"""
-@inline logicalxview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[s.rank+1:end÷2])
+@inline logicalxview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[rank(s)+1:end÷2])
 """A view of the subtableau corresponding to the logical Z operators. See also [`tab`](@ref), [`stabilizerview`](@ref), [`destabilizerview`](@ref), [`logicalxview`](@ref)"""
-@inline logicalzview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[end÷2+s.rank+1:end])
+@inline logicalzview(s::MixedDestabilizer) = Stabilizer(@view tab(s)[end÷2+rank(s)+1:end])
 
 """The number of qubits of a given state."""
 @inline nqubits(s::AbstractStabilizer) = nqubits(tab(s))

src/dense_cliffords.jl

@@ -62,7 +62,7 @@ CliffordOperator(op::CliffordOperator) = op
 CliffordOperator(paulis::AbstractVector{<:PauliOperator}) = CliffordOperator(Tableau(paulis))
 CliffordOperator(destab::Destabilizer) = CliffordOperator(tab(destab))
 
-Base.:(==)(l::CliffordOperator, r::CliffordOperator) = l.tab == r.tab
+Base.:(==)(l::CliffordOperator, r::CliffordOperator) = tab(l) == tab(r)
 Base.hash(c::T, h::UInt) where {T<:CliffordOperator} = hash(T, hash(tab(c), h))
 
 Base.getindex(c::CliffordOperator, args...) = getindex(tab(c), args...)
@@ -85,16 +85,16 @@ digits_subchars = collect("₀₁₂₃₄₅₆₇₈₉")
 digits_substr(n::Int,nwidth::Int) = join(([digits_subchars[d+1] for d in reverse(digits(n, pad=nwidth))]))
 
 function Base.copy(c::CliffordOperator)
-    CliffordOperator(copy(c.tab))
+    CliffordOperator(copy(tab(c)))
 end
 
-@inline nqubits(c::CliffordOperator) = nqubits(c.tab)
+@inline nqubits(c::CliffordOperator) = nqubits(tab(c))
 
-Base.zero(c::CliffordOperator) = CliffordOperator(zero(c.tab))
+Base.zero(c::CliffordOperator) = CliffordOperator(zero(tab(c)))
 Base.zero(::Type{<:CliffordOperator}, n) = CliffordOperator(zero(Tableau, 2n, n))
 
 function Base.:(*)(l::AbstractCliffordOperator, r::CliffordOperator)
-    tab = copy(r.tab)
+    tab = copy(QuantumClifford.tab(r))
     apply!(Stabilizer(tab),l) # TODO maybe not the most elegant way to perform apply!(::Tableau, gate)
     CliffordOperator(tab)
 end
@@ -106,7 +106,7 @@ end
 
 # TODO create Base.permute! and getindex(..., permutation_array)
 function permute(c::CliffordOperator,p) # TODO this is a slow stupid implementation
-    CliffordOperator(Tableau([c.tab[i][p] for i in 1:2*nqubits(c)][vcat(p,p.+nqubits(c))]))
+    CliffordOperator(Tableau([tab(c)[i][p] for i in 1:2*nqubits(c)][vcat(p,p.+nqubits(c))]))
 end
 
 """Nonvectorized version of `apply!` used for unit tests."""

src/ecc/circuits.jl

@@ -74,6 +74,7 @@ function perm_to_transpositions(perm)
     for i in n:-1:1
         if perm[i]!=i
             j = findfirst(==(i), perm)
+            @assert !isnothing(j)
             push!(transpositions, (i, j))
             perm[j] = perm[i]
         end

src/ecc/decoder_pipeline.jl

@@ -251,7 +251,7 @@ function create_lookup_table(code::Stabilizer)
     for bit_to_be_flipped in 1:qubits
         for error_type in [single_x, single_y, single_z]
             # Generate e⃗
-            error = error_type(qubits, bit_to_be_flipped)
+            error = error_type(qubits, bit_to_be_flipped)::PauliOperator{Array{UInt8, 0}, Vector{UInt}}
             # Calculate s⃗
             # (check which stabilizer rows do not commute with the Pauli error)
             syndrome = comm(error, code)

src/fastmemlayout.jl

@@ -20,14 +20,14 @@ fastrow(t::Tableau{Tₚᵥ,Tₘ}) where {Tₚᵥ, Tₘ<:Adjoint} = Tableau(t.pha
 fastcolumn(t::Tableau{Tₚᵥ,Tₘ}) where {Tₚᵥ, Tₘ} = Tableau(t.phases, t.nqubits, collect(t.xzs')')
 fastcolumn(t::Tableau{Tₚᵥ,Tₘ}) where {Tₚᵥ, Tₘ<:Adjoint} = t
 
-fastrow(s::Stabilizer) = Stabilizer(fastrow(s.tab))
-fastcolumn(s::Stabilizer) = Stabilizer(fastcolumn(s.tab))
+fastrow(s::Stabilizer) = Stabilizer(fastrow(tab(s)))
+fastcolumn(s::Stabilizer) = Stabilizer(fastcolumn(tab(s)))
 
-fastrow(s::Destabilizer) = Destabilizer(fastrow(s.tab))
-fastcolumn(s::Destabilizer) = Destabilizer(fastcolumn(s.tab))
+fastrow(s::Destabilizer) = Destabilizer(fastrow(tab(s)))
+fastcolumn(s::Destabilizer) = Destabilizer(fastcolumn(tab(s)))
 
-fastrow(s::MixedStabilizer) = MixedStabilizer(fastrow(s.tab), s.rank)
-fastcolumn(s::MixedStabilizer) = MixedStabilizer(fastcolumn(s.tab), s.rank)
+fastrow(s::MixedStabilizer) = MixedStabilizer(fastrow(tab(s)), rank(s))
+fastcolumn(s::MixedStabilizer) = MixedStabilizer(fastcolumn(tab(s)), rank(s))
 
-fastrow(s::MixedDestabilizer) = MixedDestabilizer(fastrow(s.tab), s.rank)
-fastcolumn(s::MixedDestabilizer) = MixedDestabilizer(fastcolumn(s.tab), s.rank)
+fastrow(s::MixedDestabilizer) = MixedDestabilizer(fastrow(tab(s)), rank(s))
+fastcolumn(s::MixedDestabilizer) = MixedDestabilizer(fastcolumn(tab(s)), rank(s))

src/linalg.jl

@@ -260,7 +260,7 @@ function tensor(ops::CliffordOperator...) # TODO implement \otimes for Destabili
     last_zrow = ntot
     last_xrow = 0
     for op in ops
-        t = op.tab
+        t = QuantumClifford.tab(op)
         _, last_zrow, _ = puttableau!(tab, (@view t[end÷2+1:end]), last_zrow, last_xrow)
         _, last_xrow, _ = puttableau!(tab, (@view t[1:end÷2]), last_xrow, last_xrow)
     end

src/mul_leftright.jl

@@ -56,11 +56,14 @@ function mul_ordered_lv!(r::AbstractVector{T}, l::AbstractVector{T}; phases::Val
 end
 =#
 
+# This method is already covered by the identical but less specific one right below. (And JET does not like it)
+#=
 function mul_ordered!(r::SubArray{T,1,P,I1,L1}, l::SubArray{T,1,P,I2,L2}; phases::Val{B}=Val(true)) where {T<:Unsigned, B, I1, I2, L1, L2, P<:Adjoint}
     # This method exists because SIMD.jl does not play well with Adjoint
     # Delete it and try `QuantumClifford.mul_left!(fastcolumn(random_stabilizer(194)), 2, 1)` # works fine for 192
     _mul_ordered_nonvec!(r,l; phases=B)
 end
+=#
 
 function mul_ordered!(r::SubArray{T,1,P,I2,L2}, l::AbstractVector{T}; phases::Val{B}=Val(true)) where {T<:Unsigned, B, I2, L2, P<:Adjoint}
     # This method exists because SIMD.jl does not play well with Adjoint

src/pauli_operator.jl

@@ -77,7 +77,7 @@ function zbit(p::PauliOperator)
     [(word>>s)&one==one for word in zview(p) for s in 0:size-1][begin:p.nqubits]
 end
 
-function _P_str(a)
+function _P_str(a::Union{String,SubString{String}})
     letters = filter(x->occursin(x,"_IZXY"),a)
     phase = phasedict[strip(filter(x->!occursin(x,"_IZXY"),a))]
     PauliOperator(phase, [l=='X'||l=='Y' for l in letters], [l=='Z'||l=='Y' for l in letters])
@@ -87,7 +87,7 @@ macro P_str(a)
     quote _P_str($a) end
 end
 
-Base.getindex(p::PauliOperator{Tₚ,Tᵥ}, i::Int) where {Tₚ, Tᵥₑ<:Unsigned, Tᵥ<:AbstractVector{Tᵥₑ}} = (p.xz[_div(Tᵥₑ, i-1)+1] & Tᵥₑ(0x1)<<_mod(Tᵥₑ,i-1))!=0x0, (p.xz[end÷2+_div(Tᵥₑ,i-1)+1] & Tᵥₑ(0x1)<<_mod(Tᵥₑ,i-1))!=0x0
+Base.getindex(p::PauliOperator{Tₚ,Tᵥ}, i::Int) where {Tₚ, Tᵥₑ<:Unsigned, Tᵥ<:AbstractVector{Tᵥₑ}} = ((p.xz[_div(Tᵥₑ, i-1)+1] & Tᵥₑ(0x1)<<_mod(Tᵥₑ,i-1))!=0x0)::Bool, ((p.xz[end÷2+_div(Tᵥₑ,i-1)+1] & Tᵥₑ(0x1)<<_mod(Tᵥₑ,i-1))!=0x0)::Bool
 Base.getindex(p::PauliOperator{Tₚ,Tᵥ}, r) where {Tₚ, Tᵥₑ<:Unsigned, Tᵥ<:AbstractVector{Tᵥₑ}} = PauliOperator(p.phase[], xbit(p)[r], zbit(p)[r])
 
 function Base.setindex!(p::PauliOperator{Tₚ,Tᵥ}, (x,z)::Tuple{Bool,Bool}, i) where {Tₚ, Tᵥₑ, Tᵥ<:AbstractVector{Tᵥₑ}}
@@ -176,7 +176,8 @@ end
 function embed(n::Int, indices, p::PauliOperator)
     if nqubits(p) == length(indices)
         pout = zero(typeof(p), n)
-        @inbounds @simd for i in eachindex(indices)
+        @inbounds @simd for i_ in eachindex(indices)
+            i = i_::Int
             pout[indices[i]] = p[i]
         end
         pout.phase[] = p.phase[]

src/project_trace_reset.jl

@@ -339,7 +339,7 @@ end
 
 function _project!(d::Destabilizer,pauli::PauliOperator;keep_result::Val{Bkr}=Val(true),phases::Val{Bp}=Val(true)) where {Bkr, Bp} # repetition between Destabilizer and MixedDestabilizer, but the redundancy makes the two codes slightly simpler and easier to infer
     anticommutes = 0
-    tab = d.tab
+    tab = QuantumClifford.tab(d)
     stabilizer = stabilizerview(d)
     destabilizer = destabilizerview(d)
     r = trusted_rank(d)
@@ -377,7 +377,7 @@ end
 
 function _project!(d::MixedDestabilizer,pauli::PauliOperator;keep_result::Val{Bkr}=Val(true),phases::Val{Bp}=Val(true)) where {Bkr, Bp} # repetition between Destabilizer and MixedDestabilizer, but the redundancy makes the two codes slightly simpler and easier to infer
     anticommutes = 0
-    tab = d.tab
+    tab = QuantumClifford.tab(d)
     stabilizer = stabilizerview(d)
     destabilizer = destabilizerview(d)
     r = trusted_rank(d)
@@ -497,7 +497,7 @@ end
 """Internal method used to implement [`projectX!`](@ref), [`projectZ!`](@ref), and [`projectY!`](@ref)."""
 function project_cond!(d::MixedDestabilizer,qubit::Int,cond::Val{IS},reset::Val{RESET};keep_result::Bool=true,phases::Val{PHASES}=Val(true)) where {IS,RESET,PHASES}
     anticommutes = 0
-    tab = d.tab
+    tab = QuantumClifford.tab(d)
     stabilizer = stabilizerview(d)
     destabilizer = destabilizerview(d)
     r = d.rank
@@ -647,7 +647,7 @@ function traceout!(s::Union{MixedStabilizer, MixedDestabilizer}, qubits; phases=
     if rank return (s, i) else return s end
 end
 
-function _expand_pauli(pauli,qubits,n) # TODO rename and make public
+function _expand_pauli(pauli::PauliOperator,qubits,n) # TODO rename and make public
     expanded = zero(PauliOperator,n)
     for (ii, i) in enumerate(qubits)
         expanded[i] = pauli[ii]
@@ -886,4 +886,4 @@ See also: [`traceout!`](@ref)
 """
 function delete_columns(𝒮::Stabilizer, subset)
     return 𝒮[:, setdiff(1:nqubits(𝒮), subset)]
-end
+end

src/symbolic_cliffords.jl

@@ -203,7 +203,7 @@ SingleQubitOperator(p::sInvSQRTY)           = SingleQubitOperator(p.q, false, tr
 SingleQubitOperator(o::SingleQubitOperator) = o
 function SingleQubitOperator(op::CliffordOperator, qubit)
     nqubits(op)==1 || throw(DimensionMismatch("You are trying to convert a multiqubit `CliffordOperator` into a symbolic `SingleQubitOperator`."))
-    SingleQubitOperator(qubit,op.tab[1,1]...,op.tab[2,1]...,(~).(iszero.(op.tab.phases))...)
+    SingleQubitOperator(qubit,tab(op)[1,1]...,tab(op)[2,1]...,(~).(iszero.(tab(op).phases))...)
 end
 SingleQubitOperator(op::CliffordOperator) = SingleQubitOperator(op, 1)