Move CSparse functions to separate package, take two

LICENSE.md

@@ -66,7 +66,6 @@ their own licenses:
 The following components of Julia's standard library have separate licenses:
 
 - base/fftw.jl (see [FFTW](http://fftw.org/doc/License-and-Copyright.html))
-- base/sparse/csparse.jl (LGPL-2.1+)
 - base/linalg/umfpack.jl (see [SUITESPARSE](http://faculty.cse.tamu.edu/davis/suitesparse.html))
 - base/linalg/cholmod.jl (see [SUITESPARSE](http://faculty.cse.tamu.edu/davis/suitesparse.html))
 

base/deprecated.jl

@@ -769,6 +769,25 @@ end
 @deprecate slice view
 @deprecate sub view
 
+# Point users to SuiteSparse
+function ereach{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, k::Integer, parent::Vector{Ti})
+    error(string("ereach(A, k, parent) now lives in package SuiteSparse.jl. Run",
+        "Pkg.add(\"SuiteSparse\") to install SuiteSparse on Julia v0.5."))
+end
+function etree{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, postorder::Bool)
+    error(string("etree(A[, post]) now lives in package SuiteSparse.jl. Run",
+        "Pkg.add(\"SuiteSparse\") to install SuiteSparse on Julia v0.5."))
+end
+etree(A::SparseMatrixCSC) = etree(A, false)
+function csc_permute{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, pinv::Vector{Ti}, q::Vector{Ti})
+    error(string("csc_permute(A, pinv, q) now lives in package SuiteSparse.jl. Run",
+        "Pkg.add(\"SuiteSparse\") to install SuiteSparse on Julia v0.5."))
+end
+function symperm{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, pinv::Vector{Ti})
+    error(string("symperm(A, pinv) now lives in package SuiteSparse.jl. Run,",
+        "Pkg.add(\"SuiteSparse\") to install SuiteSparse on Julia v0.5."))
+end
+
 # During the 0.5 development cycle, do not add any deprecations below this line
 # To be deprecated in 0.6
 

base/sparse/sparse.jl

@@ -36,7 +36,6 @@ export AbstractSparseArray, AbstractSparseMatrix, AbstractSparseVector,
 include("abstractsparse.jl")
 include("sparsematrix.jl")
 include("sparsevector.jl")
-include("csparse.jl")
 
 include("linalg.jl")
 if Base.USE_GPL_LIBS

contrib/add_license_to_files.jl

@@ -34,7 +34,6 @@ const skipfiles = [
     # files to check - already copyright
     # see: https://github.com/JuliaLang/julia/pull/11073#issuecomment-98099389
     "../base/special/trig.jl",
-    "../base/sparse/csparse.jl",
     "../base/linalg/givens.jl",
     #
     "../src/abi_llvm.cpp",

doc/stdlib/arrays.rst

@@ -986,18 +986,6 @@ dense counterparts. The following functions are specific to sparse arrays.
 
    Create a random sparse vector of length ``m`` or sparse matrix of size ``m`` by ``n`` with the specified (independent) probability ``p`` of any entry being nonzero, where nonzero values are sampled from the normal distribution. The optional ``rng`` argument specifies a random number generator, see :ref:`Random Numbers <random-numbers>`\ .
 
-.. function:: etree(A[, post])
-
-   .. Docstring generated from Julia source
-
-   Compute the elimination tree of a symmetric sparse matrix ``A`` from ``triu(A)`` and, optionally, its post-ordering permutation.
-
-.. function:: symperm(A, p)
-
-   .. Docstring generated from Julia source
-
-   Return the symmetric permutation of ``A``\ , which is ``A[p,p]``\ . ``A`` should be symmetric, sparse, and only contain nonzeros in the upper triangular part of the matrix is stored. This algorithm ignores the lower triangular part of the matrix. Only the upper triangular part of the result is returned.
-
 .. function:: nonzeros(A)
 
    .. Docstring generated from Julia source

test/sparsedir/sparse.jl

@@ -343,20 +343,6 @@ end
 @test full(spdiagm((ones(2), ones(2)), (0, -1), 3, 3)) ==
                        [1.0  0.0  0.0; 1.0  1.0  0.0;  0.0  1.0  0.0]
 
-# elimination tree
-## upper triangle of the pattern test matrix from Figure 4.2 of
-## "Direct Methods for Sparse Linear Systems" by Tim Davis, SIAM, 2006
-rowval = Int32[1,2,2,3,4,5,1,4,6,1,7,2,5,8,6,9,3,4,6,8,10,3,5,7,8,10,11]
-colval = Int32[1,2,3,3,4,5,6,6,6,7,7,8,8,8,9,9,10,10,10,10,10,11,11,11,11,11,11]
-A = sparse(rowval, colval, ones(length(rowval)))
-p = etree(A)
-P,post = etree(A, true)
-@test P == p
-@test P == Int32[6,3,8,6,8,7,9,10,10,11,0]
-@test post == Int32[2,3,5,8,1,4,6,7,9,10,11]
-@test isperm(post)
-
-
 # issue #4986, reinterpret
 sfe22 = speye(Float64, 2)
 mfe22 = eye(Float64, 2)
@@ -1043,13 +1029,9 @@ A = sparse(tril(rand(5,5)))
 @test istril(A)
 @test !istril(sparse(ones(5,5)))
 
-# symperm
-srand(1234321)
-A = triu(sprand(10,10,0.2))       # symperm operates on upper triangle
-perm = randperm(10)
-@test symperm(A,perm).colptr == [1,1,2,4,5,5,6,8,8,9,10]
-
 # droptol
+srand(1234321)
+A = triu(sprand(10,10,0.2))
 @test Base.droptol!(A,0.01).colptr == [1,1,1,2,2,3,4,6,6,7,9]
 @test isequal(Base.droptol!(sparse([1], [1], [1]), 1), SparseMatrixCSC(1,1,Int[1,1],Int[],Int[]))
 
@@ -1291,12 +1273,6 @@ if Base.USE_GPL_LIBS
 end
 @test_throws DimensionMismatch Base.SparseArrays.normestinv(sprand(3,5,.9))
 
-# csc_permute
-A = sprand(10,10,0.2)
-p = randperm(10)
-q = randperm(10)
-@test Base.SparseArrays.csc_permute(A, invperm(p), q) == full(A)[p, q]
-
 # issue #13008
 @test_throws ArgumentError sparse(collect(1:100), collect(1:100), fill(5,100), 5, 5)
 @test_throws ArgumentError sparse(Int[], collect(1:5), collect(1:5))