Move SparseArrays support to an extension (#25)

.github/workflows/Check.yml

@@ -34,19 +34,20 @@ jobs:
           Pkg.add([
               PackageSpec(name = "ExplicitImports", version = "1.9"),
               PackageSpec(name = "PartitionedArrays"),
+              PackageSpec(name = "SparseArrays"),
               PackageSpec(name = "SparseMatricesCSR"),
           ])
       - name: ExplicitImports.jl code checks
         shell: julia --project=@explicit-imports {0}
         run: |
-          using HYPRE, ExplicitImports, PartitionedArrays, SparseMatricesCSR
+          using HYPRE, ExplicitImports, PartitionedArrays, SparseArrays, SparseMatricesCSR
           # Check HYPRE
           check_no_implicit_imports(HYPRE)
           check_no_stale_explicit_imports(HYPRE)
           check_all_qualified_accesses_via_owners(HYPRE)
           check_no_self_qualified_accesses(HYPRE)
           # Check extension modules
-          for ext in (:HYPREPartitionedArrays, :HYPRESparseMatricesCSR)
+          for ext in (:HYPREPartitionedArrays, :HYPRESparseArrays, :HYPRESparseMatricesCSR)
               extmod = Base.get_extension(HYPRE, ext)
               if extmod !== nothing
                   check_no_implicit_imports(extmod)

CHANGELOG.md

@@ -11,8 +11,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
    0.5.x. ([#17], [#18])
  - CEnum.jl dependency upgraded to release series 0.5.x (release series 0.4.x still
    allowed). ([#17], [#18])
- - PartitionedArrays.jl support is now moved to a package extension. ([#23])
+ - PartitionedArrays.jl support (`PSparseMatrix`, `PVector`) is now moved to a package
- - SparseMatricesCSR.jl support is now moved to a package extension. ([#24])
+   extension. ([#23])
+ - SparseMatricesCSR.jl support (`SparseMatrixCSR`) is now moved to a package extension.
+   ([#24])
+ - SparseArrays.jl support (`SparseMatrixCSC`) is now moved to a package extension. ([#25])
 
 ## [v1.5.0] - 2023-05-26
 ### Changed
@@ -93,3 +96,5 @@ Initial release of HYPRE.jl.
 [#17]: https://github.com/fredrikekre/HYPRE.jl/issues/17
 [#18]: https://github.com/fredrikekre/HYPRE.jl/issues/18
 [#23]: https://github.com/fredrikekre/HYPRE.jl/issues/23
+[#24]: https://github.com/fredrikekre/HYPRE.jl/issues/24
+[#25]: https://github.com/fredrikekre/HYPRE.jl/issues/25

Project.toml

@@ -13,11 +13,13 @@ SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
 
 [weakdeps]
 PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
 
 [extensions]
-HYPREPartitionedArrays = ["PartitionedArrays", "SparseMatricesCSR"]
+HYPREPartitionedArrays = ["PartitionedArrays", "SparseArrays", "SparseMatricesCSR"]
-HYPRESparseMatricesCSR = "SparseMatricesCSR"
+HYPRESparseArrays = "SparseArrays"
+HYPRESparseMatricesCSR = ["SparseArrays", "SparseMatricesCSR"]
 
 [compat]
 CEnum = "0.4, 0.5"
@@ -29,8 +31,9 @@ julia = "1.6"
 [extras]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["LinearAlgebra", "PartitionedArrays", "SparseMatricesCSR", "Test"]
+test = ["LinearAlgebra", "PartitionedArrays", "SparseArrays", "SparseMatricesCSR", "Test"]

ext/HYPRESparseArrays.jl

@@ -0,0 +1,86 @@
+module HYPRESparseArrays
+
+using HYPRE.LibHYPRE: @check, HYPRE_BigInt, HYPRE_Complex, HYPRE_Int
+using HYPRE:
+    HYPRE, HYPREMatrix, HYPRESolver, HYPREVector, HYPRE_IJMatrixSetValues, Internals
+using MPI: MPI
+using SparseArrays: SparseArrays, SparseMatrixCSC, nonzeros, nzrange, rowvals
+
+##################################
+# SparseMatrixCSC -> HYPREMatrix #
+##################################
+
+function Internals.to_hypre_data(A::SparseMatrixCSC, ilower, iupper)
+    Internals.check_n_rows(A, ilower, iupper)
+    nnz = SparseArrays.nnz(A)
+    A_rows = rowvals(A)
+    A_vals = nonzeros(A)
+
+    # Initialize the data buffers HYPRE wants
+    nrows = HYPRE_Int(iupper - ilower + 1)      # Total number of rows
+    ncols = zeros(HYPRE_Int, nrows)             # Number of colums for each row
+    rows = collect(HYPRE_BigInt, ilower:iupper) # The row indices
+    cols = Vector{HYPRE_BigInt}(undef, nnz)     # The column indices
+    values = Vector{HYPRE_Complex}(undef, nnz)  # The values
+
+    # First pass to count nnz per row
+    @inbounds for j in 1:size(A, 2)
+        for i in nzrange(A, j)
+            row = A_rows[i]
+            ncols[row] += 1
+        end
+    end
+
+    # Keep track of the last index used for every row
+    lastinds = zeros(Int, nrows)
+    cumsum!((@view lastinds[2:end]), (@view ncols[1:end-1]))
+
+    # Second pass to populate the output
+    @inbounds for j in 1:size(A, 2)
+        for i in nzrange(A, j)
+            row = A_rows[i]
+            k = lastinds[row] += 1
+            val = A_vals[i]
+            cols[k] = j
+            values[k] = val
+        end
+    end
+    @assert nrows == length(ncols) == length(rows)
+    return nrows, ncols, rows, cols, values
+end
+
+# Note: keep in sync with the SparseMatrixCSR method
+function HYPRE.HYPREMatrix(comm::MPI.Comm, B::SparseMatrixCSC, ilower, iupper)
+    A = HYPREMatrix(comm, ilower, iupper)
+    nrows, ncols, rows, cols, values = Internals.to_hypre_data(B, ilower, iupper)
+    @check HYPRE_IJMatrixSetValues(A, nrows, ncols, rows, cols, values)
+    Internals.assemble_matrix(A)
+    return A
+end
+
+# Note: keep in sync with the SparseMatrixCSC method
+function HYPRE.HYPREMatrix(B::SparseMatrixCSC, ilower=1, iupper=size(B, 1))
+    return HYPREMatrix(MPI.COMM_SELF, B, ilower, iupper)
+end
+
+
+####################################
+# SparseMatrixCSC solver interface #
+####################################
+
+# Note: keep in sync with the SparseMatrixCSR method
+function HYPRE.solve(solver::HYPRESolver, A::SparseMatrixCSC, b::Vector)
+    hypre_x = HYPRE.solve(solver, HYPREMatrix(A), HYPREVector(b))
+    x = copy!(similar(b, HYPRE_Complex), hypre_x)
+    return x
+end
+
+# Note: keep in sync with the SparseMatrixCSR method
+function HYPRE.solve!(solver::HYPRESolver, x::Vector, A::SparseMatrixCSC, b::Vector)
+    hypre_x = HYPREVector(x)
+    HYPRE.solve!(solver, hypre_x, HYPREMatrix(A), HYPREVector(b))
+    copy!(x, hypre_x)
+    return x
+end
+
+end # module HYPRESparseMatricesCSR

src/HYPRE.jl

@@ -3,7 +3,6 @@
 module HYPRE
 
 using MPI: MPI
-using SparseArrays: SparseArrays, SparseMatrixCSC, nonzeros, nzrange, rowvals
 
 export HYPREMatrix, HYPREVector
 
@@ -183,9 +182,10 @@ function Base.zero(b::HYPREVector)
     return x
 end
 
-##################################
+
-# SparseMatrixCSC -> HYPREMatrix #
+#########################
-##################################
+# Vector -> HYPREVector #
+#########################
 
 function Internals.check_n_rows(A, ilower, iupper)
     if size(A, 1) != (iupper - ilower + 1)
@@ -193,63 +193,6 @@ function Internals.check_n_rows(A, ilower, iupper)
     end
 end
 
-function Internals.to_hypre_data(A::SparseMatrixCSC, ilower, iupper)
-    Internals.check_n_rows(A, ilower, iupper)
-    nnz = SparseArrays.nnz(A)
-    A_rows = rowvals(A)
-    A_vals = nonzeros(A)
-
-    # Initialize the data buffers HYPRE wants
-    nrows = HYPRE_Int(iupper - ilower + 1)      # Total number of rows
-    ncols = zeros(HYPRE_Int, nrows)             # Number of colums for each row
-    rows = collect(HYPRE_BigInt, ilower:iupper) # The row indices
-    cols = Vector{HYPRE_BigInt}(undef, nnz)     # The column indices
-    values = Vector{HYPRE_Complex}(undef, nnz)  # The values
-
-    # First pass to count nnz per row
-    @inbounds for j in 1:size(A, 2)
-        for i in nzrange(A, j)
-            row = A_rows[i]
-            ncols[row] += 1
-        end
-    end
-
-    # Keep track of the last index used for every row
-    lastinds = zeros(Int, nrows)
-    cumsum!((@view lastinds[2:end]), (@view ncols[1:end-1]))
-
-    # Second pass to populate the output
-    @inbounds for j in 1:size(A, 2)
-        for i in nzrange(A, j)
-            row = A_rows[i]
-            k = lastinds[row] += 1
-            val = A_vals[i]
-            cols[k] = j
-            values[k] = val
-        end
-    end
-    @assert nrows == length(ncols) == length(rows)
-    return nrows, ncols, rows, cols, values
-end
-
-# Note: keep in sync with the SparseMatrixCSR method
-function HYPREMatrix(comm::MPI.Comm, B::SparseMatrixCSC, ilower, iupper)
-    A = HYPREMatrix(comm, ilower, iupper)
-    nrows, ncols, rows, cols, values = Internals.to_hypre_data(B, ilower, iupper)
-    @check HYPRE_IJMatrixSetValues(A, nrows, ncols, rows, cols, values)
-    Internals.assemble_matrix(A)
-    return A
-end
-
-# Note: keep in sync with the SparseMatrixCSC method
-function HYPREMatrix(B::SparseMatrixCSC, ilower=1, iupper=size(B, 1))
-    return HYPREMatrix(MPI.COMM_SELF, B, ilower, iupper)
-end
-
-#########################
-# Vector -> HYPREVector #
-#########################
-
 function Internals.to_hypre_data(x::Vector, ilower, iupper)
     Internals.check_n_rows(x, ilower, iupper)
     indices = collect(HYPRE_BigInt, ilower:iupper)
@@ -475,6 +418,7 @@ include("solver_options.jl")
 # Compatibility for Julias that doesn't support package extensions
 if !(isdefined(Base, :get_extension))
     include("../ext/HYPREPartitionedArrays.jl")
+    include("../ext/HYPRESparseArrays.jl")
     include("../ext/HYPRESparseMatricesCSR.jl")
 end
 

src/solvers.jl

@@ -51,26 +51,6 @@ See also [`solve`](@ref).
 solve!(pcg::HYPRESolver, x::HYPREVector, A::HYPREMatrix, ::HYPREVector)
 
 
-####################################
-# SparseMatrixCSC solver interface #
-####################################
-
-# Note: keep in sync with the SparseMatrixCSR method
-function solve(solver::HYPRESolver, A::SparseMatrixCSC, b::Vector)
-    hypre_x = solve(solver, HYPREMatrix(A), HYPREVector(b))
-    x = copy!(similar(b, HYPRE_Complex), hypre_x)
-    return x
-end
-
-# Note: keep in sync with the SparseMatrixCSR method
-function solve!(solver::HYPRESolver, x::Vector, A::SparseMatrixCSC, b::Vector)
-    hypre_x = HYPREVector(x)
-    solve!(solver, hypre_x, HYPREMatrix(A), HYPREVector(b))
-    copy!(x, hypre_x)
-    return x
-end
-
-
 #####################################
 ## Concrete solver implementations ##
 #####################################