Sage 5.5 released

[Jeroen Demeyer]

Sage 5.5 was released on 21 December 2012. 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 59 people contributed to this release. Of those, 4 made
their first contribution to Sage:

- Alexander Dreyer
- Aly Deines
- Andrew Mathas
- André Apitzsch
- Anne Schilling
- Ben Hutz [first contribution]
- Benjamin Jones
- Burcin Erocal
- Charles Bouillaguet
- Chris Berg
- Christian Stump
- Daniel Bump
- David Coudert
- David Eklund
- David Roe
- Dmitrii Pasechnik
- Franco Saliola
- François Bissey
- Frédéric Chapoton
- Hugh Thomas
- Jan Groenewald
- Jason Bandlow
- Jason Grout
- Jean-Pierre Flori
- Jeroen Demeyer
- John Cremona
- John Palmieri
- Joris Vankerschaver
- Julian Rueth
- Julien Puydt
- Karl-Dieter Crisman
- Kevin Halasz
- Luis Serrano [first contribution]
- Marco Streng
- Marshall Hampton
- Martin Albrecht
- Mathieu Guay-Paquet
- Michael Brickenstein
- Mike Hansen
- Mike Zabrocki
- Moritz Minzlaff
- Nathann Cohen
- Nicolas M. Thiéry
- Nils Bruin
- Philipp Jovanovic [first contribution]
- Punarbasu Purkayastha
- R. Andrew Ohana
- Risan [first contribution]
- Robert Bradshaw
- Sarah Chisholm
- Sebastian Luther
- Simon King
- Sébastien Labbé
- Timo Jolivet
- Timo Kluck
- Travis Scrimshaw
- Volker Braun
- William Stein
- Xavier Caruso

* Release manager: Jeroen Demeyer.

* We closed 92 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.5/tickets.html

Closed tickets:

#11708: maxima doesn't build on Linux ppc64 (silius on skynet) [Reviewed
by Jeroen Demeyer]
#13210: ATLAS: flush output before os.system() [Reviewed by Jeroen Demeyer]
#13333: Copy libpari.dll.a on Cygwin [Reviewed by Dmitrii Pasechnik,
Jean-Pierre Flori]
#13408: atlas-3.8.4 package does not compile on rhel 5 systems, upgrade
to atlas-3.10.0 [Reviewed by Karl-Dieter Crisman]
#13450: Fix refcounting of libsingular rings [Reviewed by Nils Bruin]

Merged in sage-5.5.beta0:

#715: Simon King, Jean-Pierre Flori: Parents probably not reclaimed due
to too much caching [Reviewed by Jean-Pierre Flori, Simon King, Nils Bruin]
#9265: Jason Bandlow, Andrew Mathas: Remove `CombinatorialClass` from
sage.combinat.tableau [Reviewed by Andrew Mathas, Anne Schilling]
#10527: Christian Stump: Implementation of quiver mutation type
[Reviewed by Hugh Thomas]
#11521: Simon King, Nils Bruin: Use weak references to cache homsets
[Reviewed by Jean-Pierre Flori, Nils Bruin, Simon King]
#12995: Moritz Minzlaff: A first step towards linear systems of
hypersurfaces in Sage [Reviewed by David Eklund]
#13188: Nathann Cohen: Boring paperwork in the graph/ files [Reviewed by
Travis Scrimshaw]
#13244: John Palmieri: make some simplicial complexes faster [Reviewed
by Travis Scrimshaw]
#13306: David Coudert: Generators for chessboard graphs: King, Queen,
Knight, Bishop, Rooks [Reviewed by Sebastian Luther, Nathann Cohen]
#13406: Nicolas M. Thiéry: Optimize
CombinatorialFreeModule.Element._vector_ [Reviewed by Mathieu
Guay-Paquet, Franco Saliola,]
#13411: Frédéric Chapoton: implement the Holt Graph [Reviewed by Nathann
Cohen]
#13461: Daniel Bump: Another WeylCharacterRing speedup [Reviewed by Anne
Schilling]
#13519: Joris Vankerschaver: Spline is not recomputed when interpolation
points change [Reviewed by Travis Scrimshaw]
#13534: Jean-Pierre Flori, Jeroen Demeyer: Upgrade to PARI-2.5.3
[Reviewed by Dmitrii Pasechnik, François Bissey]
#13562: Robert Bradshaw: lazily import graph_generators [Reviewed by
David Coudert]
#13575: Philipp Jovanovic: Add flexibility when creating
exclusion-clauses using 'solve' from boolean_polynomials.py [Reviewed by
Martin Albrecht]
#13586: Burcin Erocal: BuiltinFunction expects to be instantiated only
once [Reviewed by Karl-Dieter Crisman]
#13590: John Palmieri: Fix random simplicial complexes [Reviewed by
Travis Scrimshaw]
#13592: Julian Rueth: padics should not be iterable [Reviewed by David Roe]

Merged in sage-5.5.beta1:

#4453: William Stein: elliptic curves -- heegner_index command gives
nonsense when rank > 1 [Reviewed by John Cremona, Robert Bradshaw]
#6822: John Palmieri: "empty" .spkg files in binary builds confusing
[Reviewed by Jeroen Demeyer]
#9191: Karl-Dieter Crisman, Jeroen Demeyer: Running .spyx files from the
command line doesn't work anymore [Reviewed by Jeroen Demeyer,
Karl-Dieter Crisman]
#11353: David Coudert: bitset complement [Reviewed by Nathann Cohen]
#11395: Marshall Hampton, François Bissey: Upgrade Gfan to latest
release (version 0.5) [Reviewed by François Bissey, Volker Braun]
#11403: Jeroen Demeyer, David Roe: NTL error while inverting q-adic
number with fixed modulus precision [Reviewed by Julian Rueth]
#12341: R. Andrew Ohana: Empty (full) cremona database in Sage 4.8
causes tests to fail [Reviewed by John Cremona]
#12513: Robert Bradshaw: Slow CDF fast_callable powers [Reviewed by Timo
Kluck, Jeroen Demeyer]
#12584: David Roe: coercing large numbers into elements of GF fails
[Reviewed by Travis Scrimshaw]
#12586: Julien Puydt: [ARM] Maxima has a strange numerical precision
issue [Reviewed by Dmitrii Pasechnik]
#12905: Nathann Cohen: Memory leaks with Cliquer [Reviewed by David Coudert]
#12943: Hugh Thomas: Tableau_class.__div__, Partition_class.__div__ are
checking domination when they should check inclusion [Reviewed by Mike
Hansen, Andrew Mathas]
#13072: Andrew Mathas: Implementation of PartitionTuple + some minor
fixes to partition.py [Reviewed by Travis Scrimshaw]
#13082: Robert Bradshaw: Powering rings to a 2-tuple should create
matrix spaces. [Reviewed by Jason Grout]
#13147: David Roe, Mike Hansen: Delay the evaluation of SAGE_TMP in
order to facilitate forking in doctesting [Reviewed by John Palmieri]
#13159: Simon King: Cache the number of arguments of a cached method
[Reviewed by David Roe]
#13365: Kevin Halasz: Add Semidirect Product Method for Permutation
Groups [Reviewed by Benjamin Jones]
#13412: Simon King: PowerSeriesRing should call Ring.__init__ [Reviewed
by Travis Scrimshaw]
#13501: Nicolas M. Thiéry, Simon King: Fix two bugs in sage.misc.c3's
implementation of the algorithm C3 [Reviewed by Simon King]
#13506: Chris Berg: Monomial basis of NCSF [Reviewed by Luis Serrano,
Mike Zabrocki]
#13520: Joris Vankerschaver: Derivative/integral of cubic splines in
sage/gsl/interpolation.pyx [Reviewed by Travis Scrimshaw]
#13563: Anne Schilling: KR crystals for spinors in type D [Reviewed by
Daniel Bump, Nicolas M. Thiéry]
#13574: Jeroen Demeyer: sage-spkg: check much earlier whether package is
already installed [Reviewed by John Palmieri]
#13578: David Coudert: Generator for Ringed-Tree graphs [Reviewed by
Nathann Cohen]
#13599: Nathann Cohen: Bugfix in is_cartesian_product [Reviewed by David
Coudert]
#13634: Travis Scrimshaw: Fix to output of scientific notation for real
interval field [Reviewed by Robert Bradshaw]
#13639: Jeroen Demeyer: Inverting 0 mod 1 [Reviewed by Robert Bradshaw]
#13643: Jason Grout: default norm for RDF/CDF matrices is inconsistent
with other types of matrices [Reviewed by Punarbasu Purkayastha]
#13646: Nathann Cohen, Volker Braun: Bug in p.add_constraint (when input
is True/False) [Reviewed by Dmitrii Pasechnik]
#13653: Volker Braun: Missing Exception type in element.pyx [Reviewed by
Robert Bradshaw]

Merged in sage-5.5.beta2:

#7797: Simon King, Michael Brickenstein, Burcin Erocal: Full interface
to letterplace from singular [Reviewed by Alexander Dreyer]
#11476: Andrew Mathas: PartitionTuples.cardinality has problems
[Reviewed by Travis Scrimshaw]
#12533: Risan: arbitrary precision LP solver backend [Reviewed by David
Coudert, Nathann Cohen, Dmitrii Pasechnik]
#12565: R. Andrew Ohana: E = EllipticCurve('10a1') gives a stupid
traceback (rather than a smart one) [Reviewed by John Cremona]
#13143: John Palmieri: Use MathJax by default when building docs from
Makefile [Reviewed by Dmitrii Pasechnik]
#13180: Martin Albrecht: Compare elements of finite fields somehow
consistently [Reviewed by André Apitzsch]
#13419: Frédéric Chapoton: 100% doc for quartic curves [Reviewed by
André Apitzsch]
#13530: Joris Vankerschaver: Hide sage/gsl/interpolation/Spline
internals [Reviewed by Travis Scrimshaw]
#13550: Mike Zabrocki: improvements and additions to dyck_words.py
[Reviewed by Christian Stump]
#13572: Chris Berg: Implement the immaculate basis of NCSF [Reviewed by
Luis Serrano, Mike Zabrocki]
#13635: Nathann Cohen: sage.isgci.update_db is broken [Reviewed by David
Coudert]
#13640: Xavier Caruso: q-numbers coutings flags stable under a nilpotent
endomorphism [Reviewed by Frédéric Chapoton]
#13641: Xavier Caruso: Short representation of morphisms [Reviewed by
Travis Scrimshaw]
#13663: Punarbasu Purkayastha: Implement __len__ in LinearCode [Reviewed
by Dmitrii Pasechnik]
#13665: David Coudert: New implementation of the blocks_and_cut_vertices
method [Reviewed by Nathann Cohen]
#13670: Charles Bouillaguet: Inversion in polynomial quotient rings
could give clearer error message when element is non-invertible
[Reviewed by Marco Streng]
#13671: Charles Bouillaguet: p.lift(...) results are non-deterministic
and incoherent for multivariate polynomials [Reviewed by Marco Streng]
#13675: Charles Bouillaguet: multivariate polynomials lack the
inverse_mod(...) method [Reviewed by Marco Streng]
#13676: Sébastien Labbé: Add _latex_ method for WordMorphism [Reviewed
by Timo Jolivet]
#13692: Nils Bruin: factor_trial_division returns Python longs as
exponents [Reviewed by Dmitrii Pasechnik]
#13704: Punarbasu Purkayastha: Fix _div_ in multivariate rings [Reviewed
by Ben Hutz]

Merged in sage-5.5.rc0:

#12091: Volker Braun: chained inequalities bug in add_constraint to
MixedIntegerLinearProgram [Reviewed by Dmitrii Pasechnik]
#13075: Nathann Cohen: Toroidal6RegularGrid2dGraph [Reviewed by David
Coudert]
#13226: John Palmieri: pseudomanifold test for simplicial complexes
[Reviewed by Volker Braun]
#13513: Sarah Chisholm: Has standard involution function for algebras.
[Reviewed by Aly Deines]
#13573: Chris Berg: Implement the dual immaculate basis of QSym
[Reviewed by Luis Serrano, Mike Zabrocki]
#13650: Volker Braun, Dmitrii Pasechnik: Base rings for MIP backends
[Reviewed by Dmitrii Pasechnik, Volker Braun]
#13664: Nathann Cohen: Another bug in add_edge [Reviewed by David Coudert]
#13668: Sébastien Labbé: MemoryError raised by WordMorphism.fixed_points
method [Reviewed by Timo Jolivet]
#13677: Sébastien Labbé: Improve __repr__ and __str__ methods of
WordMorphism [Reviewed by Timo Jolivet]
#13699: Nathann Cohen, David Coudert: Another bug in graph products....
[Reviewed by David Coudert]

Merged in sage-5.5.rc1:

#13616: David Roe: SIGABRT in unit_part() for padic extension elements
[Reviewed by Volker Braun]
#13702: Jan Groenewald: Fix path in SAGE_ROOT/spkg/README.txt [Reviewed
by Karl-Dieter Crisman]
#13741: Simon King: Proper deallocation of the (unique) pari instance
[Reviewed by Volker Braun]
#13745: Jean-Pierre Flori: Typo in lcalc.py [Reviewed by Volker Braun]
#13746: Jean-Pierre Flori, Simon King: Do not delete a borrowed
reference to reduction strategies in pbori [Reviewed by Alexander Dreyer]
#13794: Jeroen Demeyer, John Palmieri: sage -n is broken in 5.5rc0
[Reviewed by Punarbasu Purkayastha]
#13797: Volker Braun: LinearFunction.__hash__ overflow [Reviewed by
Dmitrii Pasechnik]
#13807: John Palmieri: Fix remaining temporary filename issues (like in
animate.py) [Reviewed by Karl-Dieter Crisman]