path: root/libre/sagemath/linbox-1.4.patch

diff --git a/src/module_list.py b/src/module_list.py
index a49ed36..7798cb8 100644
--- a/src/module_list.py
+++ b/src/module_list.py
@@ -27,6 +27,18 @@ lapack_libs = list(lapack_pc['libraries'])
 lapack_library_dirs = list(lapack_pc['library_dirs'])
 lapack_include_dirs = list(lapack_pc['include_dirs'])
 
+# FFLAS-FFPACK
+fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
+fflas_ffpack_libs = list(fflas_ffpack_pc['libraries'])
+fflas_ffpack_library_dirs = list(fflas_ffpack_pc['library_dirs'])
+fflas_ffpack_cflags = pkgconfig.cflags('fflas-ffpack').split()
+
+# Givaro
+givaro_pc = pkgconfig.parse('givaro')
+givaro_libs = list(givaro_pc['libraries'])
+givaro_library_dirs = list(givaro_pc['library_dirs'])
+givaro_cflags = pkgconfig.cflags('givaro').split()
+
 # GNU Scientific Library
 # Note we replace the built-in gslcblas with the above cblas
 gsl_pc = pkgconfig.parse('gsl')
@@ -40,6 +52,12 @@ gd_libs = list(gd_pc['libraries'])
 gd_library_dirs = list(gd_pc['library_dirs'])
 gd_include_dirs = list(gd_pc['include_dirs'])
 
+# LinBox
+linbox_pc = pkgconfig.parse('linbox')
+linbox_libs = list(linbox_pc['libraries'])
+linbox_library_dirs = list(linbox_pc['library_dirs'])
+linbox_cflags = pkgconfig.cflags('linbox').split()
+
 # PNG image library
 png_pc = pkgconfig.parse('libpng')
 png_libs = list(png_pc['libraries'])
@@ -58,9 +76,18 @@ zlib_include_dirs = list(zlib_pc['include_dirs'])
 #########################################################
 
 aliases = dict(
+    FFLASFFPACK_CFLAGS=fflas_ffpack_cflags,
+    FFLASFFPACK_LIBRARIES=fflas_ffpack_libs,
+    FFLASFFPACK_LIBDIR=fflas_ffpack_library_dirs,
+    GIVARO_CFLAGS=givaro_cflags,
+    GIVARO_LIBRARIES=givaro_libs,
+    GIVARO_LIBDIR=givaro_library_dirs,
     GSL_LIBRARIES=gsl_libs,
     GSL_LIBDIR=gsl_library_dirs,
     GSL_INCDIR=gsl_include_dirs,
+    LINBOX_CFLAGS=linbox_cflags,
+    LINBOX_LIBRARIES=linbox_libs,
+    LINBOX_LIBDIR=linbox_library_dirs,
 )
 
 #########################################################
@@ -85,12 +112,6 @@ except ValueError:
 singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
 
 #########################################################
-### Givaro flags
-#########################################################
-
-givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
-
-#########################################################
 ### Library order
 #########################################################
 
@@ -105,8 +126,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
 # at the very end of the list.
 library_order_list = [
     "singular", "ec", "ecm",
-    "linboxsage", "ntl", "iml", "linbox", "givaro",
-] + gsl_libs + [
+] + linbox_libs  + gsl_libs + [
     "pari", "flint", "ratpoints", "ecl", "glpk", "ppl",
     "arb", "fplll", "mpfi", "mpfr", "mpc", "gmp", "gmpxx",
     "polybori",
@@ -593,13 +613,10 @@ ext_modules = [
 
     Extension('sage.libs.linbox.linbox',
               sources = ['sage/libs/linbox/linbox.pyx'],
-              libraries = ['linboxsage', 'ntl', 'iml', 'linbox',
-                           'givaro', 'mpfr', 'gmp', 'gmpxx'] + cblas_libs,
+              libraries = linbox_libs,
               language = 'c++',
               library_dirs = cblas_library_dirs,
-              include_dirs = cblas_include_dirs,
-              extra_compile_args = givaro_extra_compile_args,
-              depends = [os.path.join(SAGE_INC, 'givaro', 'givconfig.h')]),
+              include_dirs = cblas_include_dirs),
 
     Extension('sage.libs.lcalc.lcalc_Lfunction',
               sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
@@ -645,9 +662,8 @@ ext_modules = [
 
     Extension('sage.libs.singular.singular',
               sources = ['sage/libs/singular/singular.pyx'],
-              libraries = ['givaro'] + singular_libs,
-              language="c++",
-              extra_compile_args = givaro_extra_compile_args),
+              libraries = singular_libs,
+              language="c++"),
 
     Extension('sage.libs.singular.polynomial',
               sources = ['sage/libs/singular/polynomial.pyx'],
@@ -667,8 +683,7 @@ ext_modules = [
     Extension('sage.libs.singular.function',
               sources = ['sage/libs/singular/function.pyx'],
               libraries = singular_libs,
-              language="c++",
-              extra_compile_args = givaro_extra_compile_args),
+              language="c++"),
 
     Extension('sage.libs.singular.option',
               sources = ['sage/libs/singular/option.pyx'],
@@ -923,19 +938,17 @@ ext_modules = [
     Extension('sage.matrix.matrix_modn_dense_float',
               sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
               language="c++",
-              libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
+              libraries = linbox_libs + cblas_libs,
               library_dirs = cblas_library_dirs,
-              include_dirs = cblas_include_dirs,
-              extra_compile_args = ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
+              include_dirs = cblas_include_dirs),
 
     Extension('sage.matrix.matrix_modn_dense_double',
               sources = ['sage/matrix/matrix_modn_dense_double.pyx'],
               language="c++",
-              libraries = ['ntl', 'linbox', 'givaro', 'mpfr', 'gmpxx', 'gmp'] + cblas_libs,
+              libraries = linbox_libs + cblas_libs,
               library_dirs = cblas_library_dirs,
               include_dirs = cblas_include_dirs,
-              extra_compile_args = ["-D_XPG6", "-DDISABLE_COMMENTATOR"]
-                    + m4ri_extra_compile_args + givaro_extra_compile_args),
+              extra_compile_args = ["-D_XPG6"]),
 
     Extension('sage.matrix.matrix_modn_sparse',
               sources = ['sage/matrix/matrix_modn_sparse.pyx']),
@@ -1374,8 +1387,7 @@ ext_modules = [
     Extension('sage.rings.finite_rings.element_givaro',
               sources = ["sage/rings/finite_rings/element_givaro.pyx"],
               libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
-              language='c++',
-              extra_compile_args = givaro_extra_compile_args),
+              language='c++'),
 
     Extension('sage.rings.finite_rings.element_ntl_gf2e',
               sources = ['sage/rings/finite_rings/element_ntl_gf2e.pyx'],
@@ -1395,8 +1407,7 @@ ext_modules = [
               sources = ["sage/rings/finite_rings/hom_finite_field_givaro.pyx"],
               # this order is needed to compile under windows.
               libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
-              language='c++',
-              extra_compile_args = givaro_extra_compile_args),
+              language='c++'),
 
     ################################
     ##
@@ -1548,8 +1559,7 @@ ext_modules = [
     Extension('sage.rings.polynomial.plural',
               sources = ['sage/rings/polynomial/plural.pyx'],
               libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
-              language="c++",
-              extra_compile_args = givaro_extra_compile_args),
+              language="c++"),
 
     Extension('sage.rings.polynomial.multi_polynomial_libsingular',
               sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx'],
diff --git a/src/sage/libs/linbox/echelonform.pxd b/src/sage/libs/linbox/echelonform.pxd
index 3097c8b..cf4902d 100644
--- a/src/sage/libs/linbox/echelonform.pxd
+++ b/src/sage/libs/linbox/echelonform.pxd
@@ -1,23 +1,27 @@
+# distutils: extra_compile_args = LINBOX_CFLAGS
+# distutils: libraries = LINBOX_LIBRARIES
+# distutils: library_dirs = LINBOX_LIBDIR
+
 from sage.libs.linbox.modular cimport ModDoubleField, ModDoubleFieldElement, ModFloatField, ModFloatFieldElement
 from libc.stdint cimport uint64_t
 
-cdef extern from "linbox/matrix/blas-matrix.h" namespace "LinBox":
-    cdef cppclass BlasMatrixDouble "LinBox::BlasMatrix<LinBox::Modular<double> >":
+cdef extern from "linbox/matrix/dense-matrix.h" namespace "LinBox":
+    cdef cppclass BlasMatrixDouble "LinBox::DenseMatrix<Givaro::Modular<double> >":
         BlasMatrixDouble(ModDoubleField F, uint64_t nrows, uint64_t ncols)
         void setEntry(size_t i, size_t j, ModDoubleFieldElement t)
         ModDoubleFieldElement &getEntry(size_t i, size_t j)
 
-    cdef cppclass BlasMatrixFloat "LinBox::BlasMatrix<LinBox::Modular<float> >":
+    cdef cppclass BlasMatrixFloat "LinBox::DenseMatrix<Givaro::Modular<float> >":
         BlasMatrixFloat(ModFloatField F, uint64_t nrows, uint64_t ncols)
         void setEntry(size_t i, size_t j, ModFloatFieldElement t)
         ModFloatFieldElement &getEntry(size_t i, size_t j)
 
 cdef extern from "linbox/algorithms/echelon-form.h":
-    cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<LinBox::Modular<double> >":
+    cdef cppclass EchelonFormDomainDouble "LinBox::EchelonFormDomain<Givaro::Modular<double> >":
         EchelonFormDomainDouble(ModDoubleField)
         int rowReducedEchelon(BlasMatrixDouble, BlasMatrixDouble)
 
-    cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<LinBox::Modular<float> >":
+    cdef cppclass EchelonFormDomainFloat "LinBox::EchelonFormDomain<Givaro::Modular<float> >":
         EchelonFormDomainFloat(ModFloatField)
         int rowReducedEchelon(BlasMatrixFloat, BlasMatrixFloat)
 
diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
index e102004..01ab1b1 100644
--- a/src/sage/libs/linbox/fflas.pxd
+++ b/src/sage/libs/linbox/fflas.pxd
@@ -1,3 +1,7 @@
+# distutils: extra_compile_args = FFLASFFPACK_CFLAGS
+# distutils: libraries = FFLASFFPACK_LIBRARIES
+# distutils: library_dirs = FFLASFFPACK_LIBDIR
+
 from modular cimport ModDoubleField, ModFloatField, ModDoubleFieldElement, ModFloatFieldElement
 
 cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
diff --git a/src/sage/libs/linbox/linbox.pyx b/src/sage/libs/linbox/linbox.pyx
index e932347..a9bd6d1 100644
--- a/src/sage/libs/linbox/linbox.pyx
+++ b/src/sage/libs/linbox/linbox.pyx
@@ -1,3 +1,7 @@
+# distutils: extra_compile_args = LINBOX_CFLAGS
+# distutils: libraries = LINBOX_LIBRARIES
+# distutils: library_dirs = LINBOX_LIBDIR
+
 r"""
 Linbox interface
 """
diff --git a/src/sage/libs/linbox/modular.pxd b/src/sage/libs/linbox/modular.pxd
index 7ef204c..ea5fb29 100644
--- a/src/sage/libs/linbox/modular.pxd
+++ b/src/sage/libs/linbox/modular.pxd
@@ -1,10 +1,10 @@
-cdef extern from "linbox/field/modular.h":
+cdef extern from "givaro/modular.h":
     # double
 
-    cdef cppclass ModDoubleFieldElement "LinBox::Modular<double>::Element":
+    cdef cppclass ModDoubleFieldElement "Givaro::Modular<double>::Element":
         pass
 
-    cdef cppclass ModDoubleField "LinBox::Modular<double>":
+    cdef cppclass ModDoubleField "Givaro::Modular<double>":
         ModDoubleField(int modulus)
         ModDoubleFieldElement init(ModDoubleFieldElement res, int v)
         ModDoubleFieldElement init(ModDoubleFieldElement res, double v)
@@ -20,10 +20,10 @@ cdef extern from "linbox/field/modular.h":
 
 
     # float
-    cdef cppclass ModFloatFieldElement "LinBox::Modular<float>::Element":
+    cdef cppclass ModFloatFieldElement "Givaro::Modular<float>::Element":
         pass
 
-    cdef cppclass ModFloatField "LinBox::Modular<float>":
+    cdef cppclass ModFloatField "Givaro::Modular<float>":
         ModFloatField(int modulus)
         ModFloatFieldElement init(ModFloatFieldElement res, int v)
         ModFloatFieldElement init(ModFloatFieldElement res, double v)
diff --git a/src/sage/libs/singular/singular.pyx b/src/sage/libs/singular/singular.pyx
index 33d7f7ec..77f6e0a 100644
--- a/src/sage/libs/singular/singular.pyx
+++ b/src/sage/libs/singular/singular.pyx
@@ -22,6 +22,7 @@ cdef extern from "limits.h":
 
 import os
 
+from libc.stdint cimport int64_t
 from sage.libs.singular.decl cimport intvec
 from sage.libs.singular.decl cimport SR_HDL, SR_INT, SR_TO_INT
 from sage.libs.singular.decl cimport singular_options, singular_verbose_options
@@ -155,7 +156,7 @@ cdef FFgivE si2sa_GFqGivaro(number *n, ring *_ring, Cache_givaro cache):
     order = cache.objectptr.cardinality() - 1
 
     while z:
-        c = cache.objectptr.initi(c, <long>napGetCoeff(z))
+        c = cache.objectptr.initi(c, <int64_t>napGetCoeff(z))
         e = napGetExpFrom(z,1, _ring)
         if e == 0:
             ret = cache.objectptr.add(ret, c, ret)
diff --git a/src/sage/rings/finite_rings/element_givaro.pxd b/src/sage/rings/finite_rings/element_givaro.pxd
index 68def46..91c4ed7 100644
--- a/src/sage/rings/finite_rings/element_givaro.pxd
+++ b/src/sage/rings/finite_rings/element_givaro.pxd
@@ -1,9 +1,15 @@
-from sage.structure.element cimport Element, RingElement, ModuleElement
-from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
+# distutils: extra_compile_args = GIVARO_CFLAGS
+
+from libcpp.vector cimport vector
+ctypedef vector[int] intvec
+
+from libc.stdint cimport int64_t
 
-from sage.structure.parent  cimport Parent
+from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
+from sage.structure.parent cimport Parent
 from sage.structure.sage_object cimport SageObject
 
+
 cdef extern from "givaro/givconfig.h":
     pass
 
@@ -13,16 +19,7 @@ cdef extern from "givaro/givrandom.h":
 
     GivRandom GivRandomSeeded  "Givaro::GivRandom"(unsigned long seed)
 
-cdef extern from "givaro/givgfq.h":
-    ctypedef struct intvec "std::vector<unsigned int>":
-        void (* push_back)(int elem)
-
-    ctypedef struct constintvec "const std::vector<unsigned int>"
-
-    intvec intvec_factory "std::vector<unsigned int>"(int len)
-
-cdef extern from "givaro/givgfq.h":
-
+cdef extern from "givaro/gfq.h":
     ctypedef struct GivaroGfq "Givaro::GFqDom<int>":
         #attributes
         unsigned int one
@@ -40,10 +37,10 @@ cdef extern from "givaro/givgfq.h":
         unsigned int (* cardinality)()
         int (* exponent)()
         int (* random)(GivRandom gen, int res)
-        int (* initi "init")(int res, int e)
+        int (* initi "init")(int res, int64_t e)
         int (* initd "init")(int res, double e)
         int (* indeterminate)()
-        int (* convert)(int r, int p)
+        int (* convert)(int64_t r, int p)
         int (* read)(int r, int p)
         int (* axpyin)(int r, int a, int x)
         int (* axpy)(int r, int a, int b, int c)
@@ -60,7 +57,12 @@ cdef extern from "givaro/givgfq.h":
     void delete "delete "(void *o)
     int gfq_element_factory "Givaro::GFqDom<int>::Element"()
 
-cdef class FiniteField_givaroElement(FinitePolyExtElement) #forward declaration
+
+cdef class FiniteField_givaroElement(FinitePolyExtElement):
+    cdef int element
+    cdef Cache_givaro _cache
+    cdef object _multiplicative_order
+    cdef FiniteField_givaroElement _new_c(self, int value)
 
 cdef class Cache_givaro(SageObject):
     cdef GivaroGfq *objectptr # C++ object
@@ -85,11 +87,4 @@ cdef class FiniteField_givaro_iterator:
     cdef int iterator
     cdef Cache_givaro _cache
 
-cdef class FiniteField_givaroElement(FinitePolyExtElement):
-    cdef int element
-    cdef Cache_givaro _cache
-    cdef object _multiplicative_order
-    cdef FiniteField_givaroElement _new_c(self, int value)
-
-
 cdef inline FiniteField_givaroElement make_FiniteField_givaroElement(Cache_givaro cache, int x)
diff --git a/src/sage/rings/finite_rings/element_givaro.pyx b/src/sage/rings/finite_rings/element_givaro.pyx
index d32b5cf..f2afa44 100644
--- a/src/sage/rings/finite_rings/element_givaro.pyx
+++ b/src/sage/rings/finite_rings/element_givaro.pyx
@@ -58,8 +58,9 @@ from sage.misc.randstate cimport randstate, current_randstate
 from sage.rings.finite_rings.finite_field_base cimport FiniteField
 from sage.rings.ring cimport Ring
 from element_ext_pari import FiniteField_ext_pariElement
-from element_pari_ffelt import FiniteFieldElement_pari_ffelt
+from element_pari_ffelt cimport FiniteFieldElement_pari_ffelt
 from sage.structure.sage_object cimport SageObject
+from sage.structure.element cimport Element, ModuleElement, RingElement
 import operator
 import sage.arith.all
 import finite_field_constructor as finite_field
@@ -373,18 +374,16 @@ cdef class Cache_givaro(SageObject):
         elif isinstance(e, int) or \
              isinstance(e, Integer) or \
              isinstance(e, long) or is_IntegerMod(e):
-            try:
-                e_int = e
-            except OverflowError:
-                e_int = e % self.characteristic()
+            e_int = e % self.characteristic()
             res = self.objectptr.initi(res, e_int)
 
         elif e is None:
             e_int = 0
-            res = self.objectptr.initi(res,e_int)
+            res = self.objectptr.initi(res, e_int)
 
         elif isinstance(e, float):
-            res = self.objectptr.initd(res,e)
+            e_int = int(e) % self.characteristic()
+            res = self.objectptr.initd(res, e_int)
 
         elif isinstance(e, str):
             return self.parent(eval(e.replace("^","**"),self.parent.gens_dict()))
@@ -394,8 +393,8 @@ cdef class Cache_givaro(SageObject):
                 raise TypeError, "e.parent must match self.vector_space"
             ret = self._zero_element
             for i in range(len(e)):
-                e_entry = e[i] % self.characteristic()
-                res = self.objectptr.initi(res, int(e_entry))
+                e_int = e[i] % self.characteristic()
+                res = self.objectptr.initi(res, e_int)
                 to_add = make_FiniteField_givaroElement(self, res)
                 ret = ret + to_add*self.parent.gen()**i
             return ret
@@ -434,8 +433,8 @@ cdef class Cache_givaro(SageObject):
                 raise ValueError, "list is too long"
             ret = self._zero_element
             for i in range(len(e)):
-                e_entry = e[i] % self.characteristic()
-                res = self.objectptr.initi(res, int(e_entry))
+                e_int = e[i] % self.characteristic()
+                res = self.objectptr.initi(res, e_int)
                 to_add = make_FiniteField_givaroElement(self, res)
                 ret = ret + to_add*self.parent.gen()**i
             return ret
@@ -572,19 +571,17 @@ cdef class Cache_givaro(SageObject):
         cdef int ret = k.zero
         cdef int a = k.indeterminate()
         cdef int at = k.one
-        cdef unsigned int ch = k.characteristic()
-        cdef int _n, t, i
+        cdef int ch = k.characteristic()
+        cdef int t, i
 
         if n<0 or n>k.cardinality():
             raise TypeError, "n must be between 0 and self.order()"
 
-        _n = n
-
         for i from 0 <= i < k.exponent():
-            t = k.initi(t, _n%ch)
+            t = k.initi(t, n % ch)
             ret = k.axpy(ret, t, at, ret)
             at = k.mul(at,at,a)
-            _n = _n/ch
+            n //= ch
         return make_FiniteField_givaroElement(self, ret)
 
     def _element_repr(self, FiniteField_givaroElement e):
diff --git a/src/sage/rings/finite_rings/finite_field_givaro.py b/src/sage/rings/finite_rings/finite_field_givaro.py
index adbaab3..c431f6d 100644
--- a/src/sage/rings/finite_rings/finite_field_givaro.py
+++ b/src/sage/rings/finite_rings/finite_field_givaro.py
@@ -269,7 +269,8 @@ class FiniteField_givaro(FiniteField):
             sage: k(2) # indirect doctest
             0
 
-            Floats coerce in:
+        Floats are converted like integers::
+
             sage: k(float(2.0))
             0
 
@@ -343,7 +344,7 @@ class FiniteField_givaro(FiniteField):
             sage: k(pari('Mod(1,2)'))
             1
             sage: k(pari('Mod(2,3)'))
-            0
+            a
             sage: k(pari('Mod(1,3)*a^20'))
             a^7 + a^5 + a^4 + a^2