Replace Base.convert(::Type{SparseArrays.SparseMatrixCSC}, J::SUNMatrix) with copyto!

Fix for #315

Proximate cause was that the SUNMatrix sparse Jacobian was not fully initialised,
hence failed the SparseMatrixCSC consistency checks introduces with
Julia 1.7

More fundamentally, given that Sundials uses zero-based index arrays,
convert(::Type{SparseArrays.SparseMatrixCSC}, J::SUNMatrix)
would either need to allocate, or is inherently unsafe as an in-place
version that applied a 1-based index conversion would create an
invalid SUNMatrix.
Also the convert code here looks like it modified colptr but
not rowptr, so couldn't have worked anyway... (cvodejac and similar
used to overwrite this, which is why those calls worked).

Author: Stuart Daines

src/common_interface/function_types.jl

@@ -65,16 +65,14 @@ function cvodejac(
     tmp3::N_Vector,
 )
     jac_prototype = funjac.jac_prototype
-    J = convert(SparseArrays.SparseMatrixCSC, _J)
-
+   
     funjac.u = unsafe_wrap(Vector{Float64}, N_VGetArrayPointer_Serial(u), length(funjac.u))
     _u = funjac.u
 
     funjac.jac(jac_prototype, _u, funjac.p, t)
-    J.nzval .= jac_prototype.nzval
-    # Sundials resets the value pointers each time, so reset it too
-    @. J.rowval = jac_prototype.rowval - 1
-    @. J.colptr = jac_prototype.colptr - 1
+
+    copyto!(_J, jac_prototype)
+    
     return CV_SUCCESS
 end
 
@@ -128,7 +126,6 @@ function idajac(
 )
 
     jac_prototype = funjac.jac_prototype
-    J = convert(SparseArrays.SparseMatrixCSC, _J)
 
     funjac.u = unsafe_wrap(Vector{Float64}, N_VGetArrayPointer_Serial(u), length(funjac.u))
     _u = funjac.u
@@ -137,10 +134,8 @@ function idajac(
     _du = funjac.du
 
     funjac.jac(jac_prototype, _du, _u, funjac.p, cj, t)
-    J.nzval .= jac_prototype.nzval
-    # Sundials resets the value pointers each time, so reset it too
-    @. J.rowval = jac_prototype.rowval - 1
-    @. J.colptr = jac_prototype.colptr - 1
+
+    copyto!(_J, jac_prototype)
 
     return IDA_SUCCESS
 end
@@ -155,10 +150,10 @@ function massmat(
 )
     if typeof(mmf.mass_matrix) <: Array
         M = convert(Matrix, _M)
+        M .= mmf.mass_matrix
     else
-        M = convert(SparseArrays.SparseMatrixCSC, _M)
+        copyto!(_M, mmf.mass_matrix)
     end
-    M .= mmf.mass_matrix
 
     return IDA_SUCCESS
 end

src/types_and_consts_additions.jl

@@ -39,19 +39,21 @@ function Base.convert(::Type{Matrix}, J::SUNMatrix)
     unsafe_wrap(Array, mat.data, (mat.M, mat.N), own = false)
 end
 
-function Base.convert(::Type{SparseArrays.SparseMatrixCSC}, J::SUNMatrix)
-    _sunmat = unsafe_load(J)
+# sparse SUNMatrix uses zero-offset indices, so provide copyto!, not convert
+function Base.copyto!(Asun::SUNMatrix, Acsc::SparseArrays.SparseMatrixCSC)
+    _sunmat = unsafe_load(Asun)
     _mat = convert(SUNMatrixContent_Sparse, _sunmat.content)
     mat = unsafe_load(_mat)
-    # own is false as memory is allocated by sundials
-    # TODO: Get rid of allocation for 1-based index change
-    rowval = unsafe_wrap(Array, mat.indexvals, (mat.NNZ), own = false)
-    colptr = unsafe_wrap(Array, mat.indexptrs, (mat.NP + 1), own = false)
-    colptr .+= 1
-    m = mat.M
-    n = mat.N
-    nzval = unsafe_wrap(Array, mat.data, (mat.NNZ), own = false)
-    SparseArrays.SparseMatrixCSC(m, n, colptr, rowval, nzval)
+    # own is false as memory is allocated by sundials    
+    indexvals = unsafe_wrap(Array, mat.indexvals, (mat.NNZ), own = false)
+    indexptrs = unsafe_wrap(Array, mat.indexptrs, (mat.NP + 1), own = false)
+    data = unsafe_wrap(Array, mat.data, (mat.NNZ), own = false)
+
+    @. indexvals = Acsc.rowval - 1
+    @. indexptrs = Acsc.colptr - 1
+    data .= Acsc.nzval
+    
+    return nothing
 end
 
 abstract type SundialsMatrix end