Sage 5.4 released

[Jeroen Demeyer]

Sage 5.4 was released on 08 November 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 80 people contributed to this release. Of those, 11 made
their first contribution to Sage:

- Alejandro Morales [first contribution]
- Alex Csar [first contribution]
- Alexander Dreyer
- Aly Deines
- Andrew Mathas
- Andrey Novoseltsev
- André Apitzsch
- Anne Schilling
- Armin Straub
- Benjamin Jones
- Bjarke Hammersholt Roune
- Burcin Erocal
- Charles Bouillaguet
- Chris Berg
- Dan Bump
- Dan Drake
- Daniel Bump
- David Coudert
- David Kirkby
- David Roe
- Davide Cervone [first contribution]
- Dmitrii Pasechnik
- Francis Clarke
- Franco Saliola
- François Bissey
- Frédéric Chapoton
- Hugh Thomas
- Jason Bandlow
- Jason Grout
- Jean-Philippe Labbé [first contribution]
- Jean-Pierre Flori
- Jeroen Demeyer
- John Cremona
- John Palmieri
- John Perry
- Jonathan Gutow
- Julian Rueth
- Karl-Dieter Crisman
- Kelvin Li
- Keshav Kini
- Kevin Halasz
- Kiran Kedlaya
- Leif Leonhardy
- Luis Felipe Tabera Alonso
- Luiz Aquino [first contribution]
- Maarten Derickx
- Marco Streng
- Mariah Lenox
- Marshall Hampton
- Martin Albrecht
- Michael Welsh [first contribution]
- Mike Hansen
- Mike Zabrocki
- Nathan Carter
- Nathann Cohen
- Nicolas M. Thiéry
- Nils Bruin
- Paul Zimmermann
- Paul-Olivier Dehaye
- Paulo César Pereira de Andrade
- Punarbasu Purkayastha
- R. Andrew Ohana
- Rob Beezer
- Robert Bradshaw
- Robert Harron
- Samuel Lelievre [first contribution]
- Sarah Chisholm [first contribution]
- Sebastian Luther [first contribution]
- Simon King
- Stefano Leucci [first contribution]
- Stepan Starosta
- Stephen Montgomery-Smith
- Steven Trogdon
- Thomas Feulner [first contribution]
- Tim Dumol
- Titus Nicolae
- Travis Scrimshaw
- Valentin Féray
- Volker Braun
- William Stein

* Release manager: Jeroen Demeyer.

* We closed 127 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.4/tickets.html

Closed tickets:

#9238: J. Gutow's update to Jmol in the notebook... [Reviewed by Jason
Grout, Karl-Dieter Crisman, William Stein, Jonathan Gutow]
#9428: Internationalize the Sage Notebook [Reviewed by Keshav Kini, Luiz
Aquino, Dan Drake, Tim Dumol]
#11471: Add i18n capabilities to the Flask notebook [Reviewed by Keshav
kini, Luiz Aquino, Dan Drake, Tim Dumol, Mike Hansen]
#11789: compile python with ssl-support if possible [Reviewed by Jeroen
Demeyer]
#11805: Update optional MPC spkg to version 0.9 [Reviewed by Jean-Pierre
Flori]
#12089: Dmitrii Pasechnik, Karl-Dieter Crisman, Jean-Pierre Flori:
Singular does not build on Cygwin - static libs problem [Reviewed by
Karl-Dieter Crisman, Dmitrii Pasechnik, Jean-Pierre Flori]
#12846: Multivariate Factorisation can be randomly slow (over extension
fields) [Reviewed by Jeroen Demeyer]
#12918: segmentation fault with multivariate polynomial factorization
[Reviewed by Jeroen Demeyer]
#12928: critical bug in multivariate polynomial factorization over GF(2)
[Reviewed by Jeroen Demeyer]
#13129: libSingular segmentation fault in factor [Reviewed by Jeroen
Demeyer]
#13344: Jean-Pierre Flori, Alexander Dreyer, Jeroen Demeyer: on CYGWIN,
Singular LIB files get copied to SAGELOCAL/lib [Reviewed by Dmitrii
Pasechnik, Jean-Pierre Flori]
#13384: Keshav Kini: pyOpenSSL SPKG [Reviewed by John Palmieri]
#13410: Robert Bradshaw: Patchbot timeouts [Reviewed by Volker Braun]
#6003: Additions to Cholesky decomposition [Reviewed by Rob Beezer]
#9511: Upgrade Givaro to version 3.7.0 [Reviewed by Volker Braun]
#10153: Canonical generator matrices for linear codes and their
automorphism groups [Reviewed by Thomas Feulner]
#11718: Upgrade LinBox to version 1.1.7 [Reviewed by Volker Braun,
Martin Albrecht]
#13340: log scale plot fails if xmin > xmax [Reviewed by Punarbasu
Purkayastha]
#4319: Update Italian tutorial for #4285 [Reviewed by Jeroen Demeyer]
#7832: singular-3-1-0-4-20090818.p2 - fix compilation on FreeBSD
[Reviewed by Stephen Montgomery-Smith]
#13499: Volker Braun: Update TOPCOM to 0.17.4 [Reviewed by Marshall Hampton]
#9965: Make SYMPOW not write to files under global Sage installations
[Reviewed by Jeroen Demeyer]
#3302: python_gnutls fails to upgrade on OSX in case Sage was moved
[Reviewed by Jeroen Demeyer]
#4797: Run sage -ba instead of sage -b after upgrading Cython [Reviewed
by Jeroen Demeyer]
#7511: gnutls-2.2.1 fails to build on HP-UX [Reviewed by Jeroen Demeyer]
#7542: Security issues in gnutls-2.2.1 [Reviewed by Jeroen Demeyer]
#8437: wrong unix rights/permissions of some files after make dist
[Reviewed by Jeroen Demeyer]
#9308: Add an spkg-check file for GnuTLS [Reviewed by David Kirkby,
Jeroen Demeyer]
#9974: The current (rather old) version of GnuTLS fails to install on
AIX 5.3 [Reviewed by Jeroen Demeyer]
#9975: Update GnuTLS and clean up the package [Reviewed by Mariah
Lenox, Jeroen Demeyer]
#10624: Slashes disappear in docstrings [Reviewed by John Palmieri]
#12331: updating an spkg may render Sage non-relocatable [Reviewed by
Jeroen Demeyer]
#12785: update the faq: no need for gfortran... [Reviewed by Jeroen Demeyer]
#13545: Can't create a symbolic variable named 'lambda' [Reviewed by
Nils Bruin, Burcin Erocal]
#13551: Autotools spkg does not build correctly on systems without
autotools installed [Reviewed by Jeroen Demeyer]
#12707: Keshav Kini, John Palmieri, Jeroen Demeyer: Update the git spkg
[Reviewed by Leif Leonhardy, Volker Braun]
#13150: Jeroen Demeyer: Create an optional GCC-4.7.2 package [Reviewed
by Volker Braun]
#13292: Jeroen Demeyer: Bad symlink SAGE_DATA/graphs/graphs.db in binary
distributions [Reviewed by Leif Leonhardy]
#13295: Simon King: p_group_cohomology 2.1.3 [Reviewed by John Palmieri]
#13302: Matrix constructor does not return over padic field [Reviewed by
Julian Rueth]
#13602: partition distinct parts max part error [Reviewed by Alejandro
Morales]

Merged in sage-5.4.beta0:

#5457: Mike Zabrocki, Anne Schilling, Jason Bandlow: Refactor symmetric
functions and k-bounded subspace [Reviewed by Dan Bump, Nicolas M.
Thiéry, Jeroen Demeyer]
#5489: Mike Hansen, Bjarke Hammersholt Roune: Add an interface for 4ti2
to Sage [Reviewed by Martin Albrecht, John Palmieri, Marshall Hampton,
Frédéric Chapoton]
#9774: Rob Beezer, Davide Cervone, John Palmieri, Jason Grout, Nathan
Carter: Use MathJax instead of jsMath [Reviewed by Jason Grout, John
Palmieri, Punarbasu Purkayastha, Keshav Kini]
#11021: Leif Leonhardy, Kelvin Li, Jeroen Demeyer: Fix install_package()
library function [Reviewed by Kelvin Li, Leif Leonhardy, John Palmieri]
#11305: Travis Scrimshaw: Bijection between Rigged Configurations and
Crystal Paths [Reviewed by Anne Schilling]
#11440: Paul-Olivier Dehaye: compute the dimension of partition
[Reviewed by Frédéric Chapoton]
#11913: John Palmieri: Notebook hang in ?? source display Trackback
[Reviewed by Keshav Kini]
#12299: Jonathan Gutow: Upgrade Jmol to 12.3.27, Advance Jmol
Interactive Features in Flask Notebook [Reviewed by Karl-Dieter Crisman,
Steven Trogdon, Punarbasu Purkayastha, John Palmieri, Dan Drake]
#12606: Jeroen Demeyer: Fix sage --info <package> [Reviewed by John
Palmieri]
#12946: Mike Hansen: Bug in Compositions [Reviewed by Andrew Mathas]
#13121: Keshav Kini: Upgrade sagenb to 0.10.x [Reviewed by John
Palmieri, Jonathan Gutow]
#13157: Jeroen Demeyer: inline_fortran is STILL broken on OS X [Reviewed
by Karl-Dieter Crisman, Benjamin Jones]
#13231: Alex Csar: Check if a lattice is atomic [Reviewed by Frédéric
Chapoton]
#13237: Jeroen Demeyer, Alexander Dreyer, Dmitrii Pasechnik, Karl-Dieter
Crisman, Jean-Pierre Flori: Upgrade Singular [Reviewed by Alexander
Dreyer, François Bissey]
#13253: Maarten Derickx: galois_action on cusps has a bug and incorrect
documentation [Reviewed by Marco Streng]
#13259: Andrew Mathas: Correcting implementation of "negative" quantum
integers [Reviewed by Armin Straub, Nicolas Thiery]
#13294: Stefano Leucci: Add test for not necessarily induced subgraphs
to Graph.is_subgraph() method [Reviewed by David Coudert]
#13314: Paul Zimmermann, Jeroen Demeyer: segmentation fault with roots
over ComplexField [Reviewed by John Cremona]
#13385: John Palmieri, Keshav Kini: Remove OpenSSL dependency from Sage
[Reviewed by Keshav Kini, John Palmieri]
#13389: Keshav Kini: Minor fix to LiE optional SPKG [Reviewed by John
Palmieri]
#13390: Stepan Starosta: Non Negative Integers: fix contains method
[Reviewed by Mike Hansen]

Merged in sage-5.4.beta1:

#6654: Valentin Féray: New features in group algebra category [Reviewed
by Frédéric Chapoton]
#8899: Jason Bandlow, Chris Berg, Franco Saliola, Nicolas M. Thiéry:
Implement non commutative symmetric functions [Reviewed by Mike
Zabrocki, Franco Saliola, Mike Hansen]
#9906: Leif Leonhardy, Jeroen Demeyer: Move the RPy package outside of
the R package [Reviewed by Karl-Dieter Crisman, John Palmieri]
#12883: Paulo César Pereira de Andrade, Martin Albrecht: Update LinBox
to most recent upstream release [Reviewed by Volker Braun, Jeroen Demeyer]
#12972: John Cremona: Fix small bug in elliptic curve saturation
[Reviewed by Volker Braun]
#12994: R. Andrew Ohana: Serialization of setuptools targets in
spkg/standard/deps [Reviewed by Jeroen Demeyer]
#13145: David Roe: Sage's noncommutative rings don't always increment a
refcount [Reviewed by Martin Albrecht]
#13164: Paulo César Pereira de Andrade, Martin Albrecht, Jean-Pierre
Flori: Update Givaro to 3.7.1 [Reviewed by Volker Braun]
#13284: Alexander Dreyer: Some conversion between BooleanPolynomialRing
and QQ[.....] are missing [Reviewed by Charles Bouillaguet]
#13298: John Cremona: Update Cremona's table of elliptic curves to
270000 [Reviewed by R. Andrew Ohana]
#13327: Andrey Novoseltsev: Allow conversion of strings to iterated
polynomial rings [Reviewed by Frédéric Chapoton]
#13391: Daniel Bump: WeylCharacterRing improvement [Reviewed by Anne
Schilling]
#13395: Jeroen Demeyer: Fix upgrading with GCC [Reviewed by John Palmieri]
#13404: Nicolas M. Thiéry, Mike Zabrocki: Improved printing for
symmetric function bases and misc refactoring [Reviewed by Anne Schilling]
#13416: Jeroen Demeyer: Fix GAP dependencies [Reviewed by Volker Braun]
#13427: David Kirkby: Numerical noise causing sage/numerical/optimize.py
to fail on SPARC [Reviewed by Volker Braun]
#13428: Jeroen Demeyer: Race condition in R installation [Reviewed by
John Palmieri]

Merged in sage-5.4.beta2:

#8908: Jean-Philippe Labbé: Add the Young subgroup method to symmetric
groups [Reviewed by Mike Hansen, Frédéric Chapoton]
#11442: Paul-Olivier Dehaye: Computes the Plancherel measure of an
individual partition [Reviewed by Frédéric Chapoton]
#13065: Francis Clarke: simon_two_descent not working [Reviewed by John
Cremona]
#13107: Titus Nicolae, Burcin Erocal: python long division causing
infinite loop [Reviewed by Burcin Erocal, Jean-Pierre Flori]
#13123: R. Andrew Ohana, Jeroen Demeyer: Move SAGE_DATA to
SAGE_LOCAL/share [Reviewed by François Bissey, Jeroen Demeyer]
#13316: Jean-Pierre Flori: Update pynac to version 0.2.5 [Reviewed by
Burcin Erocal]
#13348: Jeroen Demeyer: Set CPATH in sage-env [Reviewed by Volker Braun]
#13361: Volker Braun: Report startuptime exclusive children [Reviewed by
John Palmieri]
#13362: David Coudert: Fix bug in build_flow_graph [Reviewed by Keshav
Kini, Nathann Cohen]
#13397: Jeroen Demeyer: sage-location: handle lib64 also [Reviewed by
John Palmieri]
#13399: Anne Schilling, Mike Zabrocki: Fixes to symmetric functions
[Reviewed by Mike Zabrocki, Anne Schilling]
#13415: Jeroen Demeyer: Prevent unneeded rebuilding when upgrading
[Reviewed by John Palmieri]
#13420: Jeroen Demeyer: The usual #long time additions [Reviewed by
Volker Braun]
#13431: Kevin Halasz: Add sign as an alias for signature for
permutations [Reviewed by Rob Beezer, John Cremona]
#13443: Jeroen Demeyer: Some clean up of R spkg [Reviewed by Karl-Dieter
Crisman, John Palmieri]
#13449: Jonathan Gutow: Problem with testjava.sh in jmol package finding
bash [Reviewed by Dmitrii Pasechnik]
#13454: Jeroen Demeyer: Fix odlyzko database doctests [Reviewed by
Volker Braun]
#13455: Andrey Novoseltsev: Remove jsMath <> workaround [Reviewed by
John Palmieri]
#13457: Jeroen Demeyer: Various small fixes to sage-bdist [Reviewed by
John Palmieri]
#13462: Aly Deines: quaternion algebra discriminant generalized to
number fields [Reviewed by Sarah Chisholm]
#13497: Jeroen Demeyer, John Palmieri: Disable sage --info test for
bdists [Reviewed by John Palmieri]
#13502: Jason Grout: vector norm doesn't work with python integers
[Reviewed by Rob Beezer]
#13508: John Palmieri: deprecate jsmath_avoid_list etc. [Reviewed by
Nicolas M. Thiéry]

Merged in sage-5.4.rc0:

#3979: Francis Clarke: Power series composition messes up precision
[Reviewed by Kiran Kedlaya, Luis Felipe Tabera Alonso, Frédéric Chapoton]
#5160: Jeroen Demeyer: Change name of misc/sagex_ds.pyx [Reviewed by
Karl-Dieter Crisman]
#11446: Paul-Olivier Dehaye: compute the outline of a partition
[Reviewed by Frédéric Chapoton]
#11770: Robert Harron: Add ability to detect CM number fields and take
complex conjugate of their elements [Reviewed by Francis Clarke, Jeroen
Demeyer]
#12496: Samuel Lelievre, Hugh Thomas: Improve doctest coverage for
integer_ring.pyx [Reviewed by Hugh Thomas, Jeroen Demeyer]
#12802: John Perry: test containment of ideals in class MPolynomialIdeal
[Reviewed by Andrey Novoseltsev, Simon King]
#13289: David Coudert: Determine if a vertex is a cut vertex [Reviewed
by Sebastian Luther]
#13444: Anne Schilling, Mike Zabrocki: Doc Tests for book "k-Schur
Primer" [Reviewed by Anne Schilling, Mike Zabrocki]
#13459: Jeroen Demeyer: spkg/bin/sage: do not change directory [Reviewed
by John Palmieri]
#13509: Aly Deines: Pari nfhnf - hnf over number fields [Reviewed by
Jeroen Demeyer]
#13515: Jeroen Demeyer: Support the GCC spkg on Ubuntu 12.04 [Reviewed
by Volker Braun]
#13524: Michael Welsh: Error in Linear Algebra constructions [Reviewed
by Dmitrii Pasechnik]
#13527: Franco Saliola: modify repr of SubsetAlgebra (example of with
realizations) to conform to standards set out in #13404 [Reviewed by
Mike Hansen]

Merged in sage-5.4.rc1:

#13512: Francis Clarke: Docstring formatting in misc_c.pyx [Reviewed by
Jeroen Demeyer]
#13537: Julian Rueth: Stopgap for 13439 [Reviewed by Volker Braun]
#13544: John Palmieri: Omit .DS_Store when building 'all' documentation
[Reviewed by Michael Welsh]

Merged in sage-5.4.rc2:

#7688: Jeroen Demeyer: Remove byte-compiled files from extcode [Reviewed
by R. Andrew Ohana]
#9697: Paul-Olivier Dehaye: DS_Store garbage in flint spkg [Reviewed by
Karl-Dieter Crisman]
#10738: Volker Braun: insecure temp file in testcc.sh, testcxx.sh
[Reviewed by Jeroen Demeyer]
#13579: Jeroen Demeyer, Volker Braun: Python sys.path security risk
[Reviewed by Volker Braun, Jeroen Demeyer, David Roe]
#13582: John Palmieri: Add (brief) info about SAGE_TESTDIR to other
pieces of doc [Reviewed by Karl-Dieter Crisman]
#13595: Jeroen Demeyer: LD_LIBRARY_PATH potential security risk
[Reviewed by Volker Braun]

Merged in sage-5.4.rc3:

#13258: André Apitzsch: Replace some deprecated functions in the
documentation [Reviewed by Robert Bradshaw]
#13631: Jeroen Demeyer: Sage refuses to run despite safe directory
[Reviewed by Volker Braun]

Merged in sage-5.4.rc4:

#13681: Jeroen Demeyer: fix issues with SAGE_TMP [Reviewed by Volker Braun]