[sagemath] 01/04: Apply patch to work with linbox 1.4.
Tobias Hansen
thansen at moszumanska.debian.org
Fri Jul 29 17:47:46 UTC 2016
This is an automated email from the git hooks/post-receive script.
thansen pushed a commit to branch master
in repository sagemath.
commit 5c0d6fd10c6f112123d94e638a83a61c21516e39
Author: Tobias Hansen <thansen at debian.org>
Date: Fri Jul 29 13:17:53 2016 +0000
Apply patch to work with linbox 1.4.
---
debian/patches/series | 1 +
debian/patches/version-linbox-1.4.patch | 455 ++++++++++++++++++++++++++++++++
2 files changed, 456 insertions(+)
diff --git a/debian/patches/series b/debian/patches/series
index f4c14c8..be0d6ce 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -29,3 +29,4 @@ temp-disable-parallel-sphinx.patch
debian-python-2.7.11.patch
debian-ecm-7.patch
temp-cython-include-source.patch
+version-linbox-1.4.patch
diff --git a/debian/patches/version-linbox-1.4.patch b/debian/patches/version-linbox-1.4.patch
new file mode 100644
index 0000000..243cdea
--- /dev/null
+++ b/debian/patches/version-linbox-1.4.patch
@@ -0,0 +1,455 @@
+Description: Necessary changes to work with linbox 1.4.
+Origin: https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath
+
+--- a/sage/src/module_list.py
++++ b/sage/src/module_list.py
+@@ -26,6 +26,18 @@
+ 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')
+@@ -39,6 +51,12 @@
+ 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'])
+@@ -57,9 +75,18 @@
+ #########################################################
+
+ 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,
+ )
+
+ #########################################################
+@@ -84,12 +111,6 @@
+ singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
+
+ #########################################################
+-### Givaro flags
+-#########################################################
+-
+-givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+-
+-#########################################################
+ ### Library order
+ #########################################################
+
+@@ -104,8 +125,7 @@
+ # 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",
+@@ -592,13 +612,10 @@
+
+ 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'],
+@@ -644,9 +661,8 @@
+
+ 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'],
+@@ -666,8 +682,7 @@
+ 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'],
+@@ -922,19 +937,17 @@
+ 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']),
+@@ -1373,8 +1386,7 @@
+ 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'],
+@@ -1394,8 +1406,7 @@
+ 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++'),
+
+ ################################
+ ##
+@@ -1547,8 +1558,7 @@
+ 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'],
+--- a/sage/src/sage/libs/linbox/echelonform.pxd
++++ b/sage/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)
+
+--- a/sage/src/sage/libs/linbox/fflas.pxd
++++ b/sage/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":
+--- a/sage/src/sage/libs/linbox/linbox.pyx
++++ b/sage/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
+ """
+--- a/sage/src/sage/libs/linbox/modular.pxd
++++ b/sage/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 @@
+
+
+ # 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)
+--- a/sage/src/sage/libs/singular/singular.pyx
++++ b/sage/src/sage/libs/singular/singular.pyx
+@@ -22,6 +22,7 @@
+
+ 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 @@
+ 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)
+--- a/sage/src/sage/rings/finite_rings/element_givaro.pxd
++++ b/sage/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 @@
+
+ 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 @@
+ 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 @@
+ 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 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)
+--- a/sage/src/sage/rings/finite_rings/element_givaro.pyx
++++ b/sage/src/sage/rings/finite_rings/element_givaro.pyx
+@@ -58,8 +58,9 @@
+ 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 @@
+ 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 @@
+ 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 @@
+ 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 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):
+--- a/sage/src/sage/rings/finite_rings/finite_field_givaro.py
++++ b/sage/src/sage/rings/finite_rings/finite_field_givaro.py
+@@ -269,7 +269,8 @@
+ sage: k(2) # indirect doctest
+ 0
+
+- Floats coerce in:
++ Floats are converted like integers::
++
+ sage: k(float(2.0))
+ 0
+
+@@ -343,7 +344,7 @@
+ 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
+
--
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