Sage 3.1.3 released

[mabshoff]

[This is for the record only - Sage 3.2 has been released already, so
please use that. We have had some problems with getting release notes
out in a timely fashion and unfortunately the 3.1.3 as well as the
3.1.4 release announcements didn't go out in time. We have changed the
way we deal with that part of the development process, so hopefully
this problem will not happen again.

My apologies since this was largely my fault,

Michael Abshoff]

Hello folks,

Sage 3.1.3 was released on October 14th, 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 41 people contributed to this release:

* Tim Abbott
* Michael Abshoff
* Martin Albrecht
* Jason Badlaw
* Arnaud Bergeron
* Robert Bradshaw
* Michael Brickenstein
* Craig Citro
* Francis Clarke
* Timothy Clemans
* John Cremona
* Karl-Dieter Crisman
* Pablo De Napoli
* Dan Drake
* Burcin Erocal
* David Fu
* Alex Ghitza
* Andrzej Giniewicz
* Jason Grout
* Marshall Hampton
* Mike Hansen
* David Harvey
* David Joyner
* Simon King
* Emily Kirkman
* David Loeffler
* Jason Merrill
* Robert Miller
* Minh Nguyen
* Willem Jan Palenstijn
* John Palmieri
* Clement Pernet
* David Philp
* Harald Schilly
* William Stein
* Chris Swierczewski
* Nicolas Thiery
* John Voight
* Justin Walker
* Georg Weber
* Paul Zimmermann

Cheers,

Michael Abshoff (release chair), William Stein

* Major Features, New Spkgs and Bugfixes

* Mike Hansen: inclusion of Sphinx, Docutils, Jinja, and Pygments as
a step toward ReST documentation
* Robert Bradshaw: coercion improvements
* Nicolas Thiery, Mike Hansen: tighter integration with sage-
combinat, i.e. the 2144 server is now installable with vanilla Sage
* Martin Albrecht: MPolynomial_libsingular improvements for number
fields and ZZ
* Martin Albrecht: Gröbner bases over Z and Z/nZ
* William Stein, Burcin Erocal: add initial pynac-0.1.p0 package
* William Stein, Craig Citro: modular symbols -- optimize fast
computation of hecke eigenvalues on weight 2 modular symbols for
gamma0
* Michael Abshoff: numerous Solaris build fixes

For details see the Sage 3.1.3 Release Tour at

http://wiki.sagemath.org/sage-3.1.3

* Known Issues with 3.1.3:

* 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 125 tickets. For details see

http://trac.sagemath.org/sage_trac/milestone/sage-3.1.3

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

* Upcoming Releases

The next release will be 3.1.4, chaired by Michael Abshoff. It will
be a bug fixes release.

* Doctesting Coverage

For 3.1.2 we had:

Overall weighted coverage score: 60.5%
Total number of functions: 20584

We increased coverage by 1.8% in 3.1.3 while adding 836 functions:

Overall weighted coverage score: 62.3%
Total number of functions: 21420

* Closed Tickets:

Merged in Sage 3.1.3.final:

#4271: Paul Zimmermann: improve coverage test of ell_generic.py to
100%, and fix typos [Reviewed by John Cremona]
#4272: Michael Abshoff: add the files from new coercion to the
reference manual [Reviewed by Mike Hansen]
#4279: Michael Abshoff: Sage 3.1.3.rc0: numerical noise in rings/
real_lazy.pyx [Reviewed by Mike Hansen]

Merged in Sage 3.1.3.rc0:

#1346: Martin Albrecht: fpLLL doctests don't test fpLLL [Reviewed by
Willem Jan Palenstijn]
#3945: Mike Hansen, Burcin Erocal: sage -gdb doesn't work [Reviewed by
Michael Abshoff]
#4159: Michael Abshoff: sage -bdist fails on osx 10.5 ppc and intel
with libpng errors [Reviewed by Mike Hansen]
#4214: Alex Ghitza: elliptic_logarithm gives inaccurate answers
[Reviewed by Georg Weber]
#4219: Michael Abshoff: MacOSX: work around java detection hang in r
due to "Mac OS X 10.5 Update 2" [Reviewed by Mike Hansen]
#4228: Michael Abshoff: eclib-20080310.p6.spkg is broken with 'export
MAKE="make -j4"' [Reviewed by Mike Hansen]
#4231: William Stein: magma -- long input too verbose in some cases
[Reviewed by Georg Weber]
#4240: William Stein: magma -- increase doctest coverage of magma.py
[Reviewed by Georg Weber, Michael Abshoff]
#4242: Jason Badlaw: Bugfix for dominates() method of partition.py
[Reviewed by Mike Hansen]
#4253: Martin Albrecht: polybori interface: equality operator for
navigators [Reviewed by Michael Brickenstein]
#4257: Martin Albrecht: support for Singular's 'intmat' and
'intvec' [Reviewed by Mike Hansen]
#4262: William Stein: Elliptic curve a_invariants command returns a
list reference [Reviewed by Martin Albrecht]
#4263: William Stein: elliptic curves -- point height serious stupid
bug in raising error [Reviewed by Martin Albrecht]
#4270: Nicolas Thiery: Add sage-combinat script and sage-combinat
[Reviewed by Michael Abshoff]

Merged in Sage 3.1.3.alpha3:

#3385: Jason Grout: plot_vector_field does not deal with aspect ratios
correctly [Reviewed by Mike Hansen]
#3665: Mike Hansen: add initial species code [Reviewed by Robert
Miller]
#3980: Jason Merrill: Find_root bug [Reviewed by Marshall Hampton]
#4106: Alex Ghitza: error coercing symbolic variable into polynomial
ring modulo 4 (but not mod 3) [Reviewed by William Stein]
#4220: Mike Hansen: include Sphinx, Docutils, Jinja, and Pygments in
Sage [Reviewed by Michael Abshoff]
#4224: Carl Witty: small error in new question-mark interval printing
[Reviewed by Michael Abshoff]
#4225: Robert Bradsahw: faster sqrt for complex numbers [Reviewed by
Alex Ghitza]
#4226: Robert Bradshaw: Real Lazy Field [Reviewed by Mike Hansen]
#4227: Michael Abshoff: Sage 3.1.3.alpha2: many Magma doctests that
should are not optional [Reviewed by Alex Ghitza]
#4232: Robert Bradshaw: #249 causes bug in importing large lists
[Reviewed by Jason Grout]
#4233: John Palmieri: fix doctest failure due to deprecation warning
in calculus/all.py [Reviewed by Mike Hansen]
#4234: Minh Nguyen: typos in programming guide [Reviewed by Michael
Abshoff]
#4235: Minh Nguyen: typos in and enhancement to installation guide
[Reviewed by Michael Abshoff]
#4238: David Fu, Robert Bradshaw: option to create local .so file
for .spyx modules [Reviewed by Georg Weber]
#4239: Francis Clarke: fix for problems with zero kernel and images
[Reviewed by Georg Weber]
#4247: William Stein: plotting -- bug in text and pdf export [Reviewed
by Mike Hansen]

Merged in Sage 3.1.3.alpha2:

#686: Martin Albrecht: write MPolynomial_libsingular over number
fields [Reviewed by Alex Ghitza]
#767: John Palmieri: animate has cryptic error message when
imagemagick is not installed [Reviewed by Michael Abshoff]
#1104: Alex Ghitza: Ideal() should check arguments better [Reviewed by
Martin Albrecht]
#2407: Timothy Clemans: Notebook fails without explanation when
cookies are disabled [Reviewed by Jason Grout, Dan Drake, Mike Hansen]
#2948: John Palmieri: (Additional) Docstrings and Doctests for rings/
quotient_ring.py [Reviewed by Alex Ghitza]
#3316: Pablo De Napoli: Fix a bug and improve documentation in
jordan_form [Reviewed by Alex Ghitza]
#3659: Mike Hansen: Upgrade IPython to 0.8.4 [Reviewed by Michael
Abshoff]
#3799: Emily Kirkman: degree sequence should not be a single integer
in graph_database [Reviewed by Robert Miller]
#3943: David Joyner: block designs patch [Reviewed by Robert Miller]
#4021: Martin Albrecht: MPolynomial_libsingular over ZZ [Reviewed by
Alex Ghitza]
#4022: Martin Albrecht: Gröbner bases over Z and Z/nZ [Reviewed by
Alex Ghitza]
#4096: John Cremona, Alex Ghitza: fix pari precision interface
[Reviewed by Michael Abshoff]
#4111: Robert Bradshaw: move basic types to new coercion model
[Reviewed by Mike Hansen]
#4126: William Stein: improve sage <--> magma interface for number
fields [Reviewed by Robert Bradshaw]
#4157: Michael Abshoff: add introduction to README.txt [Reviewed by
Mike Hansen]
#4169: David Harvey, Tim Abbott: zn_poly 0.9 and hypellfrob 2.1.1
[Reviewed by Martin Albrecht, Michael Abshoff]
#4189: William Stein: fix hmm documentation buglet [Reviewed by
Michael Abshoff]
#4191: Arnaud Bergeron, John Cremona: Update eclib to
eclib-20080310.p6.spkg [Reviewed by Michael Abshoff]
#4192: Mike Hansen: is_Blah functions: deprecate and then remove them
from top level imports [Reviewed by Michael Abshoff]
#4195: Martin Albrecht: implicit plotting for multivariate polynomial
ideals [Reviewed by Mike Hansen]
#4197: William Stein: weird ntl finite field modulus caching bug
[Reviewed by Michael Abshoff]
#4198: Michael Abshoff: matrix_cyclo_dense.pyx leaks in _get_unsafe
[Reviewed by Mike Hansen]
#4200: Jason Grout: Update numpy to 1.2.0 [Reviewed by Michael
Abshoff]
#4201: Mike Hansen: add .options and .reset to plot functions
[Reviewed by Jason Grout]
#4202: Jason Grout: latex derivatives of symbolic functions nicely
[Reviewed by Mike Hansen]
#4208: Michael Abshoff: Update mpfr to 2.3.2 release [Reviewed by
Robert Miller]
#4209: Michael Abshoff: upgrade maxima.spkg to 5.16.3 [Reviewed by
Robert Miller]
#4210: Michael Abshoff: Remove some deprecation warnings from
numpy-1.2.spkg [Reviewed by Mike Hansen]
#4211: Michael Abshoff: new optional spkg: guppy [Reviewed by Mike
Hansen]
#4212: Michael Abshoff, Mike Hansen: Invalid read of size 8 in
totallyreal.pyx [Reviewed by Mike Hansen, Michael Abshoff]
#4213: Mike Hansen: Bug in Permutations(n, k) [Reviewed by Arnaud
Bergeron]
#4215: Mike Hansen: Bug in creating sparse vectors using a dictionary
[Reviewed by Michael Abshoff]
#4216: John Palmieri: use sage-native-execute to run 'convert' in
animate.py [Reviewed by Michael Abshoff]
#4221: William Stein, Burcin Erocal: add initial pynac-0.1.p0 package
[Reviewed by Michael Abshoff, Robert Bradshaw]
#4222: Michael Abshoff: R fails to build when global readline headers
are not present [Reviewed by Simon King]
#4132: Alex Agitza: complex arithmetic passes via pari [Reviewed by
Robert Bradshaw]

Merged in Sage 3.1.3.alpha1:

#249: Robert Bradshaw: a much needed preparser optimization -- factor
out constants [Reviewed by Alex Ghitza]
#1932: Craig Citro: weird hg bug due to sha.py in the Sage tree
[Reviewed by Alex Ghitza]
#1951: John Cremona: reduction map modulo a number field prime ideal
still not 100% done [Reviewed by Alex Ghitza]
#2076: Mike Hansen: Inconsistent coloring of plotted points [Reviewed
by Jason Grout]
#2777: Andrzej Giniewicz: '??' can't always find the source [Reviewed
by Robert Bradshaw]
#3502: William Stein, Craig Citro: modular symbols -- optimize fast
computation of hecke eigenvalues on weight 2 modular symbols for
gamma0 [Reviewed by Craig Citro, William Stein]
#3774: Robert Bradshaw: __radd__ doesn't work when left hand side is
an Element [Reviewed by Mike Hansen]
#3838: Simon King: Element access for RElement [Reviewed by Alex
Ghitza]
#3855: Arnaud Bergeron: point3d size default is too small to see
[Reviewed by Andrzej Giniewicz]
#3897: John Cremona: bug in local_information due to the lack of
residue_field for ZZ [Reviewed by Alex Ghitza]
#3967: John Voight: Totallyreal "just print" feature added [Reviewed
by Craig Citro]
#4058: Robert Bradshaw: move integer ring to the new coercion model
[Reviewed by Mike Hanson]
#4129: Martin Albrecht: add support for ntl.mat_GF2 [Reviewed by
Robert Bradshaw]
#4151: Robert Bradshaw: implementation of Dickman's function [Reviewed
by David Loeffler]
#4155: Craig Citro: Speed up totally real field enumeration code
[Reviewed by John Voight, Michael Abshoff]
#4156: Robert Miller: fix memleak in graph_isom [Reviewed by Michael
Abshoff]
#4161: Michael Abshoff: GAP doesn't compile with CXX='ccache g+
+' [Reviewed by Harald Schilly]
#4163: Alex Ghitza: tut -- improve factorial / valuation example
[Reviewed by John Cremona]
#4165: Michael Abshoff: Doctest for lisp.py blows chunks on (some) Mac
OS X systems [Reviewed by Justin Walker]
#4170: Robert Bradshaw: symbolic ring does not accept python longs
[Reviewed by Michael Abshoff]
#4173: Michael Abshoff: Solaris: fix cddlib build problem on Solaris
x86 [Reviewed by Mike Hansen]
#4174: Michael Abshoff: Do not run "make install" in python.spkg in
parallel [Reviewed by Craig Citro]
#4175: Robert Bradshaw: cpdef arithmetic functions [Reviewed by Mike
Hansen]
#4180: Mike Hansen: magic pexpect logging switch [Reviewed by Michael
Abshoff]
#4186: Robert Bradshaw: speed up default __call__ [Reviewed by Mike
Hansen]
#4187: Michael Abshoff: Fix compilation problem for libfplll.spkg on
Solaris 10 [Reviewed by Mike Hansen]
#4188: Michael Abshoff: Fix cvxopt.spkg build on Solaris due to broken
complex.h headers [Reviewed by Craig Citro]

Merged in Sage 3.1.3.alpha0:

#2906: Timothy Clemans: notebook -- there is a "sagetex" command; it
is untested and completely broken right now. remove it (i.e., don't
export to top level all.py) [Reviewed by Alex Ghitza]
#3876: Karl-Dieter Crisman: Add plotting to sigma and Euler phi
functions [Reviewed by Chris Swierczewski]
#3981: Chris Swierczewski: finance.TimeSeries - Add candlestick plot
method [Reviewed by Mike Hansen]
#4060: Marshall Hampton: Polyhedra don't handle real coordinates
properly [Reviewed by Mike Hansen]
#4087: Francis Clarke: Improved printing of polynomials with
'negative' coefficients [Reviewed by John Cremona]
#4088: Timothy Clemans: notebook -- on list of published worksheets if
no worksheets, everyone sees welcome message [Reviewed by Mike Hansen]
#4099: Jason Merrill: Fix documentation for point2d, line2d, ...
[Reviewed by Mike Hansen]
#4100: Robert Bradshaw: comparison with None extraordinarily slow
[Reviewed by John Cremona]
#4103: Jason Grout: Delete the cmap option for vector field plots
[Reviewed by Michael Abshoff]
#4104: Jason Grout: Create plot_slope_field function [Reviewed by
David Joyner]
#4115: Robert Miller: Double coset problems [Reviewed by David Joyner]
#4127: David Philp: Python scripts to search for libraries that get
wrongly called in [Reviewed by Michael Abshoff]
#4134: Timothy Clemans: notebook -- user.py has nodoctest flag
[Reviewed by Michael Abshoff]
#4139: Mike Hansen: Improvements to permutation groups [Reviewed by
Robert Miller]
#4145: Robert Miller: linear codes list function is slow [Reviewed by
David Joyner]
#4147: Clement Pernet: Upgrade to linbox-1.1.6 [Reviewed by Michael
Abshoff]
#4148: Clement Pernet: Upgrade to givaro-3.2.13rc2 [Reviewed by
Michael Abshoff]
#4150: Robert Miller: migrate graphs to new refinement code [Reviewed
by Mike Hansen]
#4153: Robert Miller: re-enable -fwrapv option for Python on Itanium
[Reviewed by Michael Abshoff]