sagemath-7.3-3.parabola1: updating version

9 files changed, 585 insertions, 175 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
index 45d2b5e47..448bdcc17 100644
--- a/libre/sagemath/PKGBUILD
+++ b/libre/sagemath/PKGBUILD
@@ -1,4 +1,4 @@
-# $Id: PKGBUILD 183005 2016-07-16 21:09:23Z arojas $
+# $Id: PKGBUILD 185390 2016-08-05 22:06:53Z arojas $
 # Maintainer (Arch): Evgeniy Alekseev <arcanis.arch at gmail dot com>
 # Maintainer (Arch): Antonio Rojas <arojas@archlinux.org>
 # Contributor (Arch): Daniel Wallace <danielwallace at gtmanfred dot com>
@@ -10,8 +10,8 @@
 # Maintainer: André Silva <emulatorman@parabola.nu>
 
 pkgname=sagemath
-pkgver=7.2
-pkgrel=7.parabola1
+pkgver=7.3
+pkgrel=3.parabola1
 pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty support"
 arch=(i686 x86_64 armv7h)
 url="http://www.sagemath.org"
@@ -28,32 +28,35 @@ optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cyt
   'modular_decomposition: modular decomposition of graphs' 'ffmpeg: to export animations to video' 'imagemagick: to show animations'
   'coxeter3: Coxeter groups implementation' 'cryptominisat: SAT solver' 'gap-data: for computing Galois groups'
   'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
-  'python2-igraph: igraph backend for graph theory'
-  'jupyter-notebook: Jupyter notebook interface' 'atlas-lapack: improved performance for some linear algebra operations')
-makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc
+  'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+  'python2-igraph: igraph backend for graph theory' 'sage-notebook-exporter: convert flask notebooks to jupyter'
+  'jupyter-notebook: Jupyter notebook interface')
+makedepends=(cython2 boost ratpoints symmetrica fflas-ffpack python2-jinja coin-or-cbc libhomfly libbraiding
   mcqd coxeter3 cryptominisat modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe) # libfes
 conflicts=(sage-mathematics)
 replaces=(sage-mathematics)
 provides=(sage-mathematics)
 source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
         anal.h env.patch paths.patch clean.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch
-        disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch linbox-1.4.patch ecm-7.patch sagemath-ipython5.patch)
-md5sums=('2afeb8f75a33107fef5d509698c0eabc'
+        disable-fes.patch jupyter-path.patch test-optional.patch python-2.7.11.patch linbox-1.4.patch ecm-7.patch
+        sagemath-ipython5.patch increase-rtol.patch)
+md5sums=('cb2aed3d24de7b2228a9b34e81a27870'
          'a906a180d198186a39820b0a2f9a9c63'
-         'f6c62f0ccc168c5e6e3dd9d6f73f6389'
-         '52d30e91110183489f66d7bf73c36c64'
+         'd4d3c235c99b2bc92dde9f6e53935a8d'
+         '45b84ae5579273196df44f7464a01a30'
          '6d9ae0978ce6a05a0da2cafdfb178a09'
-         '5947a420a0b1483f0cbc74c76895789b'
+         '6cafcb381437d4751fd55b25d5090987'
          'a1bcdd3fe620dbae60ed8b0e98b2ece7'
-         '541988696465f204235d595a349017f3'
+         'b3ecf7c93a90e0afccbc686af9fdc85f'
          '9ba81f717ffd4e20b8b2f2a318307488'
-         '4eb23a3c7363258bc9ba764d6e5512ba'
+         '06a67e611d10aa2381efe1f08ea4ffd9'
          '16b529194c6105c3364127bd8f1efa83'
          'cdcabd475b80afe0534a5621e972736e'
          'ef927896f2071b442b1d07d7e69f5f3a'
-         '9f1cef3e477bafebe2ad301db56db8a2'
+         'a276f0fbbff6eade409d0569ebd728d4'
          '0c9a57d35de80c2cd418ebec912efbbb'
-         '55e75afd249048a8718c4377c22afa52')
+         '2bcaca7284dda963ebdc17daf78cf6c9'
+         '39d3fded716d2a7ae0ab03e0896b7497')
 
 prepare(){
   cd sage-$pkgver
@@ -87,6 +90,8 @@ prepare(){
   patch -p1 -i ../cython-sys-path.patch
 # fix regressions with ECM 7
   patch -p1 -i ../ecm-7.patch
+# increase numerical tolerance, needed by scipy 0.18
+  patch -p1 -i ../increase-rtol.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
@@ -110,9 +115,6 @@ prepare(){
 # copy required private PARI header
   mkdir -p src/pari
   cp "$srcdir"/anal.h src/pari/anal.h
-
-# remove developer interface
-  rm -r src/sage/dev
 }
 
 
diff --git a/libre/sagemath/disable-fes.patch b/libre/sagemath/disable-fes.patch
index 873a6a663..086231d70 100644
--- a/libre/sagemath/disable-fes.patch
+++ b/libre/sagemath/disable-fes.patch
@@ -1,8 +1,8 @@
 --- src/module_list.py.orig	2015-06-07 11:29:30.710612146 +0200
 +++ src/module_list.py	2015-06-07 11:30:21.877506106 +0200
-@@ -685,11 +685,11 @@
-               include_dirs = [SAGE_INC + '/ecl'],
-               depends = [SAGE_INC + '/ecl/ecl.h']),
+@@ -564,11 +564,11 @@
+               sources = ["sage/libs/ecl.pyx"],
+               libraries = ["ecl"]),
  
 -    OptionalExtension("sage.libs.fes",
 -             ["sage/libs/fes.pyx"],
diff --git a/libre/sagemath/env.patch b/libre/sagemath/env.patch
index 0ec5fc68c..5cb93b75f 100644
--- a/libre/sagemath/env.patch
+++ b/libre/sagemath/env.patch
@@ -70,11 +70,11 @@
 +export SAGE_DOC_SRC="/usr/share/doc/sage"
 +export SAGE_DOC="/usr/share/doc/sage"
  
- # We offer a toolchain option, so if $SAGE_LOCAL/toolchain/toolchain-env exists source it.
- # Since the user might do something crazy we do not do any checks, but hope for the best.
-@@ -309,9 +267,6 @@
- GIT_TEMPLATE_DIR="$SAGE_LOCAL"/share/git-core/templates && export GIT_TEMPLATE_DIR
- GIT_EXEC_PATH="$SAGE_LOCAL"/libexec/git-core && export GIT_EXEC_PATH
+ if [ "$SAGE_BANNER" = "bare" ]; then
+     export SAGE_BANNER_TEXT=$(cat "$SAGE_ROOT/VERSION.txt")
+@@ -319,9 +277,6 @@
+ GPHELP="$SAGE_LOCAL/bin/gphelp" && export GPHELP
+ GPDOCDIR="$SAGE_LOCAL/share/pari/doc" && export GPDOCDIR
  
 -SINGULARPATH="$SAGE_LOCAL/share/singular" && export SINGULARPATH
 -SINGULAR_EXECUTABLE="$SAGE_LOCAL/bin/Singular" && export SINGULAR_EXECUTABLE
@@ -82,7 +82,7 @@
  if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
      SAGE_REPO_ANONYMOUS="git://trac.sagemath.org/sage.git"
      export SAGE_REPO_ANONYMOUS
-@@ -363,38 +318,33 @@
+@@ -364,10 +319,10 @@
      export SAGE_STARTUP_FILE
  fi
  
@@ -97,48 +97,16 @@
  
  if [ "$PYTHON_EGG_CACHE" = "" ]; then
      PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
-     export PYTHON_EGG_CACHE
- fi
- 
- # Set PYTHONUSERBASE to avoid picking up non-Sage versions of
- # Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/19612.
- #
- # For more history (it used to be PYTHONNOUSERSITE=yes which killed
- # the ability to do "sage -pip install PACKAGE --user"), see
- # http://trac.sagemath.org/ticket/14243 and
- # http://trac.sagemath.org/ticket/18955.
- 
- if [ "$PYTHONUSERBASE" = "" ]; then
-     PYTHONUSERBASE="$DOT_SAGE/local"
-     export PYTHONUSERBASE
- fi
- 
--if [ -d "$SAGE_LOCAL/lib/python" ]; then
--    PYTHONPATH="$SAGE_LOCAL/lib/python:$SAGE_LOCAL/lib/python/site_packages"
--    if [ -n "$SAGE_PATH" ]; then
--        PYTHONPATH="$SAGE_PATH:$PYTHONPATH"
--    fi
--    PYTHONHOME="$SAGE_LOCAL"
--    export PYTHONPATH
--    export PYTHONHOME
--fi
-+PYTHONPATH="/usr/lib/sage/site-packages:$PYTHONPATH"
-+PYTHONHOME="$SAGE_ROOT"
-+export PYTHONPATH
-+export PYTHONHOME
- 
- if [ -z "${SAGE_ORIG_LD_LIBRARY_PATH_SET}" ]; then
-     SAGE_ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH && export SAGE_ORIG_LD_LIBRARY_PATH
-@@ -431,8 +378,6 @@
+@@ -453,8 +400,6 @@
          fi
      fi
  fi
 -MAXIMA_PREFIX="$SAGE_ROOT/local" && export MAXIMA_PREFIX
 -
- ############ architecture flags
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
  
- # Support flags to change the build architecture.  Currently, this is
-@@ -602,9 +547,6 @@
+ ############ architecture flags
+@@ -622,9 +567,6 @@
      LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
  fi
  
diff --git a/libre/sagemath/increase-rtol.patch b/libre/sagemath/increase-rtol.patch
new file mode 100644
index 000000000..dc0ff8799
--- /dev/null
+++ b/libre/sagemath/increase-rtol.patch
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py        2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py     2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+     if q < 2:   # Here we check that q is actually at least 2
+         raise ValueError("The value q must be an integer greater than 1")
+ 
+-    eps  = 4.5e-16 # find_root has about this as the default xtol
++    eps  = 4.5e-15 # find_root has about this as the default xtol
+     ymax = 1 - 1/q
+     if x <= eps:
+         return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py        2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py     2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+ 
+ 
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+     """
+     Numerically find a root of ``f`` on the closed interval `[a,b]`
+     (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx      2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx   2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+             ret = ret[0]
+         return ret
+ 
+-    def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++    def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+         """
+         Numerically find a root of self on the closed interval [a,b] (or
+         [b,a]) if possible, where self is a function in the one variable.
+
diff --git a/libre/sagemath/is-package-installed.patch b/libre/sagemath/is-package-installed.patch
index 3b6efc22b..0f1c59084 100644
--- a/libre/sagemath/is-package-installed.patch
+++ b/libre/sagemath/is-package-installed.patch
@@ -2,15 +2,15 @@ diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
 index 0a5f794..2969d92 100644
 --- a/src/sage/databases/cremona.py
 +++ b/src/sage/databases/cremona.py
-@@ -52,7 +52,6 @@ from sage.misc.prandom import randint
+@@ -53,7 +53,6 @@ from sage.misc.prandom import randint
  
  import sage.schemes.elliptic_curves.constructor as elliptic
- from sql_db import SQLDatabase, verify_column
+ from .sql_db import SQLDatabase, verify_column
 -from sage.misc.package import is_package_installed
  from sage.env import SAGE_SHARE
  from sage.misc.all import walltime
  
-@@ -827,7 +826,7 @@ class MiniCremonaDatabase(SQLDatabase):
+@@ -828,7 +827,7 @@ class MiniCremonaDatabase(SQLDatabase):
              if N < self.largest_conductor():
                  message = "There is no elliptic curve with label " + label \
                      + " in the database"
@@ -19,7 +19,7 @@ index 0a5f794..2969d92 100644
                  message = "There is no elliptic curve with label " + label \
                      + " in the currently available databases"
              else:
-@@ -1676,7 +1675,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+@@ -1677,7 +1676,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
      if name is None and not set_global:
          return _db
      if set_global and name is None:
@@ -32,7 +32,7 @@ diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/nor
 index b917d2a..80fb20c 100644
 --- a/src/sage/game_theory/normal_form_game.py
 +++ b/src/sage/game_theory/normal_form_game.py
-@@ -612,8 +612,9 @@ from sage.rings.all import QQ
+@@ -614,8 +614,9 @@ from sage.rings.all import QQ
  from sage.structure.sage_object import SageObject
  from sage.matrix.constructor import matrix
  from sage.matrix.constructor import vector
@@ -43,7 +43,7 @@ index b917d2a..80fb20c 100644
  
  try:
      from gambit import Game
-@@ -1315,13 +1316,13 @@ class NormalFormGame(SageObject, MutableMapping):
+@@ -1317,13 +1318,13 @@ class NormalFormGame(SageObject, MutableMapping):
              raise ValueError("utilities have not been populated")
  
          if not algorithm:
@@ -63,7 +63,7 @@ diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron
 index 2f58d8b..eb519a2 100644
 --- a/src/sage/geometry/polyhedron/base.py
 +++ b/src/sage/geometry/polyhedron/base.py
-@@ -20,7 +20,6 @@ import six
+@@ -21,7 +21,6 @@ import six
  from sage.structure.element import Element, coerce_binop, is_Vector
  
  from sage.misc.all import cached_method, prod
@@ -71,7 +71,7 @@ index 2f58d8b..eb519a2 100644
  
  from sage.rings.all import QQ, ZZ
  from sage.rings.real_double import RDF
-@@ -3690,7 +3689,9 @@ class Polyhedron_base(Element):
+@@ -3691,7 +3690,9 @@ class Polyhedron_base(Element):
  
               David Avis's lrs program.
          """
@@ -103,7 +103,7 @@ diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
 index 252984f..ce19682 100644
 --- a/src/sage/graphs/generic_graph.py
 +++ b/src/sage/graphs/generic_graph.py
-@@ -7833,7 +7833,6 @@ class GenericGraph(GenericGraph_pyx):
+@@ -7856,7 +7856,6 @@ class GenericGraph(GenericGraph_pyx):
             sage: abs(flow_ff-flow_igraph) < 0.00001         # optional python_igraph
             True
          """
@@ -111,7 +111,7 @@ index 252984f..ce19682 100644
          self._scream_if_not_simple(allow_loops=True)
          if vertex_bound and algorithm in ["FF", "igraph"]:
              raise ValueError("This method does not support both " +
-@@ -7851,10 +7850,12 @@ class GenericGraph(GenericGraph_pyx):
+@@ -7874,10 +7873,12 @@ class GenericGraph(GenericGraph_pyx):
          if algorithm is None:
              if vertex_bound:
                  algorithm = "LP"
@@ -127,7 +127,7 @@ index 252984f..ce19682 100644
  
          if (algorithm == "FF"):
              return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
-@@ -20134,17 +20135,22 @@ class GenericGraph(GenericGraph_pyx):
+@@ -20251,17 +20252,22 @@ class GenericGraph(GenericGraph_pyx):
              Subgroup of (Permutation Group with generators [(0,7)(1,4)(2,3)(6,8)]) generated by [(0,7)(1,4)(2,3)(6,8)]]
  
          """
@@ -156,7 +156,7 @@ index 252984f..ce19682 100644
  
              A = automorphism_group(self, partition)
  
-@@ -20786,17 +20792,22 @@ class GenericGraph(GenericGraph_pyx):
+@@ -20903,17 +20909,22 @@ class GenericGraph(GenericGraph_pyx):
              True
  
          """
@@ -189,7 +189,7 @@ diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generat
 index 5919ab3..1766796 100644
 --- a/src/sage/graphs/graph_generators.py
 +++ b/src/sage/graphs/graph_generators.py
-@@ -1192,8 +1192,9 @@ class GraphGenerators():
+@@ -1195,8 +1195,9 @@ class GraphGenerators():
          .. [buckygen] \G. Brinkmann, J. Goedgebeur and B.D. McKay, Generation of Fullerenes,
            Journal of Chemical Information and Modeling, 52(11):2910-2918, 2012.
          """
@@ -201,7 +201,7 @@ index 5919ab3..1766796 100644
              raise TypeError("the optional buckygen package is not installed")
  
          # number of vertices should be positive
-@@ -1277,8 +1278,9 @@ class GraphGenerators():
+@@ -1280,8 +1281,9 @@ class GraphGenerators():
          .. [benzene] \G. Brinkmann, G. Caporossi and P. Hansen, A Constructive Enumeration of Fusenes and Benzenoids,
            Journal of Algorithms, 45:155-166, 2002.
          """
@@ -213,7 +213,7 @@ index 5919ab3..1766796 100644
              raise TypeError("the optional benzene package is not installed")
  
          # number of hexagons should be positive
-@@ -1430,8 +1432,9 @@ class GraphGenerators():
+@@ -1433,8 +1435,9 @@ class GraphGenerators():
          .. [plantri] \G. Brinkmann and B.D. McKay, Fast generation of planar graphs,
             MATCH-Communications in Mathematical and in Computer Chemistry, 58(2):323-357, 2007.
          """
@@ -225,7 +225,7 @@ index 5919ab3..1766796 100644
              raise TypeError("the optional plantri package is not installed")
  
          # number of vertices should be positive
-@@ -1629,8 +1632,9 @@ class GraphGenerators():
+@@ -1632,8 +1635,9 @@ class GraphGenerators():
              sage: [g.size() for g in graphs.triangulations(6, minimum_connectivity=3)] # optional plantri
              [12, 12]
          """
@@ -237,7 +237,7 @@ index 5919ab3..1766796 100644
              raise TypeError("the optional plantri package is not installed")
  
          # number of vertices should be positive
-@@ -1783,8 +1787,9 @@ class GraphGenerators():
+@@ -1786,8 +1790,9 @@ class GraphGenerators():
              sage: [len(g) for g in graphs.quadrangulations(12, no_nonfacial_quadrangles=True, dual=True)]  # optional plantri
              [10, 10]
          """
@@ -293,7 +293,7 @@ diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/pe
 index e42db61..d4d5684 100644
 --- a/src/sage/groups/perm_gps/permgroup.py
 +++ b/src/sage/groups/perm_gps/permgroup.py
-@@ -143,7 +143,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
+@@ -145,7 +145,6 @@ from sage.groups.perm_gps.permgroup_element import PermutationGroupElement, stan
  from sage.groups.abelian_gps.abelian_group import AbelianGroup
  from sage.misc.cachefunc import cached_method
  from sage.groups.class_function import ClassFunction
@@ -301,7 +301,7 @@ index e42db61..d4d5684 100644
  from sage.sets.finite_enumerated_set import FiniteEnumeratedSet
  from sage.categories.all import FiniteEnumeratedSets
  from sage.groups.conjugacy_classes import ConjugacyClassGAP
-@@ -188,8 +187,6 @@ def hap_decorator(f):
+@@ -190,8 +189,6 @@ def hap_decorator(f):
      """
      @wraps(f)
      def wrapped(self, n, p=0):
@@ -310,7 +310,7 @@ index e42db61..d4d5684 100644
          load_hap()
          from sage.arith.all import is_prime
          if not (p == 0 or is_prime(p)):
-@@ -1681,9 +1678,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+@@ -1683,9 +1680,7 @@ class PermutationGroup_generic(group.FiniteGroup):
          try:
              return [Integer(n) for n in self._gap_().IdGroup()]
          except RuntimeError:
@@ -321,7 +321,7 @@ index e42db61..d4d5684 100644
  
      def id(self):
          """
-@@ -1734,9 +1729,7 @@ class PermutationGroup_generic(group.FiniteGroup):
+@@ -1736,9 +1731,7 @@ class PermutationGroup_generic(group.FiniteGroup):
          try:
              return Integer(self._gap_().PrimitiveIdentification())
          except RuntimeError:
@@ -332,7 +332,7 @@ index e42db61..d4d5684 100644
  
      def center(self):
          """
-@@ -4112,8 +4105,6 @@ class PermutationGroup_generic(group.FiniteGroup):
+@@ -4114,8 +4107,6 @@ class PermutationGroup_generic(group.FiniteGroup):
          - David Joyner and Graham Ellis
  
          """
@@ -345,23 +345,23 @@ diff --git a/src/sage/misc/all.py b/src/sage/misc/all.py
 index 90e6985..21daeb0 100644
 --- a/src/sage/misc/all.py
 +++ b/src/sage/misc/all.py
-@@ -52,11 +52,6 @@ from fpickle import pickle_function, unpickle_function
+@@ -53,11 +53,6 @@ from fpickle import pickle_function, unpickle_function
  
- from dist import install_scripts
+ from .dist import install_scripts
  
--from package import (install_package,
+-from .package import (install_package,
 -        installed_packages, is_package_installed,
 -        standard_packages, optional_packages, experimental_packages,
 -        upgrade, package_versions)
 -
- from pager import pager
+ from .pager import pager
  
  lazy_import('sage.misc.sagedoc', ['browse_sage_doc',
 diff --git a/src/sage/rings/polynomial/multi_polynomial_sequence.py b/src/sage/rings/polynomial/multi_polynomial_sequence.py
 index da41cb0..49cae0b 100644
 --- a/src/sage/rings/polynomial/multi_polynomial_sequence.py
 +++ b/src/sage/rings/polynomial/multi_polynomial_sequence.py
-@@ -158,7 +158,6 @@ from sage.misc.cachefunc import cached_method
+@@ -159,7 +159,6 @@ from sage.misc.cachefunc import cached_method
  
  from types import GeneratorType
  from sage.misc.converting_dict import KeyConvertingDict
@@ -369,7 +369,7 @@ index da41cb0..49cae0b 100644
  
  from sage.structure.sequence import Sequence, Sequence_generic
  
-@@ -1428,10 +1427,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
+@@ -1429,10 +1428,11 @@ class PolynomialSequence_gf2(PolynomialSequence_generic):
  
          if S != []:
              if algorithm == "exhaustive_search":
diff --git a/libre/sagemath/linbox-1.4.patch b/libre/sagemath/linbox-1.4.patch
index 5897df763..b3955eb51 100644
--- a/libre/sagemath/linbox-1.4.patch
+++ b/libre/sagemath/linbox-1.4.patch
@@ -53,7 +53,7 @@ index a49ed36..7798cb8 100644
  )
  
  #########################################################
-@@ -85,12 +112,6 @@ except ValueError:
+@@ -91,12 +118,6 @@ except ValueError:
  singular_libs = ['singular', 'flint', 'ntl', 'gmpxx', 'gmp', 'readline', 'm']
  
  #########################################################
@@ -66,7 +66,7 @@ index a49ed36..7798cb8 100644
  ### Library order
  #########################################################
  
-@@ -105,8 +126,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
+@@ -111,8 +132,7 @@ givaro_extra_compile_args =['-D__STDC_LIMIT_MACROS']
  # at the very end of the list.
  library_order_list = [
      "singular", "ec", "ecm",
@@ -75,8 +75,8 @@ index a49ed36..7798cb8 100644
 +] + linbox_libs  + gsl_libs + [
      "pari", "flint", "ratpoints", "ecl", "glpk", "ppl",
      "arb", "fplll", "mpfi", "mpfr", "mpc", "gmp", "gmpxx",
-     "polybori",
-@@ -593,13 +613,10 @@ ext_modules = [
+     "brial",
+@@ -611,13 +631,10 @@ ext_modules = [
  
      Extension('sage.libs.linbox.linbox',
                sources = ['sage/libs/linbox/linbox.pyx'],
@@ -92,7 +92,7 @@ index a49ed36..7798cb8 100644
  
      Extension('sage.libs.lcalc.lcalc_Lfunction',
                sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
-@@ -645,9 +662,8 @@ ext_modules = [
+@@ -665,9 +682,8 @@ ext_modules = [
  
      Extension('sage.libs.singular.singular',
                sources = ['sage/libs/singular/singular.pyx'],
@@ -104,7 +104,7 @@ index a49ed36..7798cb8 100644
  
      Extension('sage.libs.singular.polynomial',
                sources = ['sage/libs/singular/polynomial.pyx'],
-@@ -667,8 +683,7 @@ ext_modules = [
+@@ -687,8 +703,7 @@ ext_modules = [
      Extension('sage.libs.singular.function',
                sources = ['sage/libs/singular/function.pyx'],
                libraries = singular_libs,
@@ -114,7 +114,7 @@ index a49ed36..7798cb8 100644
  
      Extension('sage.libs.singular.option',
                sources = ['sage/libs/singular/option.pyx'],
-@@ -923,19 +938,17 @@ ext_modules = [
+@@ -944,19 +959,17 @@ ext_modules = [
      Extension('sage.matrix.matrix_modn_dense_float',
                sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
                language="c++",
@@ -122,7 +122,7 @@ index a49ed36..7798cb8 100644
 +              libraries = linbox_libs + cblas_libs,
                library_dirs = cblas_library_dirs,
 -              include_dirs = cblas_include_dirs,
--              extra_compile_args = ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
+-              extra_compile_args = nocxx11_args + ['-DDISABLE_COMMENTATOR'] + givaro_extra_compile_args),
 +              include_dirs = cblas_include_dirs),
  
      Extension('sage.matrix.matrix_modn_dense_double',
@@ -132,13 +132,13 @@ index a49ed36..7798cb8 100644
 +              libraries = linbox_libs + cblas_libs,
                library_dirs = cblas_library_dirs,
                include_dirs = cblas_include_dirs,
--              extra_compile_args = ["-D_XPG6", "-DDISABLE_COMMENTATOR"]
+-              extra_compile_args = nocxx11_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 = [
+@@ -1400,8 +1413,7 @@ ext_modules = [
      Extension('sage.rings.finite_rings.element_givaro',
                sources = ["sage/rings/finite_rings/element_givaro.pyx"],
                libraries = ['givaro', 'ntl', 'gmpxx', 'gmp', 'm'],
@@ -148,7 +148,7 @@ index a49ed36..7798cb8 100644
  
      Extension('sage.rings.finite_rings.element_ntl_gf2e',
                sources = ['sage/rings/finite_rings/element_ntl_gf2e.pyx'],
-@@ -1395,8 +1407,7 @@ ext_modules = [
+@@ -1421,8 +1433,7 @@ 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'],
@@ -158,7 +158,7 @@ index a49ed36..7798cb8 100644
  
      ################################
      ##
-@@ -1548,8 +1559,7 @@ ext_modules = [
+@@ -1574,8 +1585,7 @@ ext_modules = [
      Extension('sage.rings.polynomial.plural',
                sources = ['sage/rings/polynomial/plural.pyx'],
                libraries = ['m', 'readline', 'singular', 'givaro', 'gmpxx', 'gmp'],
@@ -214,7 +214,7 @@ index e102004..01ab1b1 100644
 +# distutils: libraries = FFLASFFPACK_LIBRARIES
 +# distutils: library_dirs = FFLASFFPACK_LIBDIR
 +
- from modular cimport ModDoubleField, ModFloatField, ModDoubleFieldElement, ModFloatFieldElement
+ 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
@@ -264,7 +264,7 @@ diff --git a/src/sage/libs/singular/singular.pyx b/src/sage/libs/singular/singul
 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":
+@@ -23,6 +23,7 @@ cdef extern from "limits.h":
  
  import os
  
@@ -272,7 +272,7 @@ index 33d7f7ec..77f6e0a 100644
  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):
+@@ -156,7 +157,7 @@ cdef FFgivE si2sa_GFqGivaro(number *n, ring *_ring, Cache_givaro cache):
      order = cache.objectptr.cardinality() - 1
  
      while z:
@@ -365,7 +365,7 @@ diff --git a/src/sage/rings/finite_rings/element_givaro.pyx b/src/sage/rings/fin
 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
+@@ -59,8 +59,9 @@ 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
@@ -376,7 +376,7 @@ index d32b5cf..f2afa44 100644
  import operator
  import sage.arith.all
  import finite_field_constructor as finite_field
-@@ -373,18 +374,16 @@ cdef class Cache_givaro(SageObject):
+@@ -374,18 +375,16 @@ cdef class Cache_givaro(SageObject):
          elif isinstance(e, int) or \
               isinstance(e, Integer) or \
               isinstance(e, long) or is_IntegerMod(e):
@@ -399,8 +399,8 @@ index d32b5cf..f2afa44 100644
  
          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"
+@@ -395,8 +394,8 @@ 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()
@@ -410,8 +410,8 @@ index d32b5cf..f2afa44 100644
                  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"
+@@ -435,8 +434,8 @@ 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()
@@ -421,7 +421,7 @@ index d32b5cf..f2afa44 100644
                  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):
+@@ -573,19 +572,17 @@ cdef class Cache_givaro(SageObject):
          cdef int ret = k.zero
          cdef int a = k.indeterminate()
          cdef int at = k.one
@@ -431,7 +431,7 @@ index d32b5cf..f2afa44 100644
 +        cdef int t, i
  
          if n<0 or n>k.cardinality():
-             raise TypeError, "n must be between 0 and self.order()"
+             raise TypeError("n must be between 0 and self.order()")
  
 -        _n = n
 -
@@ -449,7 +449,7 @@ diff --git a/src/sage/rings/finite_rings/finite_field_givaro.py b/src/sage/rings
 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):
+@@ -270,7 +270,8 @@ class FiniteField_givaro(FiniteField):
              sage: k(2) # indirect doctest
              0
  
@@ -459,7 +459,7 @@ index adbaab3..c431f6d 100644
              sage: k(float(2.0))
              0
  
-@@ -343,7 +344,7 @@ class FiniteField_givaro(FiniteField):
+@@ -344,7 +345,7 @@ class FiniteField_givaro(FiniteField):
              sage: k(pari('Mod(1,2)'))
              1
              sage: k(pari('Mod(2,3)'))
diff --git a/libre/sagemath/paths.patch b/libre/sagemath/paths.patch
index c8afe39bb..79b37408c 100644
--- a/libre/sagemath/paths.patch
+++ b/libre/sagemath/paths.patch
@@ -1,39 +1,13 @@
 --- src/sage/env.py.orig	2014-06-25 10:47:25.827203554 +1200
 +++ src/sage/env.py	2014-06-25 10:49:07.667402821 +1200
-@@ -87,25 +87,22 @@
- _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
+@@ -90,8 +90,8 @@
  
  # bunch of sage directories and files
--_add_variable_or_fallback('SAGE_ROOT',       None)
+ _add_variable_or_fallback('SAGE_ROOT',       None)
 -_add_variable_or_fallback('SAGE_LOCAL',      opj('$SAGE_ROOT', 'local'))
 -_add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
--_add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
--_add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
-+_add_variable_or_fallback('SAGE_ROOT',       '/usr')
 +_add_variable_or_fallback('SAGE_LOCAL',      '/usr')
 +_add_variable_or_fallback('SAGE_ETC',        '/etc/sage')
-+_add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
-+_add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share', 'sage'))
+ _add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
+ _add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
  
- _add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_ROOT', 'src'))
--_add_variable_or_fallback('SITE_PACKAGES',   site.getsitepackages())
-+_add_variable_or_fallback('SITE_PACKAGES',   site.getsitepackages()+['/usr/lib/sage/site-packages'])
- _add_variable_or_fallback('SAGE_LIB',        SITE_PACKAGES[0])
- 
- _add_variable_or_fallback('SAGE_CYTHONIZED', opj('$SAGE_SRC', 'build', 'cythonized'))
- 
--_add_variable_or_fallback('SAGE_EXTCODE',    opj('$SAGE_SHARE', 'sage', 'ext'))
--_add_variable_or_fallback('SAGE_LOGS',       opj('$SAGE_ROOT', 'logs', 'pkgs'))
--_add_variable_or_fallback('SAGE_SPKG_INST',  opj('$SAGE_LOCAL', 'var', 'lib', 'sage', 'installed'))
--_add_variable_or_fallback('SAGE_DOC_SRC',    opj('$SAGE_SRC', 'doc'))
--_add_variable_or_fallback('SAGE_DOC',        opj('$SAGE_SHARE', 'doc', 'sage'))
--_add_variable_or_fallback('DOT_SAGE',        opj(os.environ.get('HOME','$SAGE_ROOT'), '.sage'))
--_add_variable_or_fallback('SAGE_DOT_GIT',    opj('$SAGE_ROOT', '.git'))
-+_add_variable_or_fallback('SAGE_EXTCODE',    opj('$SAGE_SHARE', 'ext'))
-+_add_variable_or_fallback('SAGE_DOC_SRC',    opj('$SAGE_SRC', 'doc'))
-+_add_variable_or_fallback('SAGE_DOC',        opj('/usr/share', 'doc', 'sage'))        
-+_add_variable_or_fallback('DOT_SAGE',        opj(os.environ.get('HOME'), '.sage'))
- _add_variable_or_fallback('SAGE_DISTFILES',  opj('$SAGE_ROOT', 'upstream'))
- 
- # misc
-
diff --git a/libre/sagemath/sagemath-ipython5.patch b/libre/sagemath/sagemath-ipython5.patch
index 6d8557175..0f05de4d8 100644
--- a/libre/sagemath/sagemath-ipython5.patch
+++ b/libre/sagemath/sagemath-ipython5.patch
@@ -1,56 +1,446 @@
+diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
+index 2654016..d3daed6 100644
+--- a/src/sage/doctest/forker.py
++++ b/src/sage/doctest/forker.py
+@@ -116,10 +116,6 @@ def init_sage():
+     from sage.structure.debug_options import debug
+     debug.refine_category_hash_check = True
+ 
+-    # Disable IPython colors during doctests
+-    from sage.repl.interpreter import DEFAULT_SAGE_CONFIG
+-    DEFAULT_SAGE_CONFIG.TerminalInteractiveShell.colors = 'NoColor'
+-
+     # We import readline before forking, otherwise Pdb doesn't work
+     # os OS X: http://trac.sagemath.org/14289
+     import readline
+@@ -1088,15 +1084,13 @@ class SageDocTestRunner(doctest.DocTestRunner):
+             sage: _ = sage0.eval("import doctest, sys, os, multiprocessing, subprocess")
+             sage: _ = sage0.eval("from sage.doctest.parsing import SageOutputChecker")
+             sage: _ = sage0.eval("import sage.doctest.forker as sdf")
+-            sage: _ = sage0.eval("sdf.init_sage()")
+             sage: _ = sage0.eval("from sage.doctest.control import DocTestDefaults")
+             sage: _ = sage0.eval("DD = DocTestDefaults(debug=True)")
+             sage: _ = sage0.eval("ex1 = doctest.Example('a = 17', '')")
+             sage: _ = sage0.eval("ex2 = doctest.Example('2*a', '1')")
+             sage: _ = sage0.eval("DT = doctest.DocTest([ex1,ex2], globals(), 'doubling', None, 0, None)")
+             sage: _ = sage0.eval("DTR = sdf.SageDocTestRunner(SageOutputChecker(), verbose=False, sage_options=DD, optionflags=doctest.NORMALIZE_WHITESPACE|doctest.ELLIPSIS)")
+-            sage: sage0._prompt = r"debug: "
+-            sage: print(sage0.eval("DTR.run(DT, clear_globs=False)")) # indirect doctest
++            sage: print(sage0.eval("sdf.init_sage(); DTR.run(DT, clear_globs=False)")) # indirect doctest
+             **********************************************************************
+             Line 1, in doubling
+             Failed example:
+@@ -1110,7 +1104,6 @@ class SageDocTestRunner(doctest.DocTestRunner):
+             ...
+             sage: sage0.eval("a")
+             '...17'
+-            sage: sage0._prompt = "sage: "
+             sage: sage0.eval("quit")
+             'Returning to doctests...TestResults(failed=1, attempted=2)'
+         """
+@@ -1144,13 +1137,14 @@ class SageDocTestRunner(doctest.DocTestRunner):
+                         print(src)
+                         if ex.want:
+                             print(doctest._indent(ex.want[:-1]))
+-                    from sage.repl.interpreter import DEFAULT_SAGE_CONFIG
++                    from sage.repl.configuration import sage_ipython_config
++                    from sage.repl.prompts import DebugPrompts
+                     from IPython.terminal.embed import InteractiveShellEmbed
+-                    import copy
+-                    cfg = copy.deepcopy(DEFAULT_SAGE_CONFIG)
+-                    prompt_config = cfg.PromptManager
+-                    prompt_config.in_template = 'debug: '
+-                    prompt_config.in2_template = '.....: '
++                    cfg = sage_ipython_config.default()
++                    # Currently this doesn't work: prompts only work in pty
++                    # We keep simple_prompt=True, prompts will be "In [0]:"
++                    # cfg.InteractiveShell.prompts_class = DebugPrompts
++                    # cfg.InteractiveShell.simple_prompt = False
+                     shell = InteractiveShellEmbed(config=cfg, banner1='', user_ns=dict(globs))
+                     shell(header='', stack_depth=2)
+                 except KeyboardInterrupt:
+@@ -1248,6 +1242,7 @@ class SageDocTestRunner(doctest.DocTestRunner):
+             sage: _ = sage0.eval("ex = doctest.Example('E = EllipticCurve([0,0]); E', 'A singular Elliptic Curve')")
+             sage: _ = sage0.eval("DT = doctest.DocTest([ex], globals(), 'singular_curve', None, 0, None)")
+             sage: _ = sage0.eval("DTR = sdf.SageDocTestRunner(SageOutputChecker(), verbose=False, sage_options=DD, optionflags=doctest.NORMALIZE_WHITESPACE|doctest.ELLIPSIS)")
++            sage: old_prompt = sage0._prompt
+             sage: sage0._prompt = r"\(Pdb\) "
+             sage: sage0.eval("DTR.run(DT, clear_globs=False)") # indirect doctest
+             '... ArithmeticError("invariants " + str(ainvs) + " define a singular curve")'
+@@ -1257,7 +1252,7 @@ class SageDocTestRunner(doctest.DocTestRunner):
+             '...EllipticCurve_field.__init__(self, K, ainvs)'
+             sage: sage0.eval("p ainvs")
+             '(0, 0, 0, 0, 0)'
+-            sage: sage0._prompt = "sage: "
++            sage: sage0._prompt = old_prompt
+             sage: sage0.eval("quit")
+             'TestResults(failed=1, attempted=1)'
+         """
+diff --git a/src/sage/doctest/test.py b/src/sage/doctest/test.py
+index d69136f..a6cc4d0 100644
+--- a/src/sage/doctest/test.py
++++ b/src/sage/doctest/test.py
+@@ -360,7 +360,7 @@ Test the ``--debug`` option::
+         s...: b = 5
+         s...: a + b
+         8
+-    debug:
++    In [1]:
+     <BLANKLINE>
+     Returning to doctests...
+     **********************************************************************
+diff --git a/src/sage/interfaces/sage0.py b/src/sage/interfaces/sage0.py
+index 87bfc0b..77cd151 100644
+--- a/src/sage/interfaces/sage0.py
++++ b/src/sage/interfaces/sage0.py
+@@ -18,6 +18,7 @@ from __future__ import absolute_import
+ 
+ import cPickle
+ import os
++import re
+ 
+ from .expect import Expect, ExpectElement, FunctionElement
+ import sage.repl.preparse
+@@ -146,10 +147,17 @@ class Sage(ExtraTabCompletion, Expect):
+             if init_code is None:
+                 init_code = ['from sage.all import *', 'import cPickle']
+         else:
+-            # Disable the IPython history (implemented as SQLite database)
+-            # to avoid problems with locking.
+-            command = "sage-ipython --HistoryManager.hist_file=:memory: --colors=NoColor"
+-            prompt = "sage: "
++            command = ' '.join([
++                'sage-ipython',
++                # Disable the IPython history (implemented as SQLite database)
++                # to avoid problems with locking.
++                '--HistoryManager.hist_file=:memory:',
++                # Disable everything that prints ANSI codes
++                '--colors=NoColor',
++                '--no-term-title',
++                '--simple-prompt',
++            ])
++            prompt = re.compile('In \[\d+\]: ')
+             if init_code is None:
+                 init_code = ['import cPickle']
+ 
+diff --git a/src/sage/misc/trace.py b/src/sage/misc/trace.py
+index 0da17e7..efcaa33 100644
+--- a/src/sage/misc/trace.py
++++ b/src/sage/misc/trace.py
+@@ -54,6 +54,7 @@ def trace(code, preparse=True):
+         sage: import pexpect
+         sage: s = pexpect.spawn('sage')
+         sage: _ = s.sendline("trace('print(factor(10))'); print(3+97)")
++        sage: _ = s.expect('ipdb>', timeout=90)
+         sage: _ = s.sendline("s"); _ = s.sendline("c");
+         sage: _ = s.expect('100', timeout=90)
+ 
+diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py
+new file mode 100644
+index 0000000..5034039
+--- /dev/null
++++ b/src/sage/repl/configuration.py
+@@ -0,0 +1,152 @@
++r"""
++Sage's IPython Configuration
++"""
++
++#*****************************************************************************
++#       Copyright (C) 2016 Volker Braun <vbraun.name@gmail.com>
++#
++#  Distributed under the terms of the GNU General Public License (GPL)
++#  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 __future__ import absolute_import
++
++import sys
++import copy
++from traitlets.config.loader import Config
++
++from sage.repl.prompts import SagePrompts
++
++
++# Name of the Sage IPython extension
++SAGE_EXTENSION = 'sage'
++
++
++class SageIpythonConfiguration(object):
++
++    def _doctest_mode(self):
++        """
++        Whether we are in doctest mode
++
++        This returns ``True`` during doctests.
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config._doctest_mode()
++            True
++        """
++        from sage.doctest import DOCTEST_MODE
++        return DOCTEST_MODE
++    
++    def _allow_ansi(self):
++        """
++        Whether to allow ANSI escape sequences
++
++        This returns ``False`` during doctests to avoid ANSI escape 
++        sequences.
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config._allow_ansi()
++            False
++        """
++        return (not self._doctest_mode()) and sys.stdout.isatty()
++
++    def colors(self):
++        """
++        Return the IPython color palette
++
++        This returns ``'NoColor'`` during doctests to avoid ANSI escape 
++        sequences.
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config.simple_prompt()
++            True
++        """
++        return 'LightBG' if self._allow_ansi() else 'NoColor'
++
++    def simple_prompt(self):
++        """
++        Return whether to use the simple prompt
++
++        This returns ``True`` during doctests to avoid ANSI escape sequences.
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config.simple_prompt()
++            True
++        """
++        return not self._allow_ansi()
++
++    def term_title(self):
++        """
++        Return whether to set the terminal title
++
++        This returns false during doctests to avoid ANSI escape sequences.
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config.term_title()
++            False
++        """
++        return self._allow_ansi()
++
++    def default(self):
++        """
++        Return a new default configuration object
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config.default()
++            {'InteractiveShell': {'colors': ...
++        """
++        from sage.repl.interpreter import SageTerminalInteractiveShell
++        cfg = Config(
++            TerminalIPythonApp=Config(
++                display_banner=False,
++                verbose_crash=True,
++                test_shell=False,
++                shell_class=SageTerminalInteractiveShell,
++            ),
++            InteractiveShell=Config(
++                prompts_class=SagePrompts,
++                ast_node_interactivity='all',
++                colors=self.colors(),
++                simple_prompt=self.simple_prompt(),
++                term_title=self.term_title(),
++                confirm_exit=False,
++                separate_in=''
++            ),
++            InteractiveShellApp=Config(extensions=[SAGE_EXTENSION]),
++        )
++        if self._doctest_mode():
++            # Using the file-backed history causes problems in parallel tests
++            cfg.HistoryManager = Config(hist_file=':memory:')
++        return cfg
++
++    def copy(self):
++        """
++        Return a copy of the current configuration
++
++        EXAMPLES::
++        
++            sage: from sage.repl.configuration import sage_ipython_config
++            sage: sage_ipython_config.copy()
++            {'InteractiveShell': {'colors': ...
++        """
++        try:
++            return copy.deepcopy(get_ipython().config)
++        except NameError:
++            return self.default()
++
++
++sage_ipython_config = SageIpythonConfiguration()
 diff --git a/src/sage/repl/interpreter.py b/src/sage/repl/interpreter.py
-index ef8724d..6896985 100644
+index e0499c7..1f4eda7 100644
 --- a/src/sage/repl/interpreter.py
 +++ b/src/sage/repl/interpreter.py
-@@ -103,6 +103,7 @@ import os
+@@ -102,18 +102,15 @@ Check that Cython source code appears in tracebacks::
+ #*****************************************************************************
+ 
+ 
+-import copy
+ import os
  import re
- import sys
+-import sys
  from sage.repl.preparse import preparse
 +from sage.repl.prompts import SagePrompts, InterfacePrompts
  
- from traitlets.config.loader import Config
+-from traitlets.config.loader import Config
  from traitlets import Bool, Type
-@@ -371,11 +372,6 @@ class SageTestShell(SageShellOverride, TerminalInteractiveShell):
- ###################################################################
  
- DEFAULT_SAGE_CONFIG = Config(
+ from sage.env import SAGE_LOCAL
+-
+-SAGE_EXTENSION = 'sage'
++from sage.repl.configuration import sage_ipython_config, SAGE_EXTENSION
+ 
+ def embedded():
+     """
+@@ -370,31 +367,7 @@ class SageTestShell(SageShellOverride, TerminalInteractiveShell):
+         rc = super(SageTestShell, self).run_cell(*args, **kwds)
+ 
+ 
+-###################################################################
+-# Default configuration
+-###################################################################
+-
+-DEFAULT_SAGE_CONFIG = Config(
 -    PromptManager = Config(
 -        in_template = 'sage: ',
 -        in2_template = '....: ',
 -        justify = False,
 -        out_template = ''),
-     TerminalIPythonApp = Config(
-         display_banner = False,
-         verbose_crash = True,
-@@ -383,6 +379,7 @@ DEFAULT_SAGE_CONFIG = Config(
-         shell_class = SageTerminalInteractiveShell,
-     ),
-     InteractiveShell = Config(
-+        prompts_class = SagePrompts,
-         ast_node_interactivity = 'all',
-         colors = 'LightBG' if sys.stdout.isatty() else 'NoColor',
-         confirm_exit = False,
-@@ -616,13 +613,11 @@ def interface_shell_embed(interface):
-         cfg = copy.deepcopy(get_ipython().config)
-     except NameError:
-         cfg = copy.deepcopy(DEFAULT_SAGE_CONFIG)
+-    TerminalIPythonApp = Config(
+-        display_banner = False,
+-        verbose_crash = True,
+-        test_shell = False,
+-        shell_class = SageTerminalInteractiveShell,
+-    ),
+-    InteractiveShell = Config(
+-        ast_node_interactivity = 'all',
+-        colors = 'LightBG' if sys.stdout.isatty() else 'NoColor',
+-        confirm_exit = False,
+-        separate_in = ''),
+-    InteractiveShellApp = Config(extensions=[SAGE_EXTENSION]),
+-)
+-
+-
++    
+ ###################################################################
+ # Transformers used in the SageInputSplitter
+ ###################################################################
+@@ -614,19 +587,17 @@ def interface_shell_embed(interface):
+         sage: shell = interface_shell_embed(gap)
+         sage: shell.run_cell('List( [1..10], IsPrime )')
+         [ false, true, true, false, true, false, true, false, false, false ]
+-        <IPython.core.interactiveshell.ExecutionResult object at 0x...>
+-    """
+-    try:
+-        cfg = copy.deepcopy(get_ipython().config)
+-    except NameError:
+-        cfg = copy.deepcopy(DEFAULT_SAGE_CONFIG)
 -    cfg.PromptManager['in_template'] = interface.name() + ': '
 -    cfg.PromptManager['in2_template'] = len(interface.name())*'.' + ': '
--
++        <repr(<IPython.core.interactiveshell.ExecutionResult at 0x...>) failed: 
++        AttributeError: type object 'ExecutionResult' has no attribute '__qualname__'>
+ 
++    Note that the repr error is https://github.com/ipython/ipython/issues/9756
++    """
++    cfg = sage_ipython_config.copy()
      ipshell = InteractiveShellEmbed(config=cfg,
                                      banner1='\n  --> Switching to %s <--\n\n'%interface,
-                                     exit_msg = '\n  --> Exiting back to Sage <--\n')
+-                                    exit_msg = '\n  --> Exiting back to Sage <--\n')
++                                    exit_msg='\n  --> Exiting back to Sage <--\n')
      ipshell.interface = interface
 +    ipshell.prompts = InterfacePrompts(interface.name())
  
      while ipshell.prefilter_manager.transformers:
          ipshell.prefilter_manager.transformers.pop()
+@@ -669,7 +640,7 @@ def get_test_shell():
+         sage: out + err
+         ''
+     """
+-    config = copy.deepcopy(DEFAULT_SAGE_CONFIG)
++    config = sage_ipython_config.default()
+     config.TerminalIPythonApp.test_shell = True
+     config.TerminalIPythonApp.shell_class = SageTestShell
+     app = SageTerminalApp.instance(config=config)
+@@ -748,12 +719,9 @@ class SageTerminalApp(TerminalIPythonApp):
+             sage: os.environ['IPYTHONDIR'] = IPYTHONDIR
+         """
+         super(SageTerminalApp, self).load_config_file(*args, **kwds)
+-
+-        newconfig = copy.deepcopy(DEFAULT_SAGE_CONFIG)
+-
++        newconfig = sage_ipython_config.default()
+         # merge in the config loaded from file
+         newconfig.merge(self.config)
+-
+         self.config = newconfig
+ 
+     def init_shell(self):
+@@ -767,7 +735,7 @@ class SageTerminalApp(TerminalIPythonApp):
+ 
+         EXAMPLES::
+ 
+-            sage: from sage.repl.interpreter import SageTerminalApp, DEFAULT_SAGE_CONFIG
++            sage: from sage.repl.interpreter import SageTerminalApp
+             sage: app = SageTerminalApp.instance()
+             sage: app.shell
+             <sage.repl.interpreter.SageTestShell object at 0x...>
+@@ -776,7 +744,6 @@ class SageTerminalApp(TerminalIPythonApp):
+         self.shell = self.shell_class.instance(
+             parent=self,
+             config=self.config,
+-            display_banner=False,
+             profile_dir=self.profile_dir,
+             ipython_dir=self.ipython_dir)
+         self.shell.configurables.append(self)
+diff --git a/src/sage/repl/ipython_tests.py b/src/sage/repl/ipython_tests.py
+index 0fa568d..2bb34cd 100644
+--- a/src/sage/repl/ipython_tests.py
++++ b/src/sage/repl/ipython_tests.py
+@@ -100,6 +100,12 @@ Next, test the pinfo2 magic for Cython code::
+     ...
+     File:   .../sage/tests/stl_vector.pyx
+     Type:   type
++
++Test that there are no warnings being ignored internally::
++
++    sage: import warnings
++    sage: warnings.simplefilter('error');  get_test_shell()
++    <sage.repl.interpreter.SageTestShell object at 0x...>
+ '''
+ 
+ 
 diff --git a/src/sage/repl/prompts.py b/src/sage/repl/prompts.py
 new file mode 100644
-index 0000000..69f8cdd
+index 0000000..e885730
 --- /dev/null
 +++ b/src/sage/repl/prompts.py
-@@ -0,0 +1,67 @@
+@@ -0,0 +1,92 @@
 +r"""
 +Sage Commandline Prompts
 +"""
@@ -118,3 +508,41 @@ index 0000000..69f8cdd
 +            (Token.OutPrompt, ''),
 +        ]
 +
++
++class DebugPrompts(Prompts):
++
++    def in_prompt_tokens(self, cli=None):
++        return [
++            (Token.Prompt, 'debug: '),
++        ]
++
++    def continuation_prompt_tokens(self, cli=None, width=None):
++        return [
++            (Token.Prompt, '.....: '),
++        ]
++
++    def rewrite_prompt_tokens(self):
++        return [
++            (Token.Prompt, '-----> '),
++        ]
++
++    def out_prompt_tokens(self):
++        return [
++            (Token.OutPrompt, ''),
++        ]
++
++    
++    
+diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py
+index 0d15d82..417ec5e 100644
+--- a/src/sage/tests/cmdline.py
++++ b/src/sage/tests/cmdline.py
+@@ -385,7 +385,7 @@ def test_executable(args, input="", timeout=100.0, **kwds):
+         **********************************************************************
+         Previously executed commands:
+             s...: assert True == False
+-        debug:
++        In [1]:
+         <BLANKLINE>
+         Returning to doctests...
+         **********************************************************************
diff --git a/libre/sagemath/skip-check.patch b/libre/sagemath/skip-check.patch
index dae5f7277..48cac24b7 100644
--- a/libre/sagemath/skip-check.patch
+++ b/libre/sagemath/skip-check.patch
@@ -1,6 +1,6 @@
 --- src/bin/sage.orig	2014-12-18 09:47:27.354829070 +0100
 +++ src/bin/sage	2014-12-18 09:48:00.041563401 +0100
-@@ -286,18 +286,6 @@
+@@ -352,18 +352,6 @@
  
  # Prepare for running Sage, either interactively or non-interactively.
  sage_setup() {
@@ -16,6 +16,7 @@
 -        exit 1
 -    fi
 -
-     # Display the startup banner
+     # Display the startup banner (unless SAGE_BANNER is explictly "no")
      if [ "$SAGE_BANNER" != "no" ]; then
-         cat "$SAGE_LOCAL/bin/sage-banner"
+         # can be 'bare', or 'yes', or unspecified
+