Use set!, zero!, etc. in YET more places (#1650)

Also switch to Nemo.denominator! and Nemo.numerator!,
and remove add_two! which now is equivalent to `add!(x, 2)`.

examples/Det.jl

@@ -720,7 +720,7 @@ function add_into!(A::ZZMatrix, C::ZZMatrix, c::Int)
     A_ptr = Nemo.mat_entry_ptr(A, i+c, 1)
     C_ptr = Nemo.mat_entry_ptr(C, i, 1)
     for j=1:ncols(A)
-      ccall((:fmpz_add, Nemo.libflint), Cvoid, (Ptr{ZZRingElem}, Ptr{ZZRingElem}, Ptr{ZZRingElem}), A_ptr, A_ptr, C_ptr)
+      add!(A_ptr, C_ptr)
       A_ptr += sizeof(Clong)
       C_ptr += sizeof(Clong)
     end
@@ -1247,7 +1247,7 @@ function dixon_solve(D::DixonCtx{T}, B::ZZMatrix; block::Int = 10) where T
       for i=1:nrows(D.x)
         x_ptr = Nemo.mat_entry_ptr(D.x, i, 1)
         for j=1:ncols(D.x)
-          ccall((:fmpz_addmul_si, Nemo.libflint), Cvoid, (Ptr{ZZRingElem}, Ref{ZZRingElem}, Int), x_ptr, ppow, Int(D.y_mod[i, j]))
+          addmul!(x_ptr, ppow, Int(D.y_mod[i, j]))
           x_ptr += 8
         end
       end
@@ -1302,7 +1302,7 @@ function dixon_solve(D::DixonCtx{T}, B::ZZMatrix; block::Int = 10) where T
          ccall((:fmpz_zero, Nemo.libflint), Cvoid, (Ptr{ZZRingElem},), Ay_ptr)
          for j=1:n
            y_ptr = Nemo.mat_entry_ptr(D.y_mod, j, 1)
-           ccall((:fmpz_addmul_ui, Nemo.libflint), Cvoid, (Ptr{ZZRingElem}, Ptr{ZZRingElem}, UInt), Ay_ptr, A_ptr, unsafe_load(y_ptr))
+           addmul!(Ay_ptr, A_ptr, unsafe_load(y_ptr))
            A_ptr += sizeof(ZZRingElem)
          end
        end

src/AlgAss/Elem.jl

@@ -890,7 +890,7 @@ end
 function _addmul!(M::QQMatrix, i, j, a::QQFieldElem, b::QQFieldElem, temp = nothing)
   GC.@preserve M begin
     c = mat_entry_ptr(M, i, j)
-    ccall((:fmpq_addmul, libflint), Nothing, (Ptr{QQFieldElem}, Ref{QQFieldElem}, Ref{QQFieldElem}), c, a, b)
+    addmul!(c, a, b)
   end
 end
 

src/AlgAss/Map.jl

@@ -115,7 +115,7 @@ function __set!(c_t::QQMatrix, ca)
   GC.@preserve c_t begin
     for i in 1:length(ca)
       t = mat_entry_ptr(c_t, 1, i)
-      ccall((:fmpq_set, libflint), Cvoid, (Ptr{QQFieldElem}, Ref{QQFieldElem}), t, ca[i])
+      set!(t, ca[i])
     end
   end
 end

src/AlgAssAbsOrd/PIP/bley_johnston.jl

@@ -192,7 +192,7 @@ function _is_principal_with_data_bj(I, O; side = :right, _alpha = nothing, local
 
   F = Hecke._get_a_twosided_conductor(O, M)
   # Now make corpime to conductor
- 
+
   Iorig = I
   if F == 1*O || I + F == one(A) * O
     # I should improve this
@@ -377,7 +377,7 @@ function _old_optimization(dd, local_coeffs, dec, bases_offsets_and_lengths, H,
     end
     w = local_coeffs[1][idx[1]]
     for i in 1:dd
-      ccall((:fmpq_set, libflint), Ref{Nothing}, (Ref{QQFieldElem}, Ref{QQFieldElem}), vtemp[i], w[i])
+      set!(vtemp[i], w[i])
     end
     #@show vtemp
     for j in 2:(length(dec) - 1)
@@ -404,7 +404,7 @@ function _old_optimization(dd, local_coeffs, dec, bases_offsets_and_lengths, H,
     #@show length(ids)
     for j in ids
       #for i in 1:dd
-      #  ccall((:fmpq_set, libflint), Ref{Nothing}, (Ref{QQFieldElem}, Ref{QQFieldElem}), vtemp[i], _vtempcopy[i])
+      #  set!(vtemp[i], _vtempcopy[i])
       #end
       _vtemp = deepcopy(vtemp) .+ local_coeffs[end][j]
       if all(is_integral, _vtemp)
@@ -420,7 +420,7 @@ function _old_optimization(dd, local_coeffs, dec, bases_offsets_and_lengths, H,
 end
 
 #
-function _recursive_iterator!(x, lengths, d, elts::Vector, bases_offsets, indices_integral, indices_nonintegral, k, i, vtemp)
+function _recursive_iterator!(x, lengths, d, elts::Vector, bases_offsets, indices_integral, indices_nonintegral, k, i, vtemp::Vector{QQFieldElem})
   if i > k
     println("2", x)
   elseif i == k # unroll 1-loop base case for speed
@@ -466,18 +466,18 @@ function _recursive_iterator!(x, lengths, d, elts::Vector, bases_offsets, indice
   end
 end
 
-function _is_admissible(x, i, d, elts, bases_offsets, vtemp)
+function _is_admissible(x, i, d, elts, bases_offsets, vtemp::Vector{QQFieldElem})
   # Test if x[1,...,i] is admissible
   w = elts[1][x[1]]
   for k in 1:d
-    ccall((:fmpq_set, libflint), Ref{Nothing}, (Ref{QQFieldElem}, Ref{QQFieldElem}), vtemp[k], w[k])
+    set!(vtemp[k], w[k])
   end
   #@show vtemp
   for j in 2:i
     w = elts[j][x[j]]
     #@assert all(iszero, @view w[1:bases_offsets[j][1] - 1])
     for k in bases_offsets[j][1]:d
-      add!(vtemp[k], vtemp[k], w[k])
+      add!(vtemp[k], w[k])
     end
   end
 

src/Hecke.jl

@@ -122,7 +122,7 @@ import Nemo: acb_struct, Ring, Group, Field, zzModRing, zzModRingElem, arf_struc
              FpField, acb_vec, array, acb_vec_clear, force_coerce,
              force_op, fmpz_mod_ctx_struct, divisors, is_zero_entry, IntegerUnion, remove!,
              valuation!, is_cyclo_type, is_embedded, is_maxreal_type,
-             mat_entry_ptr, factor_trial_range, set!
+             mat_entry_ptr, factor_trial_range, set!, numerator!, denominator!
 
 AbstractAlgebra.@include_deprecated_bindings()
 Nemo.@include_deprecated_bindings()

src/LinearAlgebra/LatEnum.jl

@@ -244,12 +244,12 @@ end
 
 @inline function fmpz_mat_entry_incref!(a::ZZMatrix, r::Int, c::Int)
   z = Nemo.mat_entry_ptr(a, r, c)
-  ccall((:fmpz_add_ui, libflint), Nothing, (Ptr{ZZRingElem}, Ptr{ZZRingElem}, Int), z, z, 1)
+  add!(z, 1)
 end
 
 function fmpz_mat_entry_add_ui!(a::ZZMatrix, r::Int, c::Int, v::UInt)
   z = Nemo.mat_entry_ptr(a, r, c)
-  ccall((:fmpz_add_ui, libflint), Nothing, (Ptr{ZZRingElem}, Ptr{ZZRingElem}, Int), z, z, v)
+  add!(z, v)
 end
 
 function enum_ctx_advance_level(E::enum_ctx{A,B,C}, i::Int) where {A,B,C}

src/Misc/CRT.jl

@@ -494,13 +494,13 @@ function _num_setcoeff!(a::AbsSimpleNumFieldElem, n::Int, c::UInt)
   K = a.parent
   @assert n < degree(K) && n >=0
 
-  ra = pointer_from_objref(a)
+  ra = Ptr{ZZRingElem}(pointer_from_objref(a))
 
   if degree(K) == 1
-    ccall((:fmpz_set_ui, libflint), Nothing, (Ref{Nothing}, UInt), ra, c)
+    set!(ra, c)
     ccall((:fmpq_canonicalise, libflint), Nothing, (Ref{AbsSimpleNumFieldElem}, ), a)
   elseif degree(K) == 2
-    ccall((:fmpz_set_ui, libflint), Nothing, (Ref{Nothing}, UInt), ra+n*sizeof(Int), c)
+    set!(ra+n*sizeof(Int), c)
   else
     ccall((:fmpq_poly_set_coeff_ui, libflint), Nothing, (Ref{AbsSimpleNumFieldElem}, Int, UInt), a, n, c)
    # includes canonicalisation and treatment of den.

src/Misc/Matrix.jl

@@ -243,14 +243,14 @@ function reduce_mod_hnf_ur!(a::ZZMatrix, H::ZZMatrix)
         q = ZZRingElem()
         ccall((:fmpz_fdiv_q, libflint), Nothing, (Ref{ZZRingElem}, Ref{ZZRingElem}, Ref{ZZRingElem}), q, n, m)
         #q = fdiv(a[c, j], H[i, j])
-        fl = ccall((:fmpz_is_zero, libflint), Bool, (Ref{ZZRingElem},), q)
+        fl = is_zero(q)
         if fl
           continue
         end
         for k = j:ncols(a)
           t = mat_entry_ptr(a, c, k)
           l = mat_entry_ptr(H, i, k)
-          ccall((:fmpz_submul, libflint), Nothing, (Ref{ZZRingElem}, Ref{ZZRingElem}, Ref{ZZRingElem}), t, q, l)
+          submul!(t, q, l)
           #a[c, k] = a[c, k] - q * H[i, k]
         end
       end
@@ -275,14 +275,14 @@ function reduce_mod_hnf_ll!(a::ZZMatrix, H::ZZMatrix)
         q = ZZRingElem()
         ccall((:fmpz_fdiv_q, libflint), Nothing, (Ref{ZZRingElem}, Ref{ZZRingElem}, Ref{ZZRingElem}), q, n, m)
         #q = fdiv(a[c, j], H[i, j])
-        fl = ccall((:fmpz_is_zero, libflint), Bool, (Ref{ZZRingElem},), q)
+        fl = is_zero(q)
         if fl
           continue
         end
         for k = 1:j
           t = mat_entry_ptr(a, c, k)
           l = mat_entry_ptr(H, i, k)
-          ccall((:fmpz_submul, libflint), Nothing, (Ref{ZZRingElem}, Ref{ZZRingElem}, Ref{ZZRingElem}), t, q, l)
+          submul!(t, q, l)
         end
       end
     end
@@ -486,17 +486,17 @@ function snf_for_groups(A::ZZMatrix, mod::ZZRingElem)
   GC.@preserve S R begin
     for i=1:min(nrows(S), ncols(S))
       Sii = mat_entry_ptr(S, i, i)
-      fl = ccall((:fmpz_is_one, libflint), Bool, (Ref{ZZRingElem},), Sii)
+      fl = is_one(Sii)
       if fl
         continue
       end
       for j=i+1:min(nrows(S), ncols(S))
         Sjj = mat_entry_ptr(S, j, j)
-        fl = ccall((:fmpz_is_zero, libflint), Bool, (Ref{ZZRingElem},), Sjj)
+        fl = is_zero(Sjj)
         if fl
           continue
         end
-        fl1 = ccall((:fmpz_is_zero, libflint), Bool, (Ref{ZZRingElem},), Sii)
+        fl1 = is_zero(Sii)
         if !fl1
           fl2 = Bool(ccall((:fmpz_divisible, libflint), Cint,
               (Ref{ZZRingElem}, Ref{ZZRingElem}), Sjj, Sii))
@@ -517,13 +517,13 @@ function snf_for_groups(A::ZZMatrix, mod::ZZRingElem)
         ccall((:fmpz_tdiv_qr, libflint), Nothing,
           (Ref{ZZRingElem}, Ref{ZZRingElem}, Ptr{ZZRingElem}, Ref{ZZRingElem}), a, r, Sii, g)
         #a = divexact(S[i,i], g)
-        ccall((:fmpz_set, libflint), Nothing, (Ptr{ZZRingElem}, Ref{ZZRingElem}), Sii, g)
+        set!(Sii, g)
         #S[i,i] = g
         b = ZZRingElem()
         ccall((:fmpz_tdiv_qr, libflint), Nothing,
           (Ref{ZZRingElem}, Ref{ZZRingElem}, Ptr{ZZRingElem}, Ref{ZZRingElem}), b, r, Sjj, g)
         #b = divexact(S[j,j], g)
-        ccall((:fmpz_mul, libflint), Nothing, (Ptr{ZZRingElem}, Ptr{ZZRingElem}, Ref{ZZRingElem}), Sjj, Sjj, a)
+        Sjj = mul!(Sjj, a)
         #S[j,j] *= a
         # V = [e -b ; f a];
         # so col i and j of R will be transformed. We do it naively
@@ -532,19 +532,18 @@ function snf_for_groups(A::ZZMatrix, mod::ZZRingElem)
           Rik = mat_entry_ptr(R, i, k)
           Rjk = mat_entry_ptr(R, j, k)
           aux = ZZRingElem()
-          mul!(aux, Rik, e)
-          ccall((:fmpz_addmul, libflint), Nothing, (Ref{ZZRingElem}, Ptr{ZZRingElem}, Ref{ZZRingElem}), aux, Rjk, f)
+          aux = mul!(aux, Rik, e)
+          aux = addmul!(aux, Rjk, f)
           aux1 = ZZRingElem()
-          mul!(aux1, Rjk, a)
-          ccall((:fmpz_submul, libflint), Nothing, (Ref{ZZRingElem}, Ptr{ZZRingElem}, Ref{ZZRingElem}), aux1, Rik, b)
+          aux1 = mul!(aux1, Rjk, a)
+          aux1 = submul!(aux1, Rik, b)
           set!(Rik, aux)
           set!(Rjk, aux1)
           #R[i, k], R[j, k] = e*R[i,k]+f*R[j,k], -b*R[i,k]+a*R[j,k]
         end
       end
     end
-    ccall((:fmpz_mat_transpose, libflint), Nothing,
-         (Ref{ZZMatrix}, Ref{ZZMatrix}), R, R)
+    transpose!(R)
   end
   return S, R
 end

src/NumFieldOrd/NfOrd/Ideal/Arithmetic.jl

@@ -820,7 +820,7 @@ function _idempotents_via_matrices(x::AbsNumFieldOrderIdeal, y::AbsNumFieldOrder
   @hassert :AbsNumFieldOrder 2 -z in x
   @hassert :AbsNumFieldOrder 2 1 + z in y
 
-  ccall((:fmpz_mat_zero, libflint), Nothing, (Ref{ZZMatrix}, ), V)
+  zero!(V)
 
   return -z, 1 + z
 end

src/NumFieldOrd/NfOrd/ResidueRing.jl

@@ -498,14 +498,14 @@ function is_divisible(x::AbsOrdQuoRingElem, y::AbsOrdQuoRingElem)
   for i in 2:(d + 1)
     if !iszero(V[1, i])
   #if !iszero(sub(V, 1:1, 2:(d + 1)))
-      ccall((:fmpz_mat_zero, libflint), Nothing, (Ref{ZZMatrix}, ), V)
+      zero!(V)
       return false, zero(parent(x))
     end
   end
 
   z = R(-base_ring(R)(ZZRingElem[ V[1, i] for i in (d + 2):(2*d + 1)])) # V[1, i] is always a copy
 
-  ccall((:fmpz_mat_zero, libflint), Nothing, (Ref{ZZMatrix}, ), V)
+  zero!(V)
   @hassert :AbsOrdQuoRing 1 z*y == x
   return true, z
 end
@@ -776,7 +776,7 @@ function AbstractAlgebra.gcdxx(x::AbsSimpleNumFieldOrderQuoRingElem, y::AbsSimpl
 
   @hassert :AbsOrdQuoRing 1 Q(O(1)) == u*e - (v*(-f))
 
-  ccall((:fmpz_mat_zero, libflint), Nothing, (Ref{ZZMatrix}, ), V)
+  zero!(V)
 
   return g, u, v, -f, e
 end

src/QuadForm/Enumeration.jl

@@ -313,8 +313,7 @@ function Base.iterate(C::LatEnumCtx{X, Y, elem_type}) where {X, Y, elem_type}
 
     if _short_enough
       # t1 must be a UInt
-      #z = QQFieldElem()
-      #ccall((:fmpq_set, libflint), Cvoid, (Ref{QQFieldElem}, Ref{QQFieldElem}), z, t1)
+      #z = QQFieldElem(t1)
       # Todo
       return (pp_vector(x), pp_length(len)), i
       #y = Vector{S}(undef, n)
@@ -398,8 +397,7 @@ function Base.iterate(C::LatEnumCtx{S, W, V}, it::Int) where {S, W, V}
 
     if _short_enough
       # t1 must be a UInt
-      #z = QQFieldElem()
-      #ccall((:fmpq_set, libflint), Cvoid, (Ref{QQFieldElem}, Ref{QQFieldElem}), z, t1)
+      #z = QQFieldElem(t1)
       # Todo
       #y = __clean_and_assemble(x, transform)
       #return (y, len//scale), i
@@ -504,7 +502,7 @@ function ___enumerate_cholesky(::Type{Vector}, Q::Matrix{QQFieldElem}, l::Union{
     t2 = numerator!(t2, t1)
     _short_enough = false
     if S === Int
-      _len = ccall((:fmpz_get_si, libflint), Int, (Ref{ZZRingElem}, ), t2)
+      _len = Int(t2)
       _short_enough = _len <= c
       if !(l isa Nothing)
         _short_enough = _short_enough && _len >= l
@@ -638,8 +636,6 @@ function ___enumerate_cholesky(::Type{Vector}, Q::Matrix{S}, l::Union{Int, Nothi
   end
 end
 
-@noinline _bound_error() = error("Overflow in bound computation")
-
 @inline function _compute_bounds(Ti::QQFieldElem, Qi, Ui, t1 = QQFieldElem(),
                                              t2 = ZZRingElem(),
                                              t3 = ZZRingElem(),
@@ -649,20 +645,18 @@ end
   t2 = floor!(t2, t1, t3, t4)
   t2 = isqrt!(t2, t2)
   # Now t2 = ceil(sqrt(Ti/Qi))
-  t2 = add_two!(t2, t2)
+  t2 = add!(t2, 2)
   # Now t2 = ceil(sqrt(Ti/Qi)) + 2
 
   t1 = sub!(t1, Ui, t2)
-  t1 = neg!(t1, t1)
+  t1 = neg!(t1)
   t5 = ceil!(t5, t1, t3, t4)
-  !fits(Int, t5) && _bound_error()
-  ub = ccall((:fmpz_get_si, libflint), Int, (Ref{ZZRingElem}, ), t5)
+  ub = Int(t5)  # will throw if t5 does not fit into an Int
 
   t1 = add!(t1, Ui, t2)
-  t1 = neg!(t1, t1)
+  t1 = neg!(t1)
   t5 = floor!(t5, t1, t3, t4)
-  !fits(Int, t5) && _bound_error()
-  lb = ccall((:fmpz_get_si, libflint), Int, (Ref{ZZRingElem}, ), t5) - 1
+  lb = Int(t5) - 1   # will throw if t5 does not fit into an Int
 
   return ub, lb
 end
@@ -707,10 +701,10 @@ end
 @inline function update_U!(U, QQ::Matrix{QQFieldElem}, i, n, x, t = QQFieldElem(), t2 = ZZRingElem())
   # U[i] = sum(QQ[i, j] * x[j] for j in (i + 1):n)
   s = @inbounds U[i]
-  @inbounds ccall((:fmpz_set_si, libflint), Cvoid, (Ref{ZZRingElem}, Int), t2, x[i + 1])
+  @inbounds set!(t2, x[i + 1])
   @inbounds s = mul!(s, QQ[i, i + 1], t2)
   for j in (i + 2):n
-    @inbounds ccall((:fmpz_set_si, libflint), Cvoid, (Ref{ZZRingElem}, Int), t2, x[j])
+    @inbounds set!(t2, x[j])
     @inbounds mul!(t, QQ[i, j], t2)
     s = add!(s, s, t)
     #addmul!(s, QQ[i, j], t2, t)
@@ -1021,16 +1015,6 @@ end
 #
 ################################################################################
 
-@inline function numerator!(z::ZZRingElem, y::QQFieldElem)
-  ccall((:fmpq_numerator, libflint), Cvoid, (Ref{ZZRingElem}, Ref{QQFieldElem}), z, y)
-  return z
-end
-
-@inline function denominator!(z::ZZRingElem, y::QQFieldElem)
-  ccall((:fmpq_denominator, libflint), Cvoid, (Ref{ZZRingElem}, Ref{QQFieldElem}), z, y)
-  return z
-end
-
 @inline function floor!(z::ZZRingElem, y::QQFieldElem, t0::ZZRingElem, t1::ZZRingElem)
   numerator!(t0, y)
   denominator!(t1, y)
@@ -1045,11 +1029,6 @@ end
   return z
 end
 
-@inline function add_two!(z::ZZRingElem, x::ZZRingElem)
-  add!(z, x, 2)
-  return z
-end
-
 @inline function isqrt!(z::ZZRingElem, a::ZZRingElem)
   ccall((:fmpz_sqrt, libflint), Cvoid, (Ref{ZZRingElem}, Ref{ZZRingElem}), z, a)
   return z
@@ -1059,8 +1038,4 @@ floor!(z::Int, x::Rational{Int}, y::Int, w::Int) = Int(floor(x))
 
 isqrt!(z::Int, x::Int) = isqrt(x)
 
-add_two!(z::Int, x::Int) = x + 2
-
 ceil!(z::Int, x::Rational{Int}, y::Int, w::Int) = Int(ceil(x))
-
-numerator!(z::Int, x::Rational{Int}) = numerator(x)