Cleaning linbox interface of Matrix_integer_dense

src/doc/en/reference/libs/index.rst

@@ -41,6 +41,7 @@ to be aware of the modules described in this chapter.
    sage/libs/singular/groebner_strategy
    sage/libs/ppl
    sage/libs/linbox/linbox
+   sage/libs/linbox/linbox_flint_interface
    sage/libs/flint/flint
    sage/libs/flint/fmpz_poly
    sage/libs/flint/arith

src/sage/libs/linbox/linbox.pyx

@@ -5,6 +5,9 @@
 
 r"""
 Linbox interface
+
+The interface :class:`Linbox_integer_dense` to dense matrices is deprecated. One
+would better use :mod:`~sage.libs.linbox.linbox_flint_interface`
 """
 
 ## NOTE: The sig_on()/sig_off() stuff can't go in here -- it has to be in the
@@ -83,17 +86,30 @@ cdef extern from "linbox/linbox-sage.h":
                                         size_t nrows, size_t ncols)
 
 cdef class Linbox_integer_dense:
+    r"""
+    .. WARNING::
+
+        deprecated class
+    """
     cdef set(self, mpz_t** matrix, size_t nrows, size_t ncols):
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         self.nrows = nrows
         self.ncols = ncols
         self.matrix = matrix
 
     def minpoly(self):
         """
+        Deprecated
+
         OUTPUT:
 
         coefficients of minpoly as a Python list
         """
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         cdef mpz_t* poly
         cdef size_t degree
         verbose("using linbox poly comp")
@@ -113,10 +129,15 @@ cdef class Linbox_integer_dense:
 
     def charpoly(self):
         """
+        Deprecated
+
         OUTPUT:
 
         coefficients of charpoly or minpoly as a Python list
         """
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         cdef mpz_t* poly
         cdef size_t degree
         verbose("using linbox poly comp")
@@ -138,27 +159,41 @@ cdef class Linbox_integer_dense:
                                 mpz_t **ans,
                                 mpz_t **B,
                                 size_t B_nr, size_t B_nc):
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         cdef int e
         e = linbox_integer_dense_matrix_matrix_multiply(ans, self.matrix,  B, self.nrows, self.ncols, B_nc)
         if e:
             raise RuntimeError("error doing matrix matrix multiply over ZZ using linbox")
 
 
     cdef unsigned long rank(self) except -1:
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         return linbox_integer_dense_rank(self.matrix, self.nrows, self.ncols)
 
     def det(self):
         """
+        Deprecated
+
         OUTPUT:
 
         determinant as a sage Integer
         """
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         cdef Integer z
         z = Integer()
         linbox_integer_dense_det(z.value, self.matrix, self.nrows, self.ncols)
         return z
 
     def smithform(self):
+        from sage.misc.superseded import deprecation
+        deprecation(111111, "sage.libs.linbox.linbox.Linbox_integer_dense is deprecated, use sage.libs.linbox.linbox_flint_interface instead")
+
         raise NotImplementedError
         #cdef mpz_t* v
         #linbox_integer_dense_smithform(&v, self.matrix, self.nrows, self.ncols)

src/sage/libs/linbox/linbox_flint_interface.pxd

@@ -0,0 +1,16 @@
+from sage.libs.flint.types cimport fmpz_t, fmpz_mat_t, fmpz_poly_t
+
+# set C <- A * B
+cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B)
+
+# set cp to the characteristic polynomial of A
+cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A)
+
+# set mp to the minimal polynomial of A
+cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A)
+
+# return the rank of A
+cdef unsigned long linbox_fmpz_mat_rank(fmpz_mat_t A)
+
+# set det to the determinant of A
+cdef void linbox_fmpz_mat_det(fmpz_t det, fmpz_mat_t A)

src/sage/libs/linbox/linbox_flint_interface.pyx

@@ -0,0 +1,240 @@
+# distutils: extra_compile_args = LINBOX_CFLAGS
+# distutils: libraries = LINBOX_LIBRARIES
+# distutils: library_dirs = LINBOX_LIBDIR
+# distutils: language = c++
+r"""
+Interface between flint matrices and linbox
+
+This module only contains C++ code (and the interface is fully C
+compatible). It basically contains what used to be in the LinBox
+source code under interfaces/sage/linbox-Sage.C written by M. Albrecht
+and C. Pernet. The functions available are:
+
+- ``void  linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B)``: set
+  ``C`` to be the result of the multiplication ``A * B``
+
+- ``void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A)``: set ``cp``
+  to be the characteristic polynomial of the square matrix ``A``
+
+- ``void  linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A)``: set ``mp``
+  to be the minimal polynomial of the square matrix ``A``
+
+- ``unsigned long linbox_fmpz_mat_rank(fmpz_mat_t A)``: return the rank of the
+  matrix ``A``
+
+- ``void linbox_fmpz_mat_det(fmpz_t det, fmpz_mat_t A)``: set ``det`` to the
+  determinat of the square matrix ``A``
+"""
+#*****************************************************************************
+#       Copyright (C) 2007 Martin Albrecht
+#       Copyright (C) 2008 Clement Pernet
+#       Copyright (C) 2017 Vincent Delecroix
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  http://www.gnu.org/licenses/
+#*****************************************************************************
+
+from sage.libs.gmp.types cimport mpz_t, mpz_srcptr, mpz_ptr
+from sage.libs.gmp.mpz cimport mpz_set
+from sage.libs.flint.types cimport fmpz, fmpz_t
+from sage.libs.flint.fmpz cimport fmpz_get_mpz, fmpz_set_mpz
+from sage.libs.flint.fmpz_mat cimport fmpz_mat_entry, fmpz_mat_nrows, fmpz_mat_ncols
+from sage.libs.flint.fmpz_poly cimport fmpz_poly_set_coeff_mpz, fmpz_poly_fit_length, _fmpz_poly_set_length
+
+cdef extern from "givaro/givconfig.h":
+    pass
+cdef extern from "linbox/linbox-config.h":
+    pass
+
+cdef extern from "gmp++/gmp++.h":
+    cdef cppclass GivaroInteger "Givaro::Integer":
+        mpz_srcptr get_mpz()
+
+cdef extern from "linbox/matrix/dense-matrix.h":
+    ## template <class _Field>
+    ## using DenseMatrix = BlasMatrix<_Field> ;
+    ##
+    # indirect include from linbox/matrix/densematrix/blas-matrix.h
+    ##
+    ## template <class _Field, class _Storage>
+    ## class BlasMatrix
+    cdef cppclass LinBoxIntegerDenseMatrix "LinBox::DenseMatrix<Givaro::ZRing<Givaro::Integer>>":
+        ctypedef GivaroIntegerRing Field
+        ctypedef GivaroInteger Element
+        size_t rowdim()
+        size_t coldim()
+        LinBoxIntegerDenseMatrix(Field &F, size_t m, size_t n)
+        void setEntry(size_t i, size_t j, Element &a)
+        Element &getEntry(size_t i, size_t j)
+
+cdef extern from "givaro/zring.h":
+    cdef cppclass GivaroIntegerRing "Givaro::ZRing<Givaro::Integer>":
+        ctypedef GivaroInteger Element
+
+cdef extern from "givaro/givspyinteger.h":
+    cdef cppclass GivaroSpyInteger "Givaro::SpyInteger":
+        mpz_ptr get_mpz(GivaroInteger& i)
+        mpz_srcptr get_mpz_const(const GivaroInteger& i)
+
+cdef extern from "givaro/givpoly1.h":
+    ## template < typename T, typename A=std::allocator<T> >
+    ## class givvector : public __GIV_STANDARD_VECTOR<T,A>
+    cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]:
+        T& operator[](size_t i)
+        size_t size()
+
+cdef extern from "linbox/ring/givaro-polynomial.h":
+    ## template <class Domain, class StorageTag= Givaro::Dense>
+    ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
+    cdef cppclass LinBoxIntegerPolynomialRing "LinBox::GivPolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>":
+        ctypedef givvector[GivaroInteger] Element
+        ctypedef givvector[GivaroInteger] Polynomial
+
+cdef extern from "linbox/matrix/matrix-domain.h":
+    ## template <class Field_ >
+    ## class MatrixDomain : public MVProductDomain<Field_> {
+    cdef cppclass LinBoxIntegerDenseMatrixDomain "LinBox::MatrixDomain<Givaro::ZRing<Givaro::Integer>>":
+        LinBoxIntegerDenseMatrixDomain(GivaroIntegerRing&)
+        LinBoxIntegerDenseMatrix& mul(LinBoxIntegerDenseMatrix ans,
+                                      LinBoxIntegerDenseMatrix left,
+                                      LinBoxIntegerDenseMatrix right)
+
+cdef extern from "linbox/solutions/charpoly.h":
+    ## template<class Blackbox, class Polynomial>
+    ## Polynomial &charpoly (Polynomial & P, const Blackbox & A)
+    LinBoxIntegerPolynomialRing.Element& LinBoxIntegerDense_charpoly "LinBox::charpoly" (LinBoxIntegerPolynomialRing.Element&, LinBoxIntegerDenseMatrix&)
+
+cdef extern from "linbox/solutions/minpoly.h":
+    ## template<class Polynomial, class Blackbox>
+    ## Polynomial &minpoly (Polynomial & P, const Blackbox & A)
+    LinBoxIntegerPolynomialRing.Element& LinBoxIntegerDense_minpoly "LinBox::minpoly" (LinBoxIntegerPolynomialRing.Element&, LinBoxIntegerDenseMatrix&)
+
+cdef extern from "linbox/solutions/rank.h":
+    ## template <class Blackbox, class Method, class DomainCategory>
+    ## inline unsigned long &rank (unsigned long &r, const Blackbox &A,
+    ##                             const DomainCategory &tag, const Method &M);
+    unsigned long & LinBoxIntegerDense_rank "LinBox::rank" (unsigned long &, LinBoxIntegerDenseMatrix)
+
+cdef extern from "linbox/solutions/det.h":
+    GivaroInteger& LinBoxIntegerDense_det "LinBox::det" (GivaroInteger&, LinBoxIntegerDenseMatrix)
+
+
+
+###############################################################################
+# end of LinBox declarations -- begining of the code                          #
+###############################################################################
+
+
+cdef GivaroSpyInteger spy
+
+# set the entries of A from m (no allocation preformed)
+# NOTE: this function is not part of the interface (ie the .pxd file) to keep the
+# module C-compatible
+cdef void fmpz_mat_get_linbox(LinBoxIntegerDenseMatrix * A, fmpz_mat_t m):
+    "Set the entries of A to m"
+    cdef size_t i,j
+    cdef GivaroInteger t
+
+    for i in range(fmpz_mat_nrows(m)):
+        for j in range(fmpz_mat_ncols(m)):
+            fmpz_get_mpz(<mpz_t> spy.get_mpz(t), fmpz_mat_entry(m, i, j))
+            A.setEntry(i, j, t)
+
+
+# set the entries of m from A (no allocation performed)
+# NOTE: this function is not part of the interface (ie the .pxd file) to keep the
+# module C-compatible
+cdef void fmpz_mat_set_linbox(fmpz_mat_t m, LinBoxIntegerDenseMatrix *A):
+    "Set the entries of m to A"
+    cdef size_t i,j
+    for i in range(A.rowdim()):
+        for j in range(A.coldim()):
+            fmpz_set_mpz(fmpz_mat_entry(m, i, j), <mpz_t> spy.get_mpz(A.getEntry(i, j)))
+
+
+# set C <- A * B
+cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B):
+    cdef GivaroIntegerRing ZZ
+    cdef LinBoxIntegerDenseMatrix *LBA
+    cdef LinBoxIntegerDenseMatrix *LBB
+    cdef LinBoxIntegerDenseMatrix *LBC
+
+    LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
+    fmpz_mat_get_linbox(LBA, A)
+
+    LBB = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(B), fmpz_mat_ncols(B))
+    fmpz_mat_get_linbox(LBB, B)
+
+    LBC = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(B))
+
+    cdef LinBoxIntegerDenseMatrixDomain * MD
+    MD = new LinBoxIntegerDenseMatrixDomain(ZZ)
+    MD.mul(LBC[0], LBA[0], LBB[0])
+    del MD
+
+    fmpz_mat_set_linbox(C, LBC)
+
+
+# set p to the minpoly or the charpoly of A
+cdef inline void linbox_fmpz_mat_poly(fmpz_poly_t p, fmpz_mat_t A, int minpoly):
+    cdef GivaroIntegerRing ZZ
+    cdef LinBoxIntegerDenseMatrix * LBA
+
+    LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
+    fmpz_mat_get_linbox(LBA, A)
+
+    cdef LinBoxIntegerPolynomialRing.Element m_A
+    if minpoly:
+        LinBoxIntegerDense_minpoly(m_A, LBA[0])
+    else:
+        LinBoxIntegerDense_charpoly(m_A, LBA[0])
+
+    del LBA
+
+    fmpz_poly_fit_length(p, m_A.size())
+    _fmpz_poly_set_length(p, m_A.size())
+
+    cdef size_t i
+    for i in range(m_A.size()):
+        fmpz_poly_set_coeff_mpz(p, i, spy.get_mpz(m_A[i]))
+
+
+# set cp to the characteristic polynomial of A
+cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A):
+    linbox_fmpz_mat_poly(cp, A, False)
+
+
+# set mp to the minimal polynomial of A
+cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A):
+    linbox_fmpz_mat_poly(mp, A, True)
+
+
+# return the rank of A
+cdef unsigned long linbox_fmpz_mat_rank(fmpz_mat_t A):
+    cdef GivaroIntegerRing ZZ
+    cdef LinBoxIntegerDenseMatrix * LBA
+
+    LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
+    fmpz_mat_get_linbox(LBA, A)
+    cdef unsigned long r = 0
+    LinBoxIntegerDense_rank(r, LBA[0])
+    del LBA
+    return r
+
+
+# set det to the determinant of A
+cdef void linbox_fmpz_mat_det(fmpz_t det, fmpz_mat_t A):
+    cdef GivaroIntegerRing ZZ
+    cdef LinBoxIntegerDenseMatrix * LBA
+
+    LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
+    fmpz_mat_get_linbox(LBA, A)
+    cdef GivaroInteger d
+    LinBoxIntegerDense_det(d, LBA[0])
+    del LBA
+
+    fmpz_set_mpz(det, spy.get_mpz(d))
+

src/sage/matrix/matrix_integer_dense.pxd

@@ -8,21 +8,14 @@ from sage.ext.mod_int cimport *
 ctypedef long* GEN
 
 cdef class Matrix_integer_dense(Matrix_dense):
-    cdef fmpz_mat_t _matrix  # Always initialized in __cinit__
-    cdef bint _initialized_mpz
-    cdef mpz_t * _entries    # Only used if _initialized_mpz
-    cdef mpz_t ** _rows      # Only used if _initialized_mpz
+    cdef fmpz_mat_t _matrix
     cdef object _pivots
     cdef int mpz_height(self, mpz_t height) except -1
     cdef _mod_int_c(self, mod_int modulus)
     cdef _mod_two(self)
     cdef _pickle_version0(self)
     cdef _unpickle_version0(self, data)
     cpdef _export_as_string(self, int base=?)
-    cdef inline int _init_mpz(self) except -1
-    cdef int _init_mpz_impl(self) except -1
-    cdef inline int _init_linbox(self) except -1
-    cdef void _dealloc_mpz(self)
     cdef void set_unsafe_mpz(self, Py_ssize_t i, Py_ssize_t j, const mpz_t value)
     cdef void set_unsafe_si(self, Py_ssize_t i, Py_ssize_t j, long value)
     cdef void set_unsafe_double(self, Py_ssize_t i, Py_ssize_t j, double value)