Sage 3.2.1 released

[mabshoff]

[Note: Binaries for common platforms have been created and mirrored
out]

Hello folks,

Sage 3.2.1 was released on December 1st, 2008. It is available at

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

* About Sage (http://www.sagemath.org)

Sage is developed by volunteers and combines 71 open source packages.
It is available for download from www.sagemath.org and its mirrors in
source or binary form. If you have any questions and/or problems,
please report them to the Google groups sage-devel or sage-support.
You can also drop by in #sage-devel or #sage-support in freenode.

---------------------------------------------------------------------

The following 43 people contributed to this release:

* Michael Abshoff
* Martin Albrecht
* Nick Alexander
* Jason Bandlow
* Arnaud Bergeron
* Tom Boothby
* Robert Bradshaw
* Ondrej Certik
* Craig Citro
* Timothy Clemans
* John Cremona
* Alexander Dreyer
* Burcin Erocal
* Gary Furnish
* Alex Ghitza
* Andrzej Giniewicz
* Dan Gordan
* Jason Grout
* Carlo Hamalainen
* Marshall Hampton
* Mike Hansen
* Wilfried Huss [first contribution]
* David Joyner
* Simon King
* Sebastien Labbe
* Kwankyu Lee [first contribution]
* David Loeffler
* Robert Miller
* Guillaume Moroz [first contribution]
* Tobias Nagel
* Brett Nakashima
* Willem Jan Palenstijn
* John Palmieri
* Minh Nguyen
* Franco Saliola
* Chris Swierczewski
* Jaap Spies
* William Stein
* Philippe Theveny [first contribution]
* Nicolas Thiery
* Mark Watkins
* Carl Witty
* Paul Zimmermann

Cheers,

Michael Abshoff (release chair), William Stein

* Major Features, New Spkgs and Bugfixes

See the Sage 3.2.1 Release Tour at

http://wiki.sagemath.org/sage-3.2.1

* Known Issues with 3.2.1:

* RHEL 5 clisp build issue: the latest clisp.spkg does not build
so please use the clisp.spkg from Sage 3.0.3.

* Bug Statistics

We closed 120 tickets. For details see

http://trac.sagemath.org/sage_trac/milestone/sage-3.2.1

or check out the closed ticket section at the end of the
announcement.

* Upcoming Releases

The next release will be 3.2.2, chaired by Michael Abshoff. It will
be a release focusing on merging existing patches from trac in
preparation for the big docstring Sphinx conversion planned for Sage
3.3.
The release cycle will be on the short side, i.e. about 7 days are
planned.

* Doctesting Coverage

For 3.2 we had:

Overall weighted coverage score: 63.0%
Total number of functions: 21578

We increased coverage by 0.3% in 3.2.1 while adding 39 functions:

Overall weighted coverage score: 63.3%
Total number of functions: 21617

* Closed Tickets:

Merged in Sage 3.2.1.rc1:

#3122: Michael Abshoff: after make install, sage tries to write in /
usr/local [Reviewed by William Stein]
#4254: Martin Albrecht: mq.SR improvements for convenience [Reviewed
by William Stein]
#4261: Willem Jan Palenstijn: sympow Configure fails to handle aliases
[Reviewed by William Stein, Mark Watkins, Michael Abshoff]
#4308: Philippe Theveny: make mpc an optional spkg [Reviewed by
William Stein, Michael Abshoff]
#4317: William Stein: Fix easy-install.pth after moving Sage [Reviewed
by Michael Abshoff, Craig Citro]
#4321: Alexander Dreyer, Michael Abshoff: wrong Unix permissions in
some PolyBoRi files
#4352: Marshall Hampton: add support for weight vectors to gran/
groebner_fan [Reviewed by William Stein]
#4402: William Stein: Sage 3.1.4: magma related optional doctest
failure in tut.tex [Reviewed by Michael Abshoff]
#4412: John Cremona: extend the local information function for
elliptic curves over number fields [Reviewed by William Stein, Minh
Nguyen]
#4576: Marshall Hampton: biopython optional package upgrade to
1.49beta [Reviewed by William Stein]
#4582: Guillaume Moroz: use Singular's capabilities for computing over
fraction fields [Reviewed by Martin Albrecht]
#4619: Michael Abshoff: Sage 3.2.1.a1: Update HISTORY.txt with the
3.1.3, 3.1.4 and 3.2 release notes [Reviewed by William Stein]
#4654: John Palmieri: for 'sage -testall': put sage version in test
log [Reviewed by Michael Abshoff]
#4655: William Stein: doctest failure in plot.py with 3.2.1.rc0 on 64-
bit SuSe linux [Reviewed by Michael Abshoff]
#4657: Michael Abshoff: OSX: gnuplot doesn't start due to dreaded
libpng conflict [Reviewed by William Stein]
#4658: William Stein: magma -- get rid of redundant caching: just have
_magma_init_ [Reviewed by Michael Abshoff]
#4659: John Palmieri: remove an extra 'cdef class Integer' line from
integer.pyx [Reviewed by Robert Bradshaw]
#4660: William Stein: mark inline fortran and inline cython examples
optional [Reviewed by Michael Abshoff]
#4661: Craig Citro: clean up module_list.py [Reviewed by Michael
Abshoff]
#4664: Michael Abshoff: Sage 3.2.1.rc1: Fix documentation build issues
[Reviewed by Craig Citro]
#4668: Michael Abshoff: libSingular's header have too tight
permissions [Reviewed by Craig Citro]

Merged in Sage 3.2.1.rc0:

#815: Arnaud Bergeron: doctesting is broken on .sage files [Reviewed
by William Stein]
#3102: Gary Furnish: debugging output in p-adics with print mode
"digits" [Reviewed by William Stein, Craig Citro]
#3621: Chris Swierczewski, Brett Nakashima, William Stein:
sage.finance - add expand and refine finance.Stock [Reviewed by
William Stein, Tom Boothby]
#4057: Andrzej Giniewicz: Underlines instead of headings in notebook
version of docstring for R functions [Reviewed by William Stein]
#4266: Robert Bradshaw: overflow error in SR approx [Reviewed by
William Stein]
#4334: Jaap Spies: Updated experimental Mayavi2 spkg [Reviewed by
William Stein]
#4383: David Joyner: composition_series() returns no generators for
trivial subgroup [Reviewed by William Stein]
#4431: Wilfried Huss: conversion of maxima matrices to sage matrices
[Reviewed by Mike Hansen]
#4432: Wilfried Huss, Mike Hansen, Burcin Erocal: symbolic gamma and
factorial [Reviewed by Mike Hansen, Burcin Erocal]
#4433: Wilfried Huss: Replace factorial with a symbolic version
[Reviewed by Mike Hansen]
#4481: Nicolas Thiery: Fix cached_function to accept functions without
func_doc or func_name [Reviewed by Mike Hansen]
#4488: Timothy Clemans: notebook -- login page not given when logged
out and trying to view your worksheets [Reviewed by William Stein]
#4522: Burcin Erocal: polynomial interface improvements [Reviewed by
William Stein]
#4535: Mike Hansen: refactoring in plot/* [Reviewed by William Stein,
Michael Abshoff]
#4537: David Loeffler: inverse_mod for number field ideals [Reviewed
by William Stein]
#4568: Simon King: Dangerous doc test of save_session [Reviewed by
William Stein]
#4587: Simon King: Installation of the latest version of a package
[Reviewed by William Stein]
#4615: Michael Abshoff: Make boehm_gc a standard spkg [Reviewed by
William Stein]
#4632: Carl Witty: .roots(ring=QQbar) fails for polynomials with
enormous (rational) coefficients [Reviewed by Nick Alexander]
#4641: Kwankyu Lee: "-notebook" commandline option should take
trailing options [Reviewed by William Stein]
#4642: William Stein: Limit sage-flags.txt to vector math flags
[Reviewed by Michael Abshoff]
#4645: Michael Abshoff: in setup.py module_list.py is hidden with no
comment [Reviewed by Craig Citro]
#4647: Michael Abshoff: Disable dependency code cacheing in setup.py
for now [Reviewed by Craig Citro]

Merged in Sage 3.2.1.alpha2:

#463: William Stein: sage -upgrade: "sage -upgrade URL" will install
all *newer* spkg's from the given URL, which can also be a local
directory [Reviewed by Michael Abshoff]
#4176: William Stein: matplotlib build failure due to broken tcl/tk
detection [Reviewed by Jaap Spies, Michael Abshoff]
#4613: Robert Bradshaw: doctests for big-o [Reviewed by Craig Citro]
#4624: William Stein: Sage 3.2.1.a1: add ipy_profile_sage.py to list
of files copied when sdisting [Reviewed by Michael Abshoff]
#4627: Nick Alexander: CRT_list in HNF dominates computation [Reviewed
by Craig Citro]
#4628: William Stein: sage-3.2.1.alpha1 -- setup.py build system is
foobar'd [Reviewed by Craig Citro]
#4634: Michael Abshoff: Sage 3.2.1.a1: numerical noise in sage/
schemes/ elliptic_curves/ell_rational_field.py [Reviewed by Nick
Alexander]
#4635: Michael Abshoff, John Palmieri: Sage 3.2.1.a1: numerical noise
in sage/plot/plot.py [Reviewed by Nick Alexander]

Merged in Sage 3.2.1.alpha1:

#3891: John Palmieri: polynomial sqrt method [Reviewed by Carl Witty]
#4320: David Joyner: linear codes improvements [Reviewed By Robert
Miller, Dan Gordan, Michael Abshoff]
#4341: Carlo Hamalainen: Optimisations + corrections to latin.py
[Reviewed by David Joyner]
#4381: Mike Hansen: sage -wthread not passed correctly to ipython
[Reviewed by Jaap Spies]
#4399: William Stein: Sage 3.1.4: magma related optional doctest
failure in sage/matrix/matrix1.pyx [Reviewed by Michael Abshoff]
#4401: William Stein: Sage 3.1.4: magma related optional doctest
failure in sage/crypto/mq/mpolynomialsystem.py [Reviewed by Michael
Abshoff]
#4463: Craig Citro: modular/abvar/homspace.py doctests are long
[Reviewed by William Stein]
#4482: William Stein: Sage 3.2.rc0: optional Magma doctest failure in
devel/sage/sage/rings/polynomial/pbori.pyx [Reviewed by Michael
Abshoff]
#4525: John Cremona: LLL-reduction of elliptic curve bases (with
resulting speed enhancement to integral_points()) [Reviewed by William
Stein, Tobias Nagel]
#4536: John Cremona: Various number field order and ideal utilities
[Reviewed by David Loeffler]
#4541: Jason Bandlow: kschur functions don't properly convert to
schur's [Reviewed by Mike Hansen]
#4553: John Palmieri: a few new methods for FiniteFieldElement
[Reviewed by John Cremona]
#4572: Robert Bradshaw: maxima output has misleading precision
[Reviewed by Michael Abshoff]
#4580: Robert Bradshaw: move mpfr declarations to a pxd [Reviewed by
Carl Witty]
#4592: Craig Citro: new setup.py dependency checking does not handle
Cython built-in pxd files [Reviewed by Carl Witty]
#4597: Craig Citro: setup.py dependency checker does not invalidate
cache correctly [Reviewed by Carl Witty]
#4598: Michael Abshoff: add sage/libs/gmp/__init__.py to MANIFEST.in
[Reviewed by Ondrej Certik]
#4599: Michael Abshoff: sage/schemes/elliptic_curves/
ell_rational_field.py doctest failure due to missing
"#optional" [Reviewed by Jaap Spies]
#4600: William Stein: followup issue on sage -only_optional [Reviewed
by Michael Abshoff]
#4601: William Stein: optional magma interface -- fix all broken
optional doctests by introducing _magma_init_(self, magma) signature
[Reviewed by Michael Abshoff]
#4602: Minh Nguyen: typos in files under sage/catalogue [Reviewed by
Michael Abshoff]
#4603: Minh Nguyen: trivial typos in files under sage/categories
[Reviewed by Michael Abshoff]
#4605: Robert Bradshaw: Update Cython to 0.10.2 (latest stable
upstream) [Reviewed by Michael Abshoff]
#4609: William Stein: Sage 3.2.1.a1: Make two optional magma doctests
also depend on database_gap [Reviewed by Michael Abshoff]
#4620: Craig Citro: setup.py: if the cythonization fails then next
"sage -b" starts to build extensions [Reviewed by Michael Abshoff]

Merged in Sage 3.2.1.alpha0:

#169: Craig Citro: slice assignment not implemented for PARI C library
interface [Reviewed by Robert Bradshaw]
#846: Robert Bradshaw: Split cdefs.pxi [Reviewed by Carl Witty]
#2304: Michael Abshoff: sparse_poly should probably be removed
[Reviewed by Nick Alexander]
#4144: Martin Albrecht: allow finite field elements in SBox
constructor [Reviewed by Carl Witty]
#4168: Robert Bradshaw: native mpfr polynomials [Reviewed by Mike
Hansen]
#4273: Jason Grout: Failure on Jordan form transformation matrices
[Reviewed by Marshall Hampton]
#4287: Paul Zimmermann, John Cremona: improve elliptic curve doctest
(part 5) [Reviewed by Alex Ghitza]
#4310: Robert Bradshaw: simplification of the coercion api [Reviewed
by Mike Hansen]
#4330: Mike Hansen: interfaces function_call(...) function is a total
MESS [Reviewed by William Stein]
#4403: Minh Nguyen: Fix "Install from Source Code" section in "Sage
Installation Guide" [Reviewed by Mike Hansen]
#4419: Mike Hansen: conversion of Permutations to GAP not implemented
[Reviewed by Franco Saliola]
#4468: Sebastien Labbe: assertion error when (some) bad color map
given [Reviewed by Mike Hansen]
#4487: Franco Saliola: add method to evaluate characters of
permutation and matrix groups [Reviewed by David Joyner, Mike Hansen]
#4528: John Cremona: Implement Krull dimension for orders in number
fields [Reviewed by Craig Citro]
#4533: Robert Bradshaw: divisors function slow for integers [Reviewed
by William Stein, John Cremona, Craig Citro]
#4540: Jason Bandlow: Symmetrica segfault converting Schur functions
to k-Schurs [Reviewed by Mike Hansen]
#4542: Marshall Hampton: polyhedra bug fix and improvments [Reviewed
by Carl Witty]
#4556: John Palmieri: nth_root for finite fields: document the fact
that 'extend' is not implemented [Reviewed by Robert Bradshaw]
#4558: Ondrej Certik: update to sympy-0.6.3.spkg (latest upstream)
[Reviewed by Michael Abshoff]
#4561: Robert Bradshaw: _fast_float_ for sin/cos, etc., in caculus.py
is implemented stupidly [Reviewed by Mike Hansen]
#4562: Jason Grout: clean up a bunch of imports in matrix CDF/RDF code
[Reviewed by Carl Witty]
#4564: Robert Bradshaw: implement long long -> mpz_t [Reviewed by
Craig Citro]
#4569: Franco Saliola: problems with the Permutation constructor
function [Reviewed by Mike Hansen]
#4570: Jason Grout: change the numpy include to the standard place
[Reviewed by Robert Bradshaw]
#4573: Franco Saliola: Permutation not callable, but
PermutationGroupElement is [Reviewed by Mike Hansen]
#4577: Wilfried Huss: simple interface to scipy.optimize.leastsq
[Reviewed by Carl Witty]
#4579: Robert Bradshaw: put mpz_longlong functions in c_lib [Reviewed
by Carl Witty]
#4583: William Stein: implement "sage -t --only-optional" [Reviewed by
Michael Abshoff]
#4584: William Stein: remove doctest cruft -- delete sage-
doctest_old_ver [Reviewed by Michael Abshoff]
#4586: Michael Abshoff: delete sage/rings/number_field/todo.py
[Reviewed by Nick Alexander]
#4589: William Stein: sage/rings/polynomial/multi_polynomial_ideal.py
doctest failure due to #4583 [Reviewed by Michael Abshoff]
#4591: William Stein: magma -- EllipticCurve('37a').three_selmer_rank
() fails in Magma 2.14 [Reviewed by Michael Abshoff]
#4594: Minh Nguyen: typos in files under sage/algebras [Reviewed by
Michael Abshoff]
#4595: Minh Nguyen: typos in files under sage/calculus [Reviewed by
Michael Abshoff]
#4596: Craig Citro: delete sha.py [Reviewed by William Stein]