Sage 5.6 released

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Sage 5.6 released Jeroen Demeyer 1/25/13 1:50 AM
Sage 5.6 was released on 21 January 2013. It is available in
source and binary form from:

  * http://www.sagemath.org/download.html

Sage (http://www.sagemath.org/) is developed by volunteers and combines
over 90 open source packages. For instructions about installing Sage, see

  * http://www.sagemath.org/doc/installation

The following page lists the platforms on which Sage should work:

  * http://wiki.sagemath.org/SupportedPlatforms

If you have any questions and/or problems, please report them to any of
these Google groups:

  * sage-support: http://groups.google.com/group/sage-support
  * sage-devel: http://groups.google.com/group/sage-devel

You can also drop by in #sagemath on freenode or post your questions
at http://ask.sagemath.org/

The following 65 people contributed to this release. Of those, 9 made
their first contribution to Sage:

  - Alexander Dreyer
  - Andrew Mathas
  - Andrey Novoseltsev
  - Andrzej Giniewicz
  - Andr� Apitzsch
  - Anne Schilling
  - Burcin Erocal
  - Charles Bouillaguet
  - Chris Berg
  - Christian Kuper [first contribution]
  - Christian Nassau [first contribution]
  - Christian Stump
  - David Coudert
  - David Loeffler
  - Dmitrii Pasechnik
  - Dylan Rupel [first contribution]
  - Emil Widmann
  - Fran�ois Bissey
  - Fr�d�ric Chapoton
  - Gregg Musiker [first contribution]
  - Guillaume Moroz
  - Ivan Andrus
  - Jan Medlock
  - Jason Grout
  - Jean-Pierre Flori
  - Jernej Azarija [first contribution]
  - Jeroen Demeyer
  - John Cremona
  - John Palmieri
  - John Perry
  - Julian Rueth
  - Karl-Dieter Crisman
  - Keshav Kini
  - Kevin Halasz
  - Leif Leonhardy
  - Marco Streng
  - Marshall Hampton
  - Martin Albrecht
  - Michael Orlitzky
  - Mike Hansen
  - Mike Zabrocki
  - Nathann Cohen
  - Nicolas M. Thi�ry
  - Nils Bruin
  - Noud Aldenhoven [first contribution]
  - Paul Zimmermann
  - Peter Jeremy
  - Pierre Cagne [first contribution]
  - Punarbasu Purkayastha
  - R. Andrew Ohana
  - Rob Beezer
  - Robert Bradshaw
  - Simon King
  - Stephen Montgomery-Smith
  - Steven Trogdon
  - Taylor Dupuy
  - Thomas Feulner
  - Thomas Rehn [first contribution]
  - Timo Kluck
  - Travis Scrimshaw
  - Vincent Delecroix
  - Volker Braun
  - William Stein
  - Xavier Caruso
  - Yoora Yi Tenen [first contribution]

* Release manager: Jeroen Demeyer.

* We closed 156 tickets in this release. For details, see

  http://boxen.math.washington.edu/home/release/sage-5.6/tickets.html

Closed tickets:

#13234: Andrey Novoseltsev: Add Normaliz optional package [Reviewed by
Dmitrii Pasechnik]
#13557: Jeroen Demeyer: Make the autotools spkg an optional spkg
[Reviewed by Volker Braun]
#7712: error with polynomial with interval coefficients [Reviewed by
Travis Scrimshaw]
#11231: Sparse and dense polynomials hash differently, but are equal.
[Reviewed by Christian Nassau]
#11551: Pari segfault on Sage startup in Cygwin [Reviewed by Karl-Dieter
Crisman, Jean-Pierre Flori]
#11678: sage-4.7 gives error on relocating the root directory [Reviewed
by Punarbasu Purkayastha]
#12296: Developer Conventions: 'NOTES' inaccuracy [Reviewed by Travis
Scrimshaw]
#12931: evaluation of coefficients of polynomials [Reviewed by Travis
Scrimshaw]
#13779: Crash in graph_generators with MALLOC_CHECK_=3 [Reviewed by Nils
Bruin]
#13790: Allow SR.symbol() to return a tuple. [Reviewed by Nils Bruin]
#6391: libGAP!  -- create a Cython library interface to gap [Reviewed by
Dmitrii Pasechnik, Ivan Andrus, Volker Braun, William Stein]
#12463: Polyhedron intersection and equality inconsistencies [Reviewed
by Andrey Novoseltsev, Volker Braun]
#13877: Metaticket: Make SAGE_DEBUG work [Reviewed by Volker Braun]
#13913: Jeroen Demeyer: Provide a "stripped" gcc 4.7.2 spkg [Reviewed by
Jean-Pierre Flori]
#9298: Memory leak in libsingular polynomial evaluation [Reviewed by
Charles Bouillaguet]
#10960: Better product error messages when can't multiply [Reviewed by
Michael Orlitzky]
#13863: Segfault in pari galoisconj0 [Reviewed by Volker Braun]
#13939: Fix the "SyntaxError: Non-ASCII character '\xe2'" [Reviewed by
Volker Braun]
#7773: Test failures with Fedora 12 on intel i7 860 processor [Reviewed
by Paul Zimmermann]
#9168: cygwin: ratpoints does not work correctly [Reviewed by
Karl-Dieter Crisman]
#9606: local/bin/sage-sage assumes 'sh' is bash [Reviewed by Leif
Leonhardy, John Palmieri, Stephen Montgomery-Smith]
#12401: Get Pynac functions to work on FreeBSD [Reviewed by Stephen
Montgomery-Smith]
#12411: pre-compiled Sage 4.8 binary fails some doctests on Ubuntu
[Reviewed by Paul Zimmermann]
#13866: Volker Braun: Experimental gdb spkg [Reviewed by Jeroen Demeyer]

Merged in sage-5.6.beta0:

#1920: Karl-Dieter Crisman: 3d graphics -- constant plot3d's [Reviewed
by Punarbasu Purkayastha]
#8952: Jernej Azarija: Odd Girth [Reviewed by Rob Beezer, Nathann Cohen]
#8992: Simon King: Coercion of univariate quotient polynomial rings
[Reviewed by Mike Hansen, Travis Scrimshaw]
#11453: Taylor Dupuy: residue function for laurent series ring elements
[Reviewed by Fr�d�ric Chapoton, Travis Scrimshaw]
#11839: Michael Orlitzky: sage.symbolic.expression.Expression.collect
has no documentation [Reviewed by Karl-Dieter Crisman, Travis Scrimshaw]
#12021: Emil Widmann: Doctest failure in sage_object.pyx when test run
as root [Reviewed by Volker Braun]
#12113: Yoora Yi Tenen: Add minor clarification about logs with bases
other than e [Reviewed by Travis Scrimshaw]
#12780: Michael Orlitzky: Be more careful about setting the Maxima
'domain' [Reviewed by Burcin Erocal]
#12930: Pierre Cagne: Poset of Alternating sign matrices [Reviewed by
Fr�d�ric Chapoton, Anne Schilling]
#13181: Burcin Erocal: _limit_latex_ cannot handle direction argument
[Reviewed by Karl-Dieter Crisman]
#13303: Xavier Caruso: is_unit and __invert__ for Polynomial Quotient
Rings [Reviewed by Travis Scrimshaw]
#13319: Jean-Pierre Flori: Python 2.7.3.px spkg does not build on
Cygwin. [Reviewed by Dmitrii Pasechnik]
#13322: Marco Streng: Precision loss when converting between Magma and
Sage [Reviewed by Volker Braun]
#13325: Jean-Pierre Flori: eclib does not build on Cygwin [Reviewed by
John Cremona]
#13417: Thomas Feulner, Punarbasu Purkayastha: Improved iteration on
finite \ZZ-submodules and vector spaces over finite fields [Reviewed by
Punarbasu Purkayastha, Thomas Feulner]
#13446: Michael Orlitzky: Revert fix (but not doctests) from #11919
[Reviewed by Burcin Erocal, Karl-Dieter Crisman]
#13719: Jean-Pierre Flori: Illegal free in graph_generators [Reviewed by
Nathann Cohen]
#13723: Thomas Feulner: Moving hamming_weight from sage.coding to
sage.modules [Reviewed by Punarbasu Purkayastha, Travis Scrimshaw]
#13728: Christian Stump: Implements some standard methods for fields
[Reviewed by Fr�d�ric Chapoton]
#13731: Nils Bruin, Simon King: Fix libsingular memory management
[Reviewed by Nils Bruin]
#13737: Volker Braun: fix cython warning in pynac.pyx [Reviewed by
Burcin Erocal]
#13740: Volker Braun: Upgrade Cython to 0.17.2 [Reviewed by Robert Bradshaw]
#13756: Volker Braun: fix developer manual docstrings [Reviewed by
Keshav Kini]
#13777: Karl-Dieter Crisman: Fix TimeSeries histogram plotting [Reviewed
by Punarbasu Purkayastha]
#13782: Michael Orlitzky: Dead code cleanup in
rings/polynomial/polynomial_modn_dense_ntl.pyx [Reviewed by Andr� Apitzsch]
#13784: Nathann Cohen: Move methods from GenericGraph to Graph [Reviewed
by David Coudert]
#13791: Travis Scrimshaw: Fixes to the conventions doc [Reviewed by
Charles Bouillaguet]
#13802: Karl-Dieter Crisman: Extra includes needed for letterplace for
Cygwin on XP [Reviewed by Alexander Dreyer]
#13813: David Coudert: Fix bug in chessboard graphs generator [Reviewed
by Nathann Cohen]
#13816: Karl-Dieter Crisman: Fix very minor doc issue for generic graphs
[Reviewed by Nathann Cohen]

Merged in sage-5.6.beta1:

#9016: Burcin Erocal: make morphisms hashable [Reviewed by Robert
Bradshaw, Travis Scrimshaw]
#11366: Travis Scrimshaw: Incorrect documentation for set difference
[Reviewed by Julian Rueth]
#11763: Volker Braun: Parents for polyhedra [Reviewed by Dmitrii Pasechnik]
#11768: Simon King: Get source code for parent/element classes of
categories [Reviewed by Volker Braun]
#11795: John Palmieri: Easily customize different viewers for PNG, DVI,
PDF [Reviewed by Nathann Cohen]
#12407: Thomas Rehn: Add the set of PrimitiveGroups [Reviewed by Vincent
Delecroix, Volker Braun]
#12587: Travis Scrimshaw: simplicial complexes lack hash function
[Reviewed by Christian Stump, John Palmieri]
#13211: Volker Braun, Jeroen Demeyer: Upgrade GAP to 4.5.7 [Reviewed by
Dmitrii Pasechnik]
#13375: Thomas Rehn: MIP set_problem_name crashes with GLPK backend if
name is too long [Reviewed by Christian Kuper]
#13423: Michael Orlitzky, Punarbasu Purkayastha: arrow2d missing
'linestyle' parameter docs [Reviewed by Punarbasu Purkayastha,
Karl-Dieter Crisman]
#13503: Jernej Azarija, David Coudert: Enhancement of `is_triangle_free'
addition of `triangles_count' and a minor change in
`spanning_trees_count' [Reviewed by Jernej Azarija]
#13516: Kevin Halasz: prime_powers doesn't work with start very well
[Reviewed by Dmitrii Pasechnik, Punarbasu Purkayastha, Karl-Dieter Crisman]
#13518: Christian Kuper: Additions for sensitivity analysis in
glpk_backend [Reviewed by Nathann Cohen]
#13625: Punarbasu Purkayastha: matrix_plot and title don't mix well
(yet) [Reviewed by Karl-Dieter Crisman]
#13708: Noud Aldenhoven, Burcin Erocal: Get assumptions by variables
[Reviewed by Burcin Erocal, Noud Aldenhoven]
#13727: Christian Stump: Minor improvements for dict_addition [Reviewed
by Fr�d�ric Chapoton]
#13734: Christian Stump: Implementation of latex method for
ElementWrapper [Reviewed by Nicolas M. Thi�ry]
#13742: Nathann Cohen: No Permutation should be created that its method
cannot handle [Reviewed by Dmitrii Pasechnik]
#13755: Jean-Pierre Flori: Let LinBox build with MPIR > 2.5.0 [Reviewed
by John Palmieri, Volker Braun]
#13760: Guillaume Moroz: Wrong basic interval arithmetic in
PolynomialRing [Reviewed by Paul Zimmermann]
#13778: Vincent Delecroix: lazy list [Reviewed by Travis Scrimshaw]
#13785: Nathann Cohen: Export a graph to a dictionary [Reviewed by David
Coudert]
#13789: Xavier Caruso: Opposite of sparse polynomials [Reviewed by
Charles Bouillaguet]
#13796: John Palmieri: fix small bug in Steenrod algebra multiplication
[Reviewed by Andr� Apitzsch]
#13829: Martin Albrecht: sage.misc.messaging [Reviewed by Volker Braun]
#13852: John Palmieri: fix "SEVERE" warning during docbuilding for
matrix/benchmark.py [Reviewed by Jeroen Demeyer]

Merged in sage-5.6.beta2:

#3955: Andrzej Giniewicz: make find_minimum_on_interval use _fast_float_
[Reviewed by Timo Kluck]
#4411: Marshall Hampton: phc breaks on one-variable problems [Reviewed
by Volker Braun]
#11523: Christian Stump: Implementation of Cohen-Macaulay test for
simplicial complexes [Reviewed by Travis Scrimshaw]
#12518: Vincent Delecroix: Enumerated set from iterator [Reviewed by
Travis Scrimshaw]
#13032: R. Andrew Ohana: Add ccache as an optional spkg [Reviewed by
Punarbasu Purkayastha]
#13074: Andrew Mathas: Implementation of TableauTuples [Reviewed by
Travis Scrimshaw]
#13119: Mike Zabrocki: ._apply_module_morphism() in
combinat/free_module.py doesn't handle zero element properly [Reviewed
by Travis Scrimshaw]
#13366: Kevin Halasz: Add Semidihedral Groups and Split Metacyclic
Groups as Permutation Groups [Reviewed by Volker Braun]
#13403: Travis Scrimshaw: Implementation of bijection between
KirillovReshetikhinCrystals and KirillovReshetikhinTableaux [Reviewed by
Anne Schilling]
#13638: Volker Braun: fix adjacency of rays [Reviewed by Dmitrii Pasechnik]
#13669: Volker Braun: sage -gdb ImportError [Reviewed by Simon King]
#13691: Nathann Cohen: Graph.has_homomorphism_to [Reviewed by Volker Braun]
#13725: John Palmieri: sum complexes: another example of simplicial
complexes [Reviewed by Travis Scrimshaw]
#13739: Burcin Erocal: more informative error message from
multiplication of symbolic expressions [Reviewed by Nils Bruin,
Karl-Dieter Crisman, Michael Orlitzky]
#13747: Nathann Cohen: Change default behaviour of Poset to facade =
True [Reviewed by Christian Kuper]
#13750: Nathann Cohen: List of functions in the Permutations file
[Reviewed by Dmitrii Pasechnik]
#13762: Chris Berg, Mike Zabrocki: Implement k-bounded quotient space
[Reviewed by Anne Schilling]
#13775: Ivan Andrus, Nathann Cohen: Bug in the Graph constructor in the
presence of loops AND multiple edges [Reviewed by Ivan Andrus, Nathann
Cohen]
#13799: Jean-Pierre Flori: cvxopt needs to link against gmp/mpir on
32-bit Windows XP Cygwin [Reviewed by Karl-Dieter Crisman]
#13800: Christian Nassau: sign error in Steenrod algebra multiplication
[Reviewed by John Palmieri]
#13809: Nathann Cohen: A constructor for folded cube graphs [Reviewed by
David Coudert]
#13815: Andr� Apitzsch: Fix type + code cleanup in numerical.optimize
[Reviewed by Volker Braun]
#13832: Volker Braun: Upgrade Cython to 0.17.3 [Reviewed by Jean-Pierre
Flori]
#13845: Martin Albrecht: BooleanPolynomialRing.random_element chokes on
terms parameter of type rational [Reviewed by Alexander Dreyer]
#13859: Steven Trogdon: Failure in gp pexpect interface when $COLUMNS is
exported to Sage [Reviewed by Jeroen Demeyer, Steven Trogdon]
#13860: Dmitrii Pasechnik: Maxima 5.26.0 update to make it install with
also the new ASDF (ECL 12.x) [Reviewed by Leif Leonhardy]
#13862: Nathann Cohen: Split graph_generators into several files
[Reviewed by David Coudert]
#13865: Volker Braun: Document that SAGE_DEBUG is three-state [Reviewed
by Jeroen Demeyer]
#13873: Jason Grout: Color and get_cmap should accept unicode [Reviewed
by Keshav Kini]

Merged in sage-5.6.beta3:

#5402: Charles Bouillaguet: Sparse determinants are slow [Reviewed by
Karl-Dieter Crisman]
#10352: William Stein, Nils Bruin, Volker Braun: upgrade ZODB to version
3.10.5 [Reviewed by Jeroen Demeyer]
#10538: Christian Stump, Gregg Musiker: Implementation of the class
ClusterQuiver [Reviewed by Dylan Rupel]
#11635: Jean-Pierre Flori: Ensure that libraries link to the shared
version of NTL by default [Reviewed by Karl-Dieter Crisman]
#12193: Volker Braun: Dimension of Polyhedron is not well defined
[Reviewed by David Loeffler]
#12907: Andr� Apitzsch: Replace some deprecated python functions in
sage/calculus [Reviewed by Karl-Dieter Crisman]
#13203: Fr�d�ric Chapoton: Promotion on Tableaux should force its
argument to be an Integer. [Reviewed by Nicolas M. Thi�ry]
#13460: Travis Scrimshaw: Type D_n spinor bijection [Reviewed by Anne
Schilling]
#13748: Jeroen Demeyer: Fix sig_block() doctest [Reviewed by Volker Braun]
#13806: Jean-Pierre Flori: Building complex_double.pyx fails on Cygwin
[Reviewed by Karl-Dieter Crisman]
#13821: Punarbasu Purkayastha: Change
sage.combinat.combinat.combinations() to use Combinations [Reviewed by
Travis Scrimshaw]
#13854: Thomas Feulner: Fix of _matrix_times_vector_ [Reviewed by Travis
Scrimshaw]
#13868: Volker Braun: Deal with hooked tp_* functions when using a debug
build of Python [Reviewed by Jean-Pierre Flori]
#13880: Volker Braun: Respect ulimit -v for GAP memory pool size
[Reviewed by Dmitrii Pasechnik]
#13881: Volker Braun: Enhanced debugging: cygdb and better backtraces
[Reviewed by Jeroen Demeyer]
#13882: Simon King: Deal with a trivial case in dlx_solver [Reviewed by
Fran�ois Bissey]
#13883: Alexander Dreyer: Fix an assertion in polybori [Reviewed by
Jean-Pierre Flori]
#13887: Jeroen Demeyer: Use a temporary directory for inline_fortran
[Reviewed by Volker Braun]
#13893: Jason Grout: stabilizer doesn't work with custom domain
[Reviewed by Mike Hansen]
#13896: Robert Bradshaw: Fix cython's gc_track and gc_untrack [Reviewed
by Jeroen Demeyer]
#13899: Jeroen Demeyer: Don't use TAB characters for indentation
[Reviewed by Leif Leonhardy, Karl-Dieter Crisman]
#13900: Alexander Dreyer: Remove unused _change_ordering  from
`BooleanPolynomialRing` [Reviewed by Martin Albrecht]
#13902: Jeroen Demeyer: Slowdown for PARI integer determinant [Reviewed
by Volker Braun]
#13903: John Perry: polynomial .reduce returns type int over p-adic
field [Reviewed by Karl-Dieter Crisman]
#13909: Marshall Hampton: Add Kirkman's icosahedron to polytope library
[Reviewed by Volker Braun]
#13910: Karl-Dieter Crisman: Remove databases/conv.py [Reviewed by Andr�
Apitzsch]
#13911: Anne Schilling, Mike Zabrocki: Updated doc tests for k-Schur
function and affine Schubert calculus book [Reviewed by Mike Zabrocki,
Anne Schilling]
#13920: Jeroen Demeyer: Non-ASCII character in smallgraphs.py [Reviewed
by Nathann Cohen]
#13924: Jeroen Demeyer: A few more long times [Reviewed by Volker Braun]

Merged in sage-5.6.rc0:

#7560: Jan Medlock: len(t_span) > 2 case creates len(t_span) -  1
solutions [Reviewed by Timo Kluck]
#9543: Peter Jeremy, Jean-Pierre Flori: Enable cephes on FreeBSD and
disable it on Cygwin [Reviewed by Stephen Montgomery-Smith, Karl-Dieter
Crisman]
#12792: Charles Bouillaguet: polybori / gb computation / set error
[Reviewed by Alexander Dreyer]
#13804: Jean-Pierre Flori: libfplll fails to build in parallel on Cygwin
[Reviewed by Karl-Dieter Crisman]
#13808: David Coudert: Gromov hyperbolicity of graphs [Reviewed by
Nathann Cohen]
#13851: Martin Albrecht: Add SAT Solver Interface to Reference Manual
[Reviewed by Nathann Cohen, John Palmieri, Nicolas M. Thi�ry]
#13875: David Coudert: Test memory allocation in distances_all_pairs
[Reviewed by Nathann Cohen]
#13921: Jeroen Demeyer: Make the GP executable work with SAGE_DEBUG on
Darwin [Reviewed by Volker Braun]
#13926: Jeroen Demeyer: Undo #13014 [Reviewed by Burcin Erocal,
Punarbasu Purkayastha]
#13927: Jeroen Demeyer: Disable startuptime test [Reviewed by Volker Braun]
#13930: Nils Bruin: remove bad is_subcategory implementation [Reviewed
by Simon King]
#13936: Nathann Cohen: Add encoding to smallgraphs.py [Reviewed by
Jeroen Demeyer]
#13937: Jeroen Demeyer: Properly detect GCC-4.3 [Reviewed by John Cremona]
#13938: Jeroen Demeyer: Don't set CCACHE_DIR [Reviewed by R. Andrew
Ohana, Punarbasu Purkayastha]

Merged in sage-5.6.rc1:

#13561: Keshav Kini, Jeroen Demeyer: Supply nice error message when
starting $SAGE_ROOT/sage without compiling Sage first [Reviewed by
Jeroen Demeyer, Punarbasu Purkayastha]
#13945: John Palmieri: testcflags.sh leaves a directory in spkg/build
[Reviewed by Jeroen Demeyer]
#13952: Punarbasu Purkayastha: Add documentation about importing cython
function from cells [Reviewed by Andr� Apitzsch]
#13959: Volker Braun: Parse wonky "top" output on OSX PPC [Reviewed by
Karl-Dieter Crisman]