Move SuiteSparse to stdlib (#24648)

Remove CHOLMOD stuff from precompile.jl Move unexported SparseArrays increment and decrement APIs to SuiteSparse Update SuiteSparse tests Add license text to new files.
JuliaLang · Nov 24, 2017 · f663bae · f663bae
1 parent 99f9d9a
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Showing 17 changed files with 71 additions and 56 deletions.
diff --git a/base/precompile.jl b/base/precompile.jl
@@ -10,9 +10,6 @@
 
 precompile(Tuple{typeof(Base.pointer), Array{UInt8, 1}, UInt64})
 precompile(Tuple{typeof(Base.convert), Type{Ptr{Int32}}, Ptr{UInt8}})
-if USE_GPL_LIBS
-precompile(Tuple{typeof(Base.SparseArrays.CHOLMOD.set_print_level), Array{UInt8, 1}, Int64})
-end
 precompile(Tuple{Type{Base.Multimedia.TextDisplay}, Base.TTY})
 precompile(Tuple{typeof(Base._start)})
 precompile(Tuple{typeof(Base.copy!), Array{String, 1}, Int64, Array{Any, 1}, Int64, Int64})

diff --git a/base/sparse/linalg.jl b/base/sparse/linalg.jl
@@ -2,22 +2,6 @@
 
 import Base.LinAlg: checksquare
 
-## Functions to switch to 0-based indexing to call external sparse solvers
-
-# Convert from 1-based to 0-based indices
-function decrement!(A::AbstractArray{T}) where T<:Integer
-    for i in 1:length(A); A[i] -= oneunit(T) end
-    A
-end
-decrement(A::AbstractArray{<:Integer}) = decrement!(copy(A))
-
-# Convert from 0-based to 1-based indices
-function increment!(A::AbstractArray{T}) where T<:Integer
-    for i in 1:length(A); A[i] += oneunit(T) end
-    A
-end
-increment(A::AbstractArray{<:Integer}) = increment!(copy(A))
-
 ## sparse matrix multiplication
 
 function (*)(A::SparseMatrixCSC{TvA,TiA}, B::SparseMatrixCSC{TvB,TiB}) where {TvA,TiA,TvB,TiB}

diff --git a/base/sparse/sparse.jl b/base/sparse/sparse.jl
@@ -38,12 +38,6 @@ include("abstractsparse.jl")
 include("sparsematrix.jl")
 include("sparsevector.jl")
 include("higherorderfns.jl")
-
 include("linalg.jl")
-if Base.USE_GPL_LIBS
-    include("umfpack.jl")
-    include("cholmod.jl")
-    include("spqr.jl")
-end
 
 end
diff --git a/base/sysimg.jl b/base/sysimg.jl
@@ -488,6 +488,7 @@ unshift!(Base._included_files, (@__MODULE__, joinpath(@__DIR__, "sysimg.jl")))
 Base.require(:DelimitedFiles)
 Base.require(:Test)
 Base.require(:Dates)
+Base.require(:SuiteSparse)
 
 empty!(LOAD_PATH)
 

diff --git a/doc/src/manual/linear-algebra.md b/doc/src/manual/linear-algebra.md
@@ -275,7 +275,6 @@ of the standard library documentation.
 | `CholeskyPivoted` | [Pivoted](https://en.wikipedia.org/wiki/Pivot_element) Cholesky factorization                                  |
 | `LU`              | [LU factorization](https://en.wikipedia.org/wiki/LU_decomposition)                                             |
 | `LUTridiagonal`   | LU factorization for [`Tridiagonal`](@ref) matrices                                                            |
-| `UmfpackLU`       | LU factorization for sparse matrices (computed by UMFPack)                                                     |
 | `QR`              | [QR factorization](https://en.wikipedia.org/wiki/QR_decomposition)                                             |
 | `QRCompactWY`     | Compact WY form of the QR factorization                                                                        |
 | `QRPivoted`       | Pivoted [QR factorization](https://en.wikipedia.org/wiki/QR_decomposition)                                     |

diff --git a/stdlib/SuiteSparse/src/SuiteSparse.jl b/stdlib/SuiteSparse/src/SuiteSparse.jl
@@ -0,0 +1,30 @@
+# This file is a part of Julia. License is MIT: https://julialang.org/license
+
+module SuiteSparse
+
+import Base: At_ldiv_B, Ac_ldiv_B, A_ldiv_B!
+import Base.LinAlg: At_ldiv_B!, Ac_ldiv_B!, A_rdiv_B!, A_rdiv_Bc!
+
+## Functions to switch to 0-based indexing to call external sparse solvers
+
+# Convert from 1-based to 0-based indices
+function decrement!(A::AbstractArray{T}) where T<:Integer
+    for i in 1:length(A); A[i] -= oneunit(T) end
+    A
+end
+decrement(A::AbstractArray{<:Integer}) = decrement!(copy(A))
+
+# Convert from 0-based to 1-based indices
+function increment!(A::AbstractArray{T}) where T<:Integer
+    for i in 1:length(A); A[i] += oneunit(T) end
+    A
+end
+increment(A::AbstractArray{<:Integer}) = increment!(copy(A))
+
+if Base.USE_GPL_LIBS
+    include("umfpack.jl")
+    include("cholmod.jl")
+    include("spqr.jl")
+end
+
+end # module SuiteSparse
diff --git a/base/sparse/cholmod.jl → stdlib/SuiteSparse/src/cholmod.jl b/base/sparse/cholmod.jl → stdlib/SuiteSparse/src/cholmod.jl
@@ -16,8 +16,9 @@ export
     Factor,
     Sparse
 
-import ..SparseArrays: AbstractSparseMatrix, SparseMatrixCSC, increment, indtype, sparse,
-    spzeros, nnz
+import ..SparseArrays: AbstractSparseMatrix, SparseMatrixCSC, indtype, sparse, spzeros, nnz
+
+import ..increment, ..increment!, ..decrement, ..decrement!
 
 #########
 # Setup #

diff --git a/base/sparse/cholmod_h.jl → stdlib/SuiteSparse/src/cholmod_h.jl b/base/sparse/cholmod_h.jl → stdlib/SuiteSparse/src/cholmod_h.jl
diff --git a/base/sparse/spqr.jl → stdlib/SuiteSparse/src/spqr.jl b/base/sparse/spqr.jl → stdlib/SuiteSparse/src/spqr.jl
@@ -22,8 +22,8 @@ const ORDERING_BESTAMD = Int32(9) # try COLAMD and AMD; pick best#
 # the best of AMD and METIS. METIS is not tried if it isn't installed.
 
 using ..SparseArrays: SparseMatrixCSC
-using ..SparseArrays.CHOLMOD
-using ..SparseArrays.CHOLMOD: change_stype!, free!
+using ..SuiteSparse.CHOLMOD
+using ..SuiteSparse.CHOLMOD: change_stype!, free!
 
 function _qr!(ordering::Integer, tol::Real, econ::Integer, getCTX::Integer,
         A::Sparse{Tv},

diff --git a/base/sparse/umfpack.jl → stdlib/SuiteSparse/src/umfpack.jl b/base/sparse/umfpack.jl → stdlib/SuiteSparse/src/umfpack.jl
@@ -8,7 +8,9 @@ import Base: (\), Ac_ldiv_B, At_ldiv_B, findnz, getindex, show, size
 import Base.LinAlg: A_ldiv_B!, Ac_ldiv_B!, At_ldiv_B!, Factorization, det, lufact
 
 using ..SparseArrays
-import ..SparseArrays: increment, increment!, decrement, decrement!, nnz
+import ..SparseArrays: nnz
+
+import ..increment, ..increment!, ..decrement, ..decrement!
 
 include("umfpack_h.jl")
 struct MatrixIllConditionedException <: Exception

diff --git a/base/sparse/umfpack_h.jl → stdlib/SuiteSparse/src/umfpack_h.jl b/base/sparse/umfpack_h.jl → stdlib/SuiteSparse/src/umfpack_h.jl
diff --git a/test/sparse/cholmod.jl → stdlib/SuiteSparse/test/cholmod.jl b/test/sparse/cholmod.jl → stdlib/SuiteSparse/test/cholmod.jl
@@ -1,6 +1,6 @@
 # This file is a part of Julia. License is MIT: https://julialang.org/license
 
-using Base.SparseArrays.CHOLMOD
+using SuiteSparse.CHOLMOD
 using DelimitedFiles
 using Test
 
@@ -328,8 +328,8 @@ end
     A1pdSparse = CHOLMOD.Sparse(
         A1pd.m,
         A1pd.n,
-        Base.SparseArrays.decrement(A1pd.colptr),
-        Base.SparseArrays.decrement(A1pd.rowval),
+        SuiteSparse.decrement(A1pd.colptr),
+        SuiteSparse.decrement(A1pd.rowval),
         A1pd.nzval)
 
     ## High level interface
@@ -584,7 +584,7 @@ end
         Asp = As[p,p]
         LDp = sparse(ldltfact(Asp, perm=[1,2,3])[:LD])
         # LDp = sparse(Fs[:LD])
-        Lp, dp = Base.SparseArrays.CHOLMOD.getLd!(copy(LDp))
+        Lp, dp = SuiteSparse.CHOLMOD.getLd!(copy(LDp))
         Dp = sparse(Diagonal(dp))
         @test Fs\b ≈ Af\b
         @test Fs[:UP]\(Fs[:PtLD]\b) ≈ Af\b
@@ -634,7 +634,7 @@ end
 end
 
 @testset "Issue 14134" begin
-    A = SparseArrays.CHOLMOD.Sparse(sprandn(10,5,0.1) + I |> t -> t't)
+    A = CHOLMOD.Sparse(sprandn(10,5,0.1) + I |> t -> t't)
     b = IOBuffer()
     serialize(b, A)
     seekstart(b)
@@ -655,9 +655,9 @@ end
 end
 
 @testset "Issue with promotion during conversion to CHOLMOD.Dense" begin
-    @test SparseArrays.CHOLMOD.Dense(ones(Float32, 5)) == ones(5, 1)
-    @test SparseArrays.CHOLMOD.Dense(ones(Int, 5)) == ones(5, 1)
-    @test SparseArrays.CHOLMOD.Dense(ones(Complex{Float32}, 5, 2)) == ones(5, 2)
+    @test CHOLMOD.Dense(ones(Float32, 5)) == ones(5, 1)
+    @test CHOLMOD.Dense(ones(Int, 5)) == ones(5, 1)
+    @test CHOLMOD.Dense(ones(Complex{Float32}, 5, 2)) == ones(5, 2)
 end
 
 @testset "Further issue with promotion #14894" begin
@@ -724,7 +724,7 @@ end
 
 @testset "Check that Symmetric{SparseMatrixCSC} can be constructed from CHOLMOD.Sparse" begin
     A = sprandn(10, 10, 0.1)
-    B = SparseArrays.CHOLMOD.Sparse(A)
+    B = CHOLMOD.Sparse(A)
     C = B'B
     # Change internal representation to symmetric (upper/lower)
     o = fieldoffset(CHOLMOD.C_Sparse{eltype(C)}, find(fieldnames(CHOLMOD.C_Sparse{eltype(C)}) .== :stype)[1])

diff --git a/stdlib/SuiteSparse/test/runtests.jl b/stdlib/SuiteSparse/test/runtests.jl
@@ -0,0 +1,10 @@
+# This file is a part of Julia. License is MIT: https://julialang.org/license
+
+using Test
+using SuiteSparse
+
+if Base.USE_GPL_LIBS
+   include("umfpack.jl")
+   include("cholmod.jl")
+   include("spqr.jl")
+end
diff --git a/test/sparse/spqr.jl → stdlib/SuiteSparse/test/spqr.jl b/test/sparse/spqr.jl → stdlib/SuiteSparse/test/spqr.jl
@@ -1,7 +1,7 @@
 # This file is a part of Julia. License is MIT: https://julialang.org/license
 
-using Base.SparseArrays.SPQR
-using Base.SparseArrays.CHOLMOD
+using SuiteSparse.SPQR
+using SuiteSparse.CHOLMOD
 
 @testset "Sparse QR" begin
 m, n = 100, 10

diff --git a/test/sparse/umfpack.jl → stdlib/SuiteSparse/test/umfpack.jl b/test/sparse/umfpack.jl → stdlib/SuiteSparse/test/umfpack.jl
@@ -7,15 +7,15 @@
 
     # based on deps/Suitesparse-4.0.2/UMFPACK/Demo/umfpack_di_demo.c
 
-    using Base.SparseArrays.UMFPACK.increment!
+    using SuiteSparse.increment!
 
     A0 = sparse(increment!([0,4,1,1,2,2,0,1,2,3,4,4]),
                 increment!([0,4,0,2,1,2,1,4,3,2,1,2]),
                 [2.,1.,3.,4.,-1.,-3.,3.,6.,2.,1.,4.,2.], 5, 5)
 
     @testset "Core functionality for $Tv elements" for Tv in (Float64, Complex128)
         # We might be able to support two index sizes one day
-        for Ti in Base.uniontypes(Base.SparseArrays.UMFPACK.UMFITypes)
+        for Ti in Base.uniontypes(SuiteSparse.UMFPACK.UMFITypes)
             A = convert(SparseMatrixCSC{Tv,Ti}, A0)
             lua = lufact(A)
             @test nnz(lua) == 18
@@ -31,7 +31,7 @@
 
             @test A*x ≈ b
             z = complex.(b)
-            x = Base.SparseArrays.A_ldiv_B!(lua, z)
+            x = SuiteSparse.A_ldiv_B!(lua, z)
             @test x ≈ float([1:5;])
             @test z === x
             y = similar(z)
@@ -46,22 +46,22 @@
 
             @test A'*x ≈ b
             z = complex.(b)
-            x = Base.SparseArrays.Ac_ldiv_B!(lua, z)
+            x = SuiteSparse.Ac_ldiv_B!(lua, z)
             @test x ≈ float([1:5;])
             @test x === z
             y = similar(x)
-            Base.SparseArrays.Ac_ldiv_B!(y, lua, complex.(b))
+            SuiteSparse.Ac_ldiv_B!(y, lua, complex.(b))
             @test y ≈ x
 
             @test A'*x ≈ b
             x = lua.'\b
             @test x ≈ float([1:5;])
 
             @test A.'*x ≈ b
-            x = Base.SparseArrays.At_ldiv_B!(lua,complex.(b))
+            x = SuiteSparse.At_ldiv_B!(lua,complex.(b))
             @test x ≈ float([1:5;])
             y = similar(x)
-            Base.SparseArrays.At_ldiv_B!(y, lua,complex.(b))
+            SuiteSparse.At_ldiv_B!(y, lua,complex.(b))
             @test y ≈ x
 
             @test A.'*x ≈ b
@@ -73,7 +73,7 @@
 
     @testset "More tests for complex cases" begin
         Ac0 = complex.(A0,A0)
-        for Ti in Base.uniontypes(Base.SparseArrays.UMFPACK.UMFITypes)
+        for Ti in Base.uniontypes(SuiteSparse.UMFPACK.UMFITypes)
             Ac = convert(SparseMatrixCSC{Complex128,Ti}, Ac0)
             x  = complex.(ones(size(Ac, 1)), ones(size(Ac,1)))
             lua = lufact(Ac)
@@ -142,9 +142,9 @@
 
     @testset "Test aliasing" begin
         a = rand(5)
-        @test_throws ArgumentError Base.SparseArrays.UMFPACK.solve!(a, lufact(sparse(1.0I, 5, 5)), a, Base.SparseArrays.UMFPACK.UMFPACK_A)
+        @test_throws ArgumentError SuiteSparse.UMFPACK.solve!(a, lufact(sparse(1.0I, 5, 5)), a, SuiteSparse.UMFPACK.UMFPACK_A)
         aa = complex(a)
-        @test_throws ArgumentError Base.SparseArrays.UMFPACK.solve!(aa, lufact(sparse((1.0im)I, 5, 5)), aa, Base.SparseArrays.UMFPACK.UMFPACK_A)
+        @test_throws ArgumentError SuiteSparse.UMFPACK.solve!(aa, lufact(sparse((1.0im)I, 5, 5)), aa, SuiteSparse.UMFPACK.UMFPACK_A)
     end
 
     @testset "Issues #18246,18244 - lufact sparse pivot" begin

diff --git a/test/choosetests.jl b/test/choosetests.jl
@@ -102,9 +102,6 @@ function choosetests(choices = [])
     end
 
     sparsetests = ["sparse/sparse", "sparse/sparsevector", "sparse/higherorderfns"]
-    if Base.USE_GPL_LIBS
-        append!(sparsetests, ["sparse/umfpack", "sparse/cholmod", "sparse/spqr"])
-    end
     if "sparse" in skip_tests
         filter!(x -> (x != "sparse" && !(x in sparsetests)), tests)
     elseif "sparse" in tests

diff --git a/test/compile.jl b/test/compile.jl
@@ -218,7 +218,7 @@ try
                                     [:Base, :Core, Foo2_module, FooBase_module, :Main, :Test]),
                                # plus modules included in the system image
                                Dict(s => Base.module_uuid(Base.root_module(s)) for s in
-                                    [:DelimitedFiles, :Mmap, :Base64, :Dates]))
+                                    [:DelimitedFiles, :Mmap, :Base64, :Dates, :SuiteSparse]))
         @test discard_module.(deps) == deps1
 
         @test current_task()(0x01, 0x4000, 0x30031234) == 2