Merge branch 'develop' into public/ticket/10963-doc-distributive

* develop: (155 commits)
  Updated Sage version to 6.2.beta6
  32-bit fix
  typo fixing
  fix int/long doctest
  trac #16032: These matrices should be sparse
  trac 16032: This can be simplified... :-P
  Correct typo in sage/symbolic/ring.pyx.
  Put comment in the code and add more examples.
  trac #16032: reviewer's remarks
  FiniteStateMachine.__add__ is the same as __or__
  trac #16032: Bug in IncidenceStructure.dual_design
  final edits
  more changes -- please check if I got your algorithm right, Travis
  Review changes from Ben.
  further optimizations
  Fixed KR doctest and documentation of q_dimension.
  Fixes for q-dims for general highest weight crystals.
  more optimizations
  Partial work for general HW crystals.
  Review changes and (minor) optimizations.
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta5, released 2014-03-23
+Sage version 6.2.beta6, released 2014-04-02

build/deps

@@ -364,7 +364,7 @@ $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
 $(INST)/$(SIX): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(SIX) 2>&1" "tee -a $(SAGE_LOGS)/$(SIX).log"
 
-$(INST)/$(DATEUTIL): $(INST)/$(PYTHON) $(INST)/$(SIX)
+$(INST)/$(DATEUTIL): $(INST)/$(PYTHON) $(INST)/$(SIX) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(DATEUTIL) 2>&1" "tee -a $(SAGE_LOGS)/$(DATEUTIL).log"
 
 $(INST)/$(PYPARSING): $(INST)/$(PYTHON)

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e4f7a8b1595adc80b90d3118c35d3f8568588b8e
-md5=fb4ca501460d44ab117694de80be374c
-cksum=474790094
+sha1=0c309e33052d3847c89514d81742ecc7faaef1c3
+md5=c4a51de241dc1092d8679b5b4dd5c3a6
+cksum=1285854398

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-18
+19

build/pkgs/cryptominisat/SPKG.txt

@@ -0,0 +1,34 @@
+= CryptoMiniSat =
+
+== Description ==
+
+  CryptoMiniSat is a SAT solver that aims to become a premiere SAT
+  solver with all the features and speed of successful SAT solvers,
+  such as MiniSat and PrecoSat. The long-term goals of CryptoMiniSat
+  are to be an efficient sequential, parallel and distributed
+  solver. There are solvers that are good at one or the other,
+  e.g. ManySat (parallel) or PSolver (distributed), but we wish to
+  excel at all.
+
+  CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted
+  by researchers and industry.
+
+== License ==
+
+ * GNU General Public License Version 3 or later (see src/COPYING)
+
+== Maintainers ==
+
+ * Martin Albrecht
+
+== Upstream Contact ==
+
+ * Authors: Mate Soos
+ * Email:   soos.mate@gmail.com
+ * Website: http://www.msoos.org/cryptominisat2
+
+== Special Update/Build Instructions ==
+
+CryptoMiniSat's tarball is called cmsat-VERSION.tar.gz and unpacks to
+cmsat-VERSION. It should be unpacked, renamed to cryptominisat-VERSION and
+repackaged.

build/pkgs/cryptominisat/checksums.ini

@@ -0,0 +1,4 @@
+tarball=cryptominisat-VERSION.tar.gz
+sha1=3566754f4e1eb5aefec703f7806c74e4c3edda80
+md5=6fdabd54dc9076e0e2f28f489f5eab64
+cksum=2155609827

build/pkgs/cryptominisat/package-version.txt

@@ -0,0 +1 @@
+2.9.6

build/pkgs/cryptominisat/spkg-install

@@ -0,0 +1,76 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting"
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+unset RM
+
+INCLUDES="-I$SAGE_LOCAL/include"
+LIBDIRS="-L$SAGE_LOCAL/lib"
+
+CXXFLAGS="$CXXFLAGS $INCLUDES $LIBDIRS -g"
+
+COMPILER=`testcc.sh $CC`
+
+if [ "x$COMPILER"  = "xGNU" ] ; then
+   CXXFLAGS="$CXXFLAGS -fPIC -Wall -pedantic"
+elif [ "x$COMPILER" = "xSun_on_Solaris" ] ; then
+   CXXFLAGS="$CXXFLAGS -Kpic"
+elif [ "x$COMPILER" = "xHP_on_HPUX" ] ; then
+   CXXFLAGS="$CXXFLAGS + z"
+fi
+
+CPPFLAGS="$INCLUDES"
+
+if [ "x$SAGE_DEBUG" = "xyes" ]; then
+   CXXFLAGS="$CXXFLAGS -O0"
+   ENABLE_DEBUG="--enable-debug"
+else
+   CXXFLAGS="$CXXFLAGS -O2"
+   ENABLE_DEBUG=""
+fi
+
+if [ "x$SAGE64" = "xyes" ]; then
+    CXXFLAGS="$CXXFLAGS -m64"
+    CPPFLAGS="$CPPFLAGS -m64"
+    # FIXME: Do we need LDFLAGS here, too?
+    #        But looks as if all linking is performed by libtool/
+    #        gcc, so we do not really need it here.
+fi
+
+export CXXFLAGS
+export CPPFLAGS
+
+
+#build CryptoMiniSat
+
+cd src
+
+$MAKE clean
+
+./configure --prefix=$SAGE_LOCAL $ENABLE_DEBUG
+
+if [ $? -ne 0 ]; then
+    echo "Error configuring cryptominisat"
+    exit 1
+fi
+
+$MAKE
+
+if [ $? -ne 0 ]; then
+    echo "Error building cryptominisat"
+    exit 1
+fi
+
+$MAKE install
+
+if [ $? -ne 0 ]; then
+    echo "Error installing cryptominisat"
+    exit 1
+fi
+
+cd ..
+

build/pkgs/freetype/package-version.txt

@@ -1 +1 @@
-2.5.2.p0
+2.5.2.p1

build/pkgs/freetype/spkg-install

@@ -30,3 +30,9 @@ ${MAKE} install
 if [ $? -ne 0 ]; then
     exit 1;
 fi;
+
+# The following file may be present from old builds of freetype, and
+# its presence can break the matplotlib build. So remove it. (The
+# current version is $SAGE_LOCAL/include/freetype2/ftbuild.h.)
+
+rm -f "$SAGE_LOCAL/include/ft2build.h"

build/pkgs/pynac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pynac-VERSION.tar.bz2
-sha1=9fe3137139ecc27d1d737d9208cb1e41ecbd2979
-md5=1e1f8c545223871e5703ded52c62a723
-cksum=1549561445
+sha1=d7a80f5c96eec3ac9ecb6757d004e460fbfecece
+md5=70fae63e2c1cb4ec13eea24a4a780ba8
+cksum=1408069708

build/pkgs/pynac/package-version.txt

@@ -1 +1 @@
-0.3.1
+0.3.2

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.2.beta5, Release Date: 2014-03-23                   │
+│ Sage Version 6.2.beta6, Release Date: 2014-04-02                   │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-spkg

@@ -106,7 +106,7 @@ verify_checksum()
         actual=`md5sum $file | sed 's/[^0-9a-f].*//'`
     elif command -v md5 > /dev/null; then
         expected=`lookup_param md5 $checksums`
-        actual=`md5 $file | sed 's/[^0-9a-f].*//'`
+        actual=`md5 $file | sed 's/.*= *//'`
     else
         # POSIX; Note that Solaris is not compliant and its sed
 	# does not understand [[:space:]]

src/bin/sage-version.sh

@@ -1,4 +1,4 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='6.2.beta5'
-SAGE_RELEASE_DATE='2014-03-23'
+SAGE_VERSION='6.2.beta6'
+SAGE_RELEASE_DATE='2014-04-02'

src/doc/de/tutorial/programming.rst

@@ -104,35 +104,8 @@ Kommandozeile arbeiten, können Sie kompilierten Code genau wie
 interpretierten Code anhängen und laden. (Im Moment wird das Anhängen
 von Cythoncode vom Notebook aus nicht unterstützt).
 Die tatsächliche Kompilierung wird "hinter den Kulissen" durchgeführt
-ohne dass Sie explizit etwas tun müssen. Schauen Sie sich
-``$SAGE_ROOT/examples/programming/sagex/factorial.spyx`` an, um ein
-Beispiel einer kompilierten Implementation der Fakultätsfunktion zu
-sehen, welche die GMP-C-Bibliothek unmittelbar benutzt. Um dies
-selbst auszuprobierten, wechseln Sie in das Verzeichnis
-``$SAGE_ROOT/examples/programming/sagex/`` und führen Sie Folgendes
-aus:
-
-.. skip
-
-::
-
-    sage: load "factorial.spyx"
-    ***************************************************
-                    Recompiling factorial.spyx
-    ***************************************************
-    sage: factorial(50)
-    30414093201713378043612608166064768844377641568960512000000000000L
-    sage: time n = factorial(10000)
-    CPU times: user 0.03 s, sys: 0.00 s, total: 0.03 s
-    Wall time: 0.03
-
-Hier gibt das abschließende L ein "Python long integer" zu erkennen
-(Lesen Sie :ref:`section-mathannoy`).
-
-Beachten Sie, dass Sage ``factorial.spyx`` neu kompiliert falls Sie
-Sage beenden und neustarten.
-Die komplierte "shared object library" wird unter
-``$HOME/.sage/temp/hostname/pid/spyx`` gespeichert. Diese Dateien
+ohne dass Sie explizit etwas tun müssen. Die komplierte "shared object library"
+wird unter ``$HOME/.sage/temp/hostname/pid/spyx`` gespeichert. Diese Dateien
 werden gelöscht wenn Sie Sage beenden.
 
 Auf spyx-Dateien wird kein "preparsing" angewendet, d.h. ``1/3`` wird

src/doc/en/reference/combinat/designs.rst

@@ -16,6 +16,8 @@ Constructions
    :maxdepth: 1
 
    ../sage/combinat/designs/block_design
+   ../sage/combinat/designs/bibd
    ../sage/combinat/designs/steiner_quadruple_systems
    ../sage/combinat/designs/latin_squares
+   ../sage/combinat/designs/orthogonal_arrays
 

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

@@ -61,6 +61,7 @@ Libraries of algorithms
 
    sage/graphs/graph_coloring
    sage/graphs/cliquer
+   sage/graphs/independent_sets
    sage/graphs/comparability
    sage/graphs/line_graph
    sage/graphs/spanning_tree

src/doc/en/tutorial/programming.rst

@@ -99,32 +99,7 @@ command-line interface, you can attach and load compiled code
 exactly like with interpreted code (at the moment, attaching and
 loading Cython code is not supported with the notebook interface).
 The actual compilation is done "behind the scenes" without your
-having to do anything explicit. See
-``$SAGE_ROOT/examples/programming/sagex/factorial.spyx`` for an
-example of a compiled implementation of the factorial function that
-directly uses the GMP C library. To try this out for yourself, cd
-to ``$SAGE_ROOT/examples/programming/sagex/``, then do the
-following:
-
-.. skip
-
-::
-
-    sage: load "factorial.spyx"
-    ***************************************************
-                    Recompiling factorial.spyx
-    ***************************************************
-    sage: factorial(50)
-    30414093201713378043612608166064768844377641568960512000000000000L
-    sage: time n = factorial(10000)
-    CPU times: user 0.03 s, sys: 0.00 s, total: 0.03 s
-    Wall time: 0.03
-
-Here the trailing L indicates a Python long integer (see
-:ref:`section-mathannoy`).
-
-Note that Sage will recompile ``factorial.spyx`` if you quit and restart Sage.
-The compiled shared object library is stored under
+having to do anything explicit. The compiled shared object library is stored under
 ``$HOME/.sage/temp/hostname/pid/spyx``. These files are deleted
 when you exit Sage.
 

src/doc/fr/tutorial/programming.rst

@@ -105,33 +105,7 @@ ligne de commande, vous pouvez charger ou attacher des fichiers de code
 compilé exactement comme les fichiers interprétés. Pour l'instant,
 le *notebook* ne permet pas d'attacher des fichiers compilés. La
 compilation proprement dite a lieu « en coulisse », sans que vous ayez à
-la déclencher explicitement. Le fichier
-``$SAGE_ROOT/examples/programming/sagex/factorial.spyx`` donne un exemple
-d'implémentation compilée de la fonction factorielle, qui appelle
-directement la bibliothèque GMP. Pour l'essayer, placez-vous dans le
-répertoire ``$SAGE_ROOT/examples/programming/sagex/`` et entrez les
-commandes suivantes :
-
-
-.. skip
-
-::
-
-    sage: load "factorial.spyx"
-    ***************************************************
-                    Recompiling factorial.spyx
-    ***************************************************
-    sage: factorial(50)
-    30414093201713378043612608166064768844377641568960512000000000000L
-    sage: time n = factorial(10000)
-    CPU times: user 0.03 s, sys: 0.00 s, total: 0.03 s
-    Wall time: 0.03
-
-Le suffixe ``L`` ci-dessus dénote un entier long Python (voir
-:ref:`section-mathannoy`).
-
-Notez que si vous quittez et relancez Sage, ``factorial.spyx`` sera
-recompilé. La bibliothèque d'objets partagés compilés se trouve
+la déclencher explicitement.  La bibliothèque d'objets partagés compilés se trouve
 dans ``$HOME/.sage/temp/hostname/pid/spyx``. Ces fichiers sont supprimés
 lorsque vous quittez Sage.
 

src/doc/ru/tutorial/programming.rst

@@ -92,32 +92,8 @@ C и обработан компилятором C.
 вы можете прикреплять и загружать компилируемый код точно так же, как и
 интерпретируемый (на данный момент, прикрепление и загрузка кода на Cython не
 поддерживается в интерфейсе Notebook). Само компилирование происходит
-"за кулисами", не требуя каких-либо действий с вашей стороны. Просмотреть
-пример компилированного исполнения функции факториал, которое напрямую
-использует библиотеки GMP на C, можно в
-``$SAGE_ROOT/examples/programming/sagex/factorial.spyx``. Для того, чтобы
-опробовать это самому, перейдите в ``$SAGE_ROOT/examples/programming/sagex/``
-с помощью cd, а затем выполниет следующее:
-
-.. skip
-
-::
-
-    sage: load "factorial.spyx"
-    ***************************************************
-                    Recompiling factorial.spyx
-    ***************************************************
-    sage: factorial(50)
-    30414093201713378043612608166064768844377641568960512000000000000L
-    sage: time n = factorial(10000)
-    CPU times: user 0.03 s, sys: 0.00 s, total: 0.03 s
-    Wall time: 0.03
-
-В данном примере L в конце означает Python long integer (см.
-:ref:`section-mathannoy`).
-
-Заметьте, что Sage перекомпилирует ``factorial.spyx`` в том случае, если
-вы выйдете и перезапустите Sage. Компилированная библиотека общих объектов
+"за кулисами", не требуя каких-либо действий с вашей стороны. 
+Компилированная библиотека общих объектов
 содержится в ``$HOME/.sage/temp/hostname/pid/spyx``. Эти файлы будут удалены
 при выходе из Sage.
 

src/ext/pari/simon/ell.gp

@@ -1776,8 +1776,11 @@ if( DEBUGLEVEL_ell >= 2, print("  reduced: Y^2 = ",lift(redq[1])));
 \\ Search for a point on the quartic
       point = nfratpoint(nf,pol,LIM1,1);
       found = point != [];
-\\ If no point is found, check if it is ELS
-      if( !found && !loc,
+      if( found,
+        loc = 1
+      );
+\\ If the quartic is not known to be ELS, check if it is
+      if( !loc,
         if( bigflag,
           loc = nflocallysoluble(nf,pol,r,a,b)
         , loc = nflocallysoluble(nf,pol,0,1,1)

src/module_list.py

@@ -372,6 +372,9 @@ def uname_specific(name, value, alternative):
               sources = ['sage/graphs/cliquer.pyx', 'sage/graphs/cliquer/cl.c'],
               libraries = ['cliquer']),
 
+    Extension('sage.graphs.independent_sets',
+              sources = ['sage/graphs/independent_sets.pyx']),
+
     Extension('sage.graphs.graph_decompositions.vertex_separation',
               sources = ['sage/graphs/graph_decompositions/vertex_separation.pyx']),
 

src/sage/algebras/free_algebra.py

@@ -273,7 +273,7 @@ def create_key(self,base_ring, arg1=None, arg2=None,
                             raise TypeError
                     else:
                         raise TypeError
-            except (TypeError, NotImplementedError),msg:
+            except (TypeError, NotImplementedError) as msg:
                 raise NotImplementedError, "The letterplace implementation is not available for the free algebra you requested"
         if PolRing is not None:
             if degrees is None:

src/sage/algebras/letterplace/free_algebra_letterplace.pyx

@@ -470,7 +470,7 @@ cdef class FreeAlgebra_letterplace(Algebra):
 
             sage: F.<bla,alpha,z> = FreeAlgebra(QQ, implementation='letterplace', degrees=[1,2,3])
             sage: latex(F)
-            \Bold{Q}\langle \mbox{bla}, \alpha, z\rangle
+            \Bold{Q}\langle \mathit{bla}, \alpha, z\rangle
 
         """
         from sage.all import latex