Ticket #4300: HISTORY.txt.patch

1c1,628
< Hello folks,
---
> Sage 3.1.2 was released on September 19th, 2008. It is available at
> 
>            http://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 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 42 people contributed to this release:
> 
>  * Tim Abbott
>  * Michael Abshoff
>  * Martin Albrecht
>  * Robert Bradshaw
>  * Arnaud Bergeron [first contribution]
>  * C. Boncelet [first contribution]
>  * Tom Boothby
>  * Michael Brickenstein
>  * Ondrej Certik
>  * Craig Citro
>  * Timothy Clemans
>  * John Cremona
>  * Karl-Dieter Crisman
>  * Burcin Erocal
>  * Gary Furnish
>  * Alex Ghitza
>  * Andrzej Giniewicz
>  * Jason Grout
>  * Mike Hansen
>  * Marshall Hampton
>  * Chris Holdsworth [first contribution]
>  * Hamish Ivey-Law [first contribution]
>  * David Joyner
>  * Josh Kantor
>  * Simon King
>  * Steve Linton
>  * Jason Merrill [first contribution]
>  * Robert Miller
>  * Minh Nguyen
>  * Willem Jan Palenstijn
>  * John Palmieri
>  * David Philp [first contribution]
>  * Yi Qiang
>  * Nils-Peter Skoruppa [first contribution]
>  * Franco Saliola
>  * William Stein
>  * Griffen Thoma [first contribution]
>  * Igor Tolkov
>  * Ralf-Philipp Weinmann
>  * Georg Weber [first contribution]
>  * Carl Witty
>  * Chris Wuthrich
> 
> Cheers,
> 
> Michael Abshoff (release chair), William Stein
> 
> * Major Features, New Spkgs and Bugfixes
> 
>  * Doctest Coverage Hits 60% (Mike Hansen and others)
>  * Hidden Markov Models (William Stein)
>  * Fix various Notebook Bugs (Timothy Clemans, Mike Hansen)
>  * New Structures for Partition Refinement (Robert Miller)
>  * Improved Dense Linear Algebra over GF(2) (Martin Albrecht)
>  * Update to new PolyBoRi Version (0.5) and Improved Interface (Tim Abbott, Michael Abshoff, Martin Albrecht)
>  * QEPCAD Interface (Carl Witty)
>  * Update Developer's Handbook (John Palmieri)
>  * Improved 64-bit OSX Support (Michael Abshoff)
>  * GAP Meataxe Interface (Simon King, David Joyner)
>  * Better SymPy Integration (Ondrej Certik)
>  * Real Number Inputs Improved (Robert Bradshaw)
>  * Faster Determinants of Dense Matrices over Multivariate Polynomial Rings (Martin Albrecht)
>  * Arrow drawing improved (Jason Grout)
>  * Eigen functions for matrices (Jason Grout)
>  * Memory Leak fixes (Michael Abshoff, Craig Citro)
> 
> For details see the Sage 3.1.2 Release Tour at
> 
>   http://wiki.sagemath.org/sage-3.1.2
> 
> * Known Issues with 3.1.2:
> 
>  * 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 251 tickets. For details see
> 
>    http://trac.sagemath.org/sage_trac/milestone/sage-3.1.2
> 
> or check out the closed ticket section at the end of the 
> announcement. 
> 
> * Upcoming Releases
> 
> The next release will be 3.1.3, chaired by Michael Abshoff. It will 
> be a mix of new features and bug fixes.
> 
> * Doctesting Coverage
> 
> For 3.1.1 we had:
> 
> Overall weighted coverage score:  56.5%
> Total number of functions:  20920
> 
> We increased coverage by 4.0% in 3.1.2 while removing 336 functions:
> 
> Overall weighted coverage score:  60.5%
> Total number of functions:  20584
> 
> * Closed Tickets:
> 
> Merged in Sage 3.1.2.rc5:
> 
> #3534: William Stein, John Palmieri: plot -- fix circle example in the documentation [Reviewed by Mike Hansen]
> #3894: John Palmieri: in tutorial, live version, triple dots are not visible [Reviewed by Mike Hansen]
> #4063: Timothy Clemans: properly escape the titles of worksheets [Reviewed by Mike Hansen] 
> #4133: Mike Hansen, Michael Abshoff: sage.math - sage 3.1.2.rc4 doctest failure in interfaces/maxima.py [Reviewed By Robert Miller]
> #4130: Michael Abshoff: #4125 does not work on OS X 10.4 [Reviewed by Robert Miller]
> #4131: Michael Abshoff: unbreak sage-clone [Reviewed by Mike Hansen]
> #4137: William Stein: add doctests for user_type() in avatar.py [Reviewed by Mike Hansen]
> #4138: Michael Abshoff: Sage 3.1.2.rc5: fix documentation build issues [Reviewed by Mike Hansen]
> 
> Merged in Sage 3.1.2.rc4:
> 
> #925: Michael Abshoff: valgrind options to sage (sage -valgrind, sage -callgrind, etc.) should be more customizable [Reviewed by Robert Miller]
> #1915: Alex Ghitza: infinity doesn't behave well [Reviewed by John Cremona]
> #3563: Michael Abshoff: make "def atlas()" deal with the Accelerate Framework on OSX [Reviewed by Robert Miller]
> #3675: Michael Abshoff: upgrade optinal valgrind.spkg to the 3.3.1 release [Reviewed by Robert Miller]
> #3847: Alex Ghitza: can't make vector of ints [Reviewed by John Cremona]
> #4097: Robert Miller: matrix automorphism groups [Reviewed by David Joyner]
> #4119: Martin Albrecht: doctests + fixes for SymbolicData interface [Reviewed by Mike Hansen]
> #4121: Robert Miller: correct the translation for automorphism groups of graphs with edge labels [Reviewed by Mike Hansen]
> #4122: Michael Abshoff: build python without pymalloc for SAGE_VALGRIND, add sleep(3) for parallel make install issue [Reviewed by Robert Miller]
> #4123: Michael Abshoff: source $SAGE_ROOT/toolchain/toolchain-env if it exists [Reviewed by Robert Miller]
> #4124: Robert Miller: disable pbuild [Reviewed by Michael Abshoff]
> #4125: David Philp: Build breaks entirely or pulls in non-standard libraries with fink and macports [Reviewed by Robert Miller]
>  
> Merged in Sage 3.1.2.rc3:
> 
> #3009: Jason Merrill: remove spaces after continuation characters "\" [Reviewed by Michael Abshoff]
> #3422: Jason Merrill: Minor typo in docs for zeta_zeros() [Reviewed by Michael Abshoff]
> #4110: Michael Abshoff: Memory leak in pickling matrices of GF(2) [Reviewed by Robert Miller]
> #4112: Mike Hansen: 3.1.2.rc2 doctest failure: sage/interfaces/sage0.py [Reviewed by Craig Citro]
> #4113: Craig Citro: Doctest failure in free_module.py [Reviewed by Michael Abshoff]
> #4114: Mike Hansen: hang in lisp.py on OS X 10.5 [Reviewed by Michael Abshoff]
> #4117: Craig Citro, Michael Abshoff: number_field_* leaks caused by gen.pyx's type(gen self) [Reviewed by Michael Abshoff, Craig Citro]
> #4118: Craig Citro: fix various Pari-related issues [Reviewed by Michael Abshoff]
> 
> Merged in Sage 3.1.2.rc2:
> 
> #3957: Mike Hansen: notebook -- major bug in opening notebooks and plots [Reviewed by Timothy Clemans]
> #3978: Michael Abshoff: Sage 3.1.2.alpha1: ghmm and hmm numerical noise doctest failures [Reviewed by Robert Miller]
> #4085: Robert Bradshaw: high precision real literals [Reviewed by Mike Hansen]
> #4086: Michael Abshoff: Fix polybori-0.5rc.p3.spkg build issue from vanilla tarball [Reviewed by Martin Albrecht]
> #4090: Georg Weber, Michael Abshoff: polybori-0.5rc1.p4 fails to build on OSX 10.4 [Reviewed by Robert Miller]
> #4091: Craig Citro: Sage 3.1.2.rc1: matrix_real_double_dense.py doctest failure [Reviewed by Jason Grout]
> #4092: Martin Albrecht: libm4ri-20080904 fails to build on OSX 10.4 [Reviewed by Michael Abshoff]
> #4093: John Cremona: fix numerical fuzz in period_lattice for 3.1.2 [Reviewed by Michael Abshoff]
> #4094: Tom Boothby: evaluate all causes massive browser hang [Reviewed by Mike Hansen]
> #4098: William Stein: "T1 = M1.hecke_operator(13^9)" blows up on 32 bit builds [Reviewed by Michael Abshoff]
> #4101: Robert Bradshaw: cpdef horribly broken in last Cython [Reviewed by Michael Abshoff]
> #4107: Minh Nguyen: trivial typos in tut.tex [Reviewed by Mike Hansen, Michael Abshoff]
> #4108: Michael Abshoff: disable hmm.pyx and chmm.pyx doctests [Reviewed by Robert Miller]
> 
> Merged in Sage 3.1.2.rc1:
> 
> #1785: Alex Ghitza: bug in creating points on elliptic curves over extension fields [Reviewed by John Cremona]
> #3711: Mike Hansen: notebook -- folder of worksheets not properly saved [Reviewed by Timothy Clemans]
> #3918: Mike Hansen: notebook -- MAJOR BUG involving uploading file from URL [Reviewed by Timothy Clemans]
> #4064: Alex Ghitza, John Cremona: fix pari precision issues [Reviewed by John Cremona, Alex Ghitza]
> #4070: Michael Abshoff: fix polybori-0.5.rc1 build issues [Reviewed by Martin Albrecht]
> #4071: Mike Hansen: Fix issues in the lisp interface [Reviewed by Michael Abshoff]
> #4072: Mike Hansen: Fix issue in trait_names in the sage0 interface [Reviewed by Martin Albrecht]
> #4073: Martin Albrecht: disable colors in sage0 [Reviewed by Mike Hansen]
> #4074: Mike Hansen: the notebook is totally broken in secure mode with the new twisted spkg [Reviewed by Michael Abshoff]
> #4075: David Joyner: fix bug in BCHCode [Reviewed by Robert Miller]
> #4077: Mike Hansen: notebook - ReactorNotRunning error consistently seen in sage-3.1.2.rc0 [Reviewed by Michael Abshoff]
> #4078: Mike Hansen: evaluate all has sometimes erratic behavior [Reviewed by William Stein]
> #4080: Martin Albrecht: Symbol clash between global M4RI and PolyBoRi's M4RI [Reviewed by Michael Abshoff]
> #4081: Robert Miller: memleaks in nonlinear binary codes [Reviewed by Michael Abshoff]
> #4082: Michael Abshoff: Sage 3.1.2.rc0: numerical noise on OSX/Intel in schemes/elliptic_curves/ell_number_field.py [Reviewed by Mike Hansen]
> #4084: Jason Merrill: plot(1/cos,-1,1) fails [Reviewed by Michael Abshoff]
> 
> Merged in Sage 3.1.2.rc0:
> 
> #1115: John Cremona: Sha_an either fails or lies when prec isn't the default 53 [Reviewed by Alex Ghitza]
> #1170: John Cremona: Behaviour of the order function for infinite groups [Reviewed by Alex Ghitza]
> #1877: Griffen Thoma, Jason Merrill: same range variables -- bug in 3d plotting [Reviewed by Arnaud Bergeron]
> #3264: Tim Abbott, Martin Albrecht: Upgrade PolyBoRi to 0.5rc [Reviewed by Michael Abshoff]
> #3377: Chris Wuthrich, John Cremona: torsion and other functions for elliptic curves over number fields [Reviewed by Alex Ghitza]
> #3728: John Palmieri: tutorial: add documentation for solving matrix equations [Reviewed by John Cremona, Alex Ghitza]
> #3857: Chris Holdsworth, John Cremona, Nils Skoruppa: BinaryQF_reduced_representatives in binary_qf.py produces extra unreduced forms [Reviewed by Alex Ghitza]
> #3885: Craig Citro, Martin Albrecht: Bug in free module __call__ method [Reviewed by Mike Hansen, Robert Bradshaw]
> #3907: Mike Hansen: plot correctly up to asymptotes [Reviewed by Robert Miller]
> #3922: Jason Grout: Make nice arrows [Reviewed by Mike Hansen, Michael Abshoff]
> #3954: Alex Ghitza: bug in elliptic curve period_lattice [Reviewed by John Cremona]
> #3960: Mike Hansen: "edit this" on published worksheets doesn't work anymore in 3.1.1 [Reviewed by Michael Abshoff]
> #4023: Alex Ghitza: Sage 3.1.2.alpha3: 32 vs. 64 bit doctesting issues for gp [Reviewed by Michael Abshoff, Martin Albrecht]
> #4026: Gary Furnish: Move Macaulay2 to latest upstream 1.1-r7221 [Reviewed by Martin Albrecht]
> #4040: Marshall Hampton: Update biopython optional package to 1.47 [Reviewed by Michael Abshoff]
> #4042: Martin Albrecht: libm4ri-20080903 fails to build on Itanium Linux [Reviewed by Michael Abshoff]
> #4043: Michael Abshoff: Sage 3.1.2.alpha4: numerical noise in plot.py [Reviewed by Mike Hansen]
> #4044: Martin Albrecht: create AES equation systems for PolyBoRi [Reviewed by Ralf-Philipp Weinmann]
> #4045: Martin Albrecht: fix PolyBoRi GB calculations in some situations [Reviewed by Ralf-Philipp Weinmann]
> #4047: Robert Miller: automorphism groups/canonical labels for hypergraphs [Reviewed by Mike Hansen]
> #4049: Arnaud Bergeron: Don't use the -i option to tar as it does not exist on most BSDs [Reviewed by Michael Abshoff]
> #4050: Mike Hansen: Shared worksheets are not copied correctly [Reviewed by Michael Abshoff]
> #4051: Arnaud Bergeron: Use of tar -j in sage-pkg [Reviewed by Michael Abshoff]
> #4052: Arnaud Bergeron: readline spkg doesn't build under OpenBSD [Reviewed by Michael Abshoff] 
> #4053: Robert Miller: more checking for graph6, sparse6 and dig6 formats [Reviewed by Michael Abshoff]
> #4054: Robert Miller: shorten doctesting in graph_generators.py [Reviewed by Michael Abshoff]
> #4059: Arnaud Bergeron: libm4ri configure is seriously broken on anything not x86 [Reviewed by Martin Albrecht]
> #4066: Michael Abshoff: Sage 3.1.2.alpha3: Solaris build fixes for the Sage library [Reviewed by Martin Albrecht]
> #4067: Michael Abshoff: hmm.pyx and ghmm.pyx valgrind issues [Reviewed by Martin Albrecht]
> #4068: Martin Albrecht: determinants for matrices over multivariate polynomial rings slow [Reviewed by Mike Hansen]
> 
> Merged in Sage 3.1.2.alpha4:
> 
> #309: Alex Ghitza: rationals enumeration not monotone in height [Reviewed by John Cremona]
> #1834: Alex Ghitza: General linear group over ZZ hangs in __call__ [Reviewed by John Cremona]
> #2547: Jason Merrill: Implement gradient(), hessian() for callable symbolic expressions [Reviewed by Mike Hansen]
> #3451: Alex Ghitza: inaccurate error message in scheme morphisms [Reviewed by John Cremona]
> #3622: Robert Bradshaw: numerical fast integration using fast float [Reviewed by Jason Merrill]
> #3805: Jason Merrill: sage gets basic arithmetic with sqrt(3) wrong [Reviewed by Michael Abshoff]
> #3921: Jason Merrill: calculus -- solve(..., constant) should complain by default [Reviewed by Alex Ghitza]
> #3969: Robert Brashaw: Matrix_mod2_dense hashs follow-up (see #3724)) [Reviewed by Martin Albrecht]
> #3974: Chris Wuthrich: renaming of integral_weierstrass_model to integral_short_weierstrass_model [Reviewed by John Cremona]
> #4016: Alex Ghitza: improve doctests to schemes/generic/scheme.py [Reviewed by Robert Bradshaw]
> #4017: Michael Abshoff: Sage 3.1.2.alpha1 - PPC OSX: numerical noise in sage/stats/hmm/chmm.pyx [Reviewed by Mike Hansen]
> #4018: Robert Bradshaw: casting of non t_INT pari integers [Reviewed by Alex Ghitza]
> #4019: Robert Bradshaw: numerator and denominator for QQ[x] [Reviewed by Alex Ghitza]
> #4020: Robert Bradshaw: fraction field doctests [Reviewed by Mike Hansen]
> #4024: Martin Albrecht: upgrade M4RI to newest upstream release (20080901) [Reviewed by Michael Abshoff]
> #4025: Michael Abshoff, Mike Hansen: Sage 3.1.2.alpha3: benchmark.py runs Maple tests that should be optional [Reviewed by David Joyner]
> #4027: Martin Albrecht: Sage 3.1.2.alpha3: matrix_mod2_dense.pyx doctest failure on 32 bits [Reviewed by Michael Abshoff]
> #4028: Mike Hansen: doctest and improve sage/interfaces/axiom.py [Reviewed by Michael Abshoff]
> #4030: Jason Merrill: Vectors of callable things should be callable [Reviewed by Mike Hansen]
> #4031: Jason Merrill: Callable symbolic expressions should allow keyword args [Reviewed by Mike Hansen]
> #4032: Michael Abshoff: Add x86 Solaris build support for libSingular [Reviewed by Martin Albrecht]
> #4033: Michael Abshoff: disabled libiconv on Solaris for the r.spkg [Reviewed by Martin Albrecht]
> #4034: Michael Abshoff: Fix rubiks.spkg build on Solaris  [Reviewed by Martin Albrecht]
> #4037: Alex Ghitza: list_of_first_n() broken in interact.py [Reviewed by John Cremona]
> 
> Merged in Sage 3.1.2.alpha3:
> 
> #708: Alex Ghitza: performance issue -- Magma is way faster at testing some polynomials for irreducibility [Reviewed by Martin Albrecht]
> #1213: Jason Merrill: strange unused file sage/plot/mpl_wrapper.py should be fixed or deleted [Reviewed by Michael Abshoff]
> #1647: John Palmieri: rewrite spkg chapter in the developer handbook [Reviewed by Martin Albrecht]
> #1648: John Palmieri: add chapter in developer's handbook about bug handling via trac [Reviewed by Martin Albrecht]
> #2078: John Palmieri: programming guide: section "quick Mercurial tutorial for Sage" is wrong/misleading [Reviewed by Martin Albrecht]
> #2422: John Palmieri: Update Programming Guide [Reviewed by Martin Albrecht]
> #3324: Martin Albrecht: Matrix_mod2_dense to/from PNG routines [Reviewed by William Stein, Michael Abshoff]
> #3376: Martin Albrecht: matrix multiplication should use Strassen's algorithm [Reviewed by Robert Miller, Michael Abshoff]
> #3393: John Palmieri: fix typo in documentation related to sage_search [Reviewed by Martin Albrecht]
> #3481: Mike Hansen: remove sage/plot/plot3dsoya.py from sage [Reviewed by Michael Abshoff]
> #3780: Martin Albrecht: add fast col_swap method for dense matrices over GF(2) [Reviewed by Robert Miller]
> #3843: Robert Miller:n ice tree plotting - improve graph plotting docs [Reviewed by Franco Saliola]
> #3905: John Palmieri: revision of programming guide [Reviewed by Martin Albrecht]
> #3956: Martin Albrecht: Fast hash for matrices over finite fields [Reviewed by Robert Bradshaw]
> #3988: William Stein: interfaces -- add algorithm='magma' for polynomial factor and galois_group commands [Reviewed by Martin Albrecht]
> #3991: Martin Albrecht: Matrix_mod2_dense.__hash__ 32-bit doctest failure [Reviewed by John Cremona]
> #3992: Michael Abshoff: Sage 3.1.2.alpha2: three tests in sage/interfaces/octave.py need to be optional [Reviewed by John Cremona]
> #3995: Mike Hansen: improve and doctest the MuPAD interface [Reviewed by Michael Abshoff] 
> #3996: Mike Hansen: doctest the Singular interface [Reviewed by Martin Albrecht]
> #3997: Mike Hansen: doctest and fix the Lisp interface [Reviewed by Michael Abshoff]
> #4001: Martin Albrecht: ZZ['x'].gen()^(2^20) should work but doesn't [Reviewed by John Cremona]
> #4002: Robert Miller, Mike Hansen: raise coverage of sage.graphs to 100% [Reviewed by Mike Hansen, Robert Miller]
> #4003: Mike Hansen: increase coverage of sage/interfaces/maple.py [Reviewed by Michael Abshoff]
> #4004: Mike Hansen: increase coverage of sage/interfaces/gap.py and sage/interfaces/gp.py [Reviewed by Michael Abshoff]
> #4005: Robert Miller: sage-coverage screws up with lambda functions as default arguments [Reviewed by Michael Abshoff]
> #4006: Mike Hansen: Remove unused code in sage/libs/pari/functional.py [Reviewed by Michael Abshoff]
> #4007: Michael Abshoff: OSX 10.4/5: build libpng.dylib again [Reviewed by Robert Miller]
> #4008: Michael Abshoff: OSX 10.4/5: build python without the OSX specific extensions [Reviewed by Robert Miller]
> #4009: Michael Abshoff: OSX 10.4/5: build R without the aqua support [Reviewed by Robert Miller]
> #4014: Mike Hansen: remove sage/plot/graph.py from Sage [Reviewed by Michael Abshoff]
> #4015: Robert Miller: add docs to tests/benchmark.py [Reviewed by Michael Abshoff]
> #4016: Alex Ghitza: improve doctests to schemes/generic/scheme.py [Reviewed by Robert Bradshaw]
> 
> Merged in Sage 3.1.2.alpha2:
> 
> #132: Simon King, Mike Hansen: maxima -- implement special arithmetic for MaximaFunction class [Reviewed by Martin Albrecht]
> #772: Carl Witty, Jason Grout: create experimental QEPCAD.spkg for quantifier elimination and solving systems of inequalities [Reviewed by Michael Abshoff, Jason Grout, Carl Witty]
> #1952: Martin Albrecht, Mike Hansen: Follow up to #1940: Ideal comparison improvements [Reviewed by Mike Hansen, Martin Albrecht]
> #2209: Steve Linton: gap on itanium - incorporate steve linton's new fixes so gap builds fine with optimizations [Reviewed by William Stein]
> #2366: Mike Hansen: add docstring to sloane_find and sloane_sequence [Reviewed by Timothy Clemans]
> #3253: Alex Ghitza: f.jacob() used to work to compute jacobian ideal. Now it doesn't [Reviewed by Martin Albrecht]
> #3431: Carl Witty: QEPCAD interface [Reviewed by Jason Grout]
> #3440: Martin Albrecht: Our PolyBoRi's GB calculation in AES mode is broken [Reviewed by Burcin Erocal]
> #3630: Yi Qiang: upgrade twisted.spkg to 8.1.0 release [Reviewed by Michael Abshoff]
> #3635: Martin Albrecht: If m is a matrix, then m.plot() should call matrix_plot [Reviewed by Jason Grout] 
> #3823: Igor Tolkov: Interact - get rid of default height [Reviewed by Jason Grout]
> #3883: John Cremona: Streamline elliptic curve division (torsion) polynomials  [Reviewed by Chris Wuthrich]
> #3892: Hamish Ivey-Law, Martin Albrecht: PowerSeries random element over GF(q) (Givaro) fails [Reviewed by Alex Ghitza]
> #3909: Josh Kantor: Updating jmol package to 11.6rc8 [Reviewed by Jason Grout, Michael Abshoff]
> #3915: Martin Albrecht: PolyBoRi interface improvements [Reviewed by Michael Brickenstein]
> #3935: Jason Merrill: ode_solver __init__ method ignores many parameters [Reviewed by Jason Grout]
> #3961: John Cremona: bug in ell_finite_field.abelian_group() [Reviewed by Alex Ghitza]
> #3965: Martin Albrecht: one line fix for PolyBoRi to Magma conversion [Reviewed by Burcin Erocal]
> #3966: Jason Grout: The ode cython example gives errors [Reviewed by Jason Merrill]
> #3968: Jason Grout: Magma interface sometimes fails on long inputs [Reviewed by Willem Jan Palenstijn]
> #3971: William Stein: hidden markov models -- implement nsteps and log_likelihood_cutoff [Reviewed by Josh Kantor]
> #3972: Michael Abshoff: 3.1.2.alpha1: numerical noise in plot.py [Reviewed by Craig Citro]
> #3973: Chris Wuthrich: short_weierstrass_model in characteristic 3 [Reviewed by John Cremona]
> #3975: Arnaud Bergeron: Small mistake in the new plot() code [Reviewed by Mike Hansen]
> #3976: Mike Hansen: improve doctests to expect.py, maxima.py, and lie.py [Reviewed by Robert Miller]
> #3977: Mike Hansen: get interfaces/octave.py up to 100% coverage [Reviewed by Robert Miller]
> #3982: Robert Miller: Pipe stdout to /dev/null to help sage_timeit with "print" statements [Reviewed by Mike Hansen]
> #3983: Mike Hansen: get coverage for sage/interfaces/sage0.py up to 100% [Reviewed by Michael Abshoff]
> #3989: Michael Abshoff: fix autotools issues with gd-2.0.35 [Reviewed by Craig Citro]
> 
> Merged in Sage 3.1.2.alpha1:
> 
> #1539: William Stein: bdist of sage should include devel/doc [Reviewed by Michael Abshoff]
> #2000: Martin Albrecht: fall back to univariate factoring if possible [Reviewed by Carl Witty]
> #2410: Jason Grout: parametric_plot and constants [Reviewed by Mike Hansen]
> #2491: Mike Hansen: Showing source from sloane_functions [Reviewed by Michael Abshoff]
> #2569: Carl Witty: Add XOR to preparser [Reviewed by Mike Hansen]
> #3359: Martin Albrecht: bug/inconsistency in multivariate polynomial substitution [Reviewed by Mike Hansen]
> #3390: Jason Grout: update numpy to the 1.1.0 release [Reviewed by Michael Abshoff]
> #3392: Tim Abbott, Jason Grout: upgrade matplotlib to 0.98.3 release [Reviewed by Michael Abshoff]
> #3432: Martin Albrecht: MPolynomial_libsingular does not have a degrees method [Reviewed by Mike Hansen]
> #3653: Carl Witty: Better random complex numbers [Reviewed by Mike Hansen]
> #3654: Jason Grout: Deprecation warning function [Reviewed by Michael Abshoff, Mike Hansen]
> #3655: C. Boncelet, David Joyner: left multiplication in piecewise does not work [Reviewed by Mike Hansen]
> #3719: David Joyner: bug in group cohomology [Reviewed by Alex Ghitza]
> #3724: Martin Albrecht: faster hashs for Matrix_mod2_dense [Reviewed by Simon King]
> #3792: Ondrej Certik: fix Sage build when there is a broken systemwide freetype library [Reviewed by Michael Abshoff]
> #3794: Jason Grout: Create eigen functions for matrices [Reviewed by John Cremona]
> #3813: Franco Saliola, Arnaud Bergeron: Improve adaptive rendering in plot() [Reviewed by William Stein, Mike Hansen]
> #3826: Carl Witty: Empty string in interact prints \x00 [Reviewed by Igor Tolkov]
> #3853: Mike Hansen, Jason Grout: plot.py improvements part 1: Remove all factories [Reviewed by Jason Grout, Mike Hansen, Michael Abshoff]
> #3854: Igor Tolkov: interact needs to use "notruncate" [Reviewed by Martin Albrecht, Mike Hansen]
> #3869: John Cremona: CremonaDatabase functions iter() and isogeny_classes() sort keys wrongly [Reviewed by Carl Witty]
> #3873: Jason Grout, Carl Witty: Doctest should test for warnings [Reviewed by Carl Witty, Michael Abshoff]
> #3896: Robert Bradshaw: Upgrade Cython to 0.9.8.1.1 [Reviewed by Michael Abshoff]
> #3910: Carl Witty: adjust interval printing: precise integers print as integers [Reviewed by John Cremona]
> #3913: John Cremona: order function not defined for ideal classes [Reviewed by Alex Ghitza]
> #3926: Martin Albrecht: fix Macaulay2 building [Reviewed by Michael Abshoff]
> #3927: John Cremona: Several enhancements and bug fixes for Factorization class [Reviewed by Carl Witty]
> #3939: Martin Albrecht: copyright notice in integer.pyx [Reviewed by Michael Abshoff]
> #3942: Robert Miller: Sage interfaces vs. pyprocessing [Reviewed by William Stein]
> #3946: Chris Holdsworth: Tidier BinaryQF reductions [Reviewed by John Cremona]
> #3947: Michael Abshoff, David Philp: build python against Sage's readline [Reviewed by Mike Hansen]
> #3948: Michael Abshoff: Add 64 bit OSX build support for clisp [Reviewed by Mike Hansen]
> #3952: Mike Hansen: make plot() and parametric_plot() use fast_float on their functions [Reviewed by Carl Witty, Michael Abshoff]
> #3963: Mike Hansen: bug in converting Sage's rationals to Sympy rationals [Reviewed by Michael Abshoff]
> 
> Merged in Sage 3.1.2.alpha0:
> 
> #1300: Simon King, Martin Albrecht: Customize the output of Singular matrices [Reviewed by Martin Albrecht, Simon King]
> #1470: Michael Abshoff, Mike Hansen: upgrade maxima.spkg to 5.16.2 [Reviewed by Mike Hansen, Michael Abshoff]
> #1621: Michael Abshoff: update gd to 2.0.35/update 64 bit OSX support [Reviwed by Robert Miller]
> #3013: Michael Abshoff: bug in integrate (found during a talk!) [Reviewed by Mike Hansen]
> #3174: Michael Abshoff: add 64 bit OSX build support to flint [Reviewed by Robert Miller]
> #3175: Michael Abshoff: add 64 bit OSX build support to zlib [Reviewed by Robert Miller]
> #3194: Michael Abshoff: fix 64 bit OSX build support for singular [Reviwed by Robert Miller]
> #3195: Michael Abshoff: add 64 bit OSX build support for polybori [Reviwed by Robert Miller]
> #3199: Michael Abshoff: fix 64 bit OSX build support for zn_poly [Reviwed by Mike Hansen]
> #3641: Martin Albrecht: new Singular upstream release [Reviewed by Michael Abshoff]
> #3683: Simon King, David Joyner: Wrap GAP's meataxe implementation [Reviewed by David Joyner, Simon King]
> #3707: Ondrej Certik: Make all common Sage classes convertible to SymPy, update Sympy to 0.6.2 [Reviewed by Martin Albrecht]
> #3710: Andrzej Giniewicz: Segfault in Tachyon on some latest GCC versions [Reviewed by Michael Abshoff]
> #3726: William Stein: stats/finance -- add support for hidden markov models to sage [Reviewed by Josh Kantor]
> #3773: William Stein: hidden markov models -- part 2 [Reviewed by Josh Kantor]
> #3874: Karl-Dieter Crisman: Moebius plot bug [Reviewed by William Stein]
> #3880: Robert Miller: Bad behavior of arrows [Reviewed by Michael Abshoff]
> #3884: Michael Abshoff: change banner in "sage -advanced" [Reviewed by William Stein]
> #3887: Craig Citro, Nils-Peter Skoruppa: Fix bug in determinant [Reviewed by William Stein]
> #3888: Martin Albrecht: fix trivial indentation [Reviewed by Michael Abshoff]
> #3908: Carl Witty: fix major memory leak in fast_float [Reviewed by Michael Abshoff]
> #3919: Igor Tolkov: Selector - do not inset a lone button [Reviewed by William Stein]
> 
> ===================================================================
> 
> Sage 3.1.1 was released on August 17th, 2008. It is available at
> 
>            http://sagemath.org/download.html
> 
> Note that Sage 3.1 was never publically announced due to a grave bug 
> fixed in 3.1.1.
> 
> * About Sage (http://www.sagemath.org)
> 
> Sage is developed by volunteers and combines 71 open source packages.
> It is available for download from 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 44 people contributed to this release:
> 
>  * Tim Abbott
>  * Michael Abshoff
>  * Martin Albrecht
>  * Nick Alexander
>  * Robert Bradshaw
>  * Tom Boothby
>  * Nicolas Borie [first contribution]
>  * Dan Bump
>  * Craig Citro
>  * Francis Clarke
>  * Timothy Clemans
>  * John Cremona
>  * Didier Deshommes
>  * Tom Denton [first contribution]
>  * Tom Draper [first contribution]
>  * Bill Furnish
>  * Andrzej Giniewicz
>  * Alex Ghitza
>  * Jason Grout
>  * David Harvey
>  * Mike Hansen
>  * Waldek Hebish
>  * David Joyner
>  * Emily Kirkman
>  * David Kohel
>  * Michael Mardaus [first contribution]
>  * Robert Miller
>  * Tobias Nagel [first contribution]
>  * Brett Nakashima [first contribution]
>  * Bill Page
>  * John Palmieri
>  * Clement Pernet
>  * Pearu Peterson [first contribution]
>  * David Roe
>  * Harald Schilly [first contribution]
>  * Jaap Spies
>  * Franco Saliola
>  * Chris Swierczewski
>  * Yi Qiang
>  * Glenn Tarbox [first contribution]
>  * Nicolas Thiery
>  * Igor Tolkov
>  * William Stein
>  * Carl Witty
> 
> Cheers,
> 
> Michael Abshoff (release chair), William Stein
> 
> * Major Features, New Spkgs and Bugfixes
> 
>  * New Coercion Infrastructure (Robert Bradshaw, David Roe)
>  * Graph and Plotting Improvements (Arnaud Bergeron, Jason Grout, Robert Miller, Franco Saliola)
>  * Major Update to Root Systems: Dan Bump, Nicolas Thiery, Nicolas Borie, Mike Hansen 
>  * Steenrod Algebra Calculations (John Palmieri)
>  * Notebook improvements (Timothy Clemans)
>  * Free Modules Revision (David Kohel)
>  * Multimodular Algorithm for Bernoulli Numbers (David Harvey)
>  * Partition Refinement (Robert Miller)
>  * New sage_input Function (Carl Witty)
>  * New printing for intervals and QQbar elements (Carl Witty)
>  * Integral Point Finding for Elliptic Curves over Q (Tobias Nagel, Michael Mardaus, John Cremona)
> 
> For details see the Sage 3.1 and 3.1.1 Release Tour at
> 
>   http://wiki.sagemath.org/sage-3.1
> 
> * Known Issues with 3.1.1:
> 
>  * 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 114 tickets. For details see
> 
>    http://trac.sagemath.org/sage_trac/milestone/sage-3.1
>    http://trac.sagemath.org/sage_trac/milestone/sage-3.1.1
> 
> or check out the closed ticket section at the end of the 
> announcement. 
> 
> * Upcoming Releases
> 
> The next release will be 3.1.2, chaired by Michael Abshoff. It will 
> be a mix of new features and bug fixes.
> 
> * Doctesting Coverage
> 
> For 3.0.6 we had:
> 
> Overall weighted coverage score:  54.2%
> Total number of functions:  20237
> 
> We increased coverage by 2.3% in 3.1.1 while adding 683 functions:
> 
> Overall weighted coverage score:  56.5%
> Total number of functions:  20920
> 
> * Closed Tickets:
> 
> Merged in Sage 3.1.1.final:
> 
> William Stein: Fix a critical notebook unpickling bug
> 
> Merged in Sage 3.1.final:
> 
> #3875: William Stein: matrix/matrix_cyclo_dense.pyx segfault [Reviewed by Michael Abshoff]
> #3878: Franco Saliola: Constructing a c_graph from a DiGraph doubles the edges [Reviwed by Robert Miller]
> #3881: Michael Abshoff: Quiet three MPolynomialRing deprecation warnings [Reviwed by Robert Miller]
> 
> Merged in Sage 3.1.rc0:
> 
> #1719: Jason Grout: problems building documentation [Reviewed by Michael Abshoff]
> #3864: Craig Citro: Bug exposed by p-adic matrices [Reviewed by William Stein]
> #3738: Robert Bradshaw, David Roe: new coercion model [Reviewed by Nick Alexander, Robert Miller, Craig Citro]
> #3744: Robert Bradshaw: Coercion between isomorphic parents should result in an element of the left operand's parent [Reviewed by Nick Alexander, Robert Miller, Craig Citro]
> #3759: Robert Miller: make testlong leaves all kinds of crap in SAGE_ROOT [Reviewed by William Stein]
> #3814: Craig Citro: Bug introduced in trac #3800 fix [Reviewed by John Cremona]
> #3815: William Stein: fix plot3d segfaults [Reviewed by Michael Abshoff]
> #3822: Igor Tolkov: Interact - slider breaks defaulting on too many values [Reviewed by William Stein]
> #3825: Franco Saliola: 2d-plots has no functionality for grid lines [Reviewed by William Stein]
> #3827: Chris Swierczewski: finance.TimeSeries -- missng docstring input option [Reviewed by Andrzej Giniewicz]
> #3834: William Stein: notebook -- massive bug in the notebook -- doing full text search starts a PYthon process for every single worksheet you have!!! [Reviewed by Michael Abshoff]
> #3837: John Cremona: Performance regression in sha.py due to #3674 [Reviewed by Michael Abshoff, William Stein]
> #3842: William Stein: notebook -- major bug in how javascript <script> tags are interpreted by the notebook [Reviewed by Timothy Clemans]
> #3848: Craig Citro: Better documentation for discriminant function for modular abelian varieties' endomorphism ring [Reviewed by William Stein]
> #3850: William Stein: Sage 3.1.alpha2: matrix_space.py doctest failure (OSX only) [Reviewed by Michael Abshoff]
> #3851: John Palmieri: Steenrod algebra doctest patch: small coercion issue with 3.1alpha [Reviewed by Michael Abshoff]
> #3858: John Palmieri: 3.1alpha: fix issues with the reference manual [Reviewed by Michael Abshoff]
> #3860: Michael Abshoff: itanium -- can't build mercurial extension [Reviewed by William Stein]
> #3867: William Stein: sage-3.1.alpha2: graph.py numerical noise [Reviewed by Michael Abshoff]
> #3868: William Stein: matrix_modn_dense -- numerical noise [Reviewed by Michael Abshoff]
> 
> Merged in Sage 3.1.alpha2:
> 
> #1220: Craig Citro: ModularSymbols(GammaH) [Reviewed by John Cremona, Michael Abshoff]
> #2527: Craig Citro: get doctests for congroup.py and congroup_element.py up to 100% [Reviewed by John Cremona]
> #3383: John Cremona: division_points() fails for elliptic curve over number field [Reviewed by William Stein, Michael Abshoff]
> #3485: Carl Witty: new sage_input function gives a sequence of commands to reproduce sage values [Reviewed by William Stein]
> #3637: Emily Kirkman: Implement Jacobi sums of Dirichlet characters [Reviewed by Nick Alexander, Alex Ghitza, David Joyner]
> #3674: Tobias Nagel, Michael Mardaus, John Cremona: Implement integral point finding for elliptic curves over Q [Reviewed by William Stein, Nick Alexander]
> #3676: Robert Miller: Refactor graph isom code [Reviewed by Nick Alexander, Tom Boothby]
> #3776: Timothy Clemans: notebook -- cookies don't work for admin users [Reviewed by William Stein]
> #3786: Robert Miller: Refactor binary code isomorphism code [Reviewed by Nick Alexander]
> #3806: Mike Hansen, Robert Miller: improvements to plot.py [Reviewed by Robert Miller, Mike Hansen]
> #3807: Michael Abshoff: Fix gcc 4.3 issues in David Harvey Bernoulli modp code [Reviewed by William Stein]
> #3809: Nick Alexander: reorder checks for creating a number field; prevents some silly errors [Reviewed by William Stein]
> #3811: Nick Alexander: number fields in different polynomials compare differently [Reviewed by William Stein]
> #3816: William Stein: notebook -- SyntaxWarning in twist.py [Reviewed by Michael Abshoff]
> #3818: William Stein: COPYING.txt doesn't mention jmol but it should [Reviewed by Michael Abshoff]
> #3819: Michael Abshoff: time_series.pyx numerical noise doctest failures [Reviewed by William Stein]
> #3821: David Harvey: bernmm shouldn't depend on pyport.h [Reviewed by Michael Abshoff]
> #3824: Timothy Clemans: notebook -- clicking sign out needs to resource not found page [Reviewed by William Stein]
> #3828: Clement Pernet: Upgrade to linbox-1.1.6rc1 [Reviewed by Michael Abshoff]
> #3831: Michael Abshoff: add experimental boost-1.34-1.spkg to the repo [Reviewed by Robert Miller]
> #3832: Michael Abshoff: add experimental Quantlib.spkg and Quantlib-SWIG.spkg to the repo [Reviewed by Robert Miller]
> #3833: William Stein: calculus -- fix bug in hashing of symbolic expressions [Reviewed by Bill Furnish]
> #3840: Bill Furnish: conversion of 0 from MV polynomial rings broken [Reviewed by Nick Alexander, William Stein]
> 
> Merged in Sage 3.1.alpha1:
> 
> #1686: Michael Abshoff: arpack -- illegal instruction when built on Pentium 4 using gfortran [Reviewed by William Stein] 
> #3119: John Cremona: elliptic curves -- implement gens function for non-integral models [Reviewed by Nick Alexander]
> #3397: John Palmieri: Steenrod algebra calculations [Reviewed by William Stein]
> #3460: Nick Alexander: add power_basis() to number fields [Reviewed by David Harvey, John Cremona]
> #3484: Carl Witty: extend sage_eval (in preparation for sage_input) [Reviewed by William Stein]
> #3514: David Kohel:  Free modules revision [Reviewed by Mike Hansen, William Stein]
> #3522: Jaap Spies: New experimental mayavi2 spkg based on vtk_5.2 for linux [Reviewed by Michael Abshoff]
> #3542: David Harvey: multimodular algorithm for Bernoulli numbers [Reviewed by William Stein, Nick Alexander]
> #3591: Timothy Clemans: notebook -- remove notebook.save() from Logout [Reviewed by Nick Alexander, William Stein]
> #3613: Mike Hansen: symbolic equations are not passed to Maple correctly [Reviewed by Nick Alexander]
> #3633: Yi Qiang: use commands.getoutput in hostinfo [Reviewed by Robert Miller]
> #3649: Timothy Clemans: Add option to disable the Notebook registration email [Reviewed by William Stein]
> #3652: Carl Witty: FreeModule(ZZ, 2000).random_element() is far slower than it should be [Reviewed by Nick Alexander]
> #3662: Niclos Thiery, Mike Hansen: separate the module functionality of out CombinatorialAlgebra and move it into CombinatorialAlgebra [Reviewed by the Sage-combinat team]
> #3664: Dan Bump, Nicolas Thiery, Nicolas Borie, Mike Hansen: major updates to root systems [Reviewed by the Sage-combinat team]
> #3673: Francis Clarke: NumberFieldElement class unreasonably privileges the polynomial variable 'x' [Reviewed by John Cremona]
> #3727: Harald Schilly: bug report link in notebook [Reviewed by Timothy Clemans]
> #3731: John Palmieri: missing some derivatives in wester [Reviewed by Nick Alexander]
> #3735: William Stein: Interact - header Javascript code executes on update [Reviewed by Igor Tolkov]
> #3736: Mike Hansen: pairwise_product fails for vectors over CDF [Reviewed by Robert Bradshaw]
> #3741: Timothy Clemans: notebook -- the files for the revision history of a worksheet *do* get published [Reviewed by William Stein]
> #3743: Timothy Clemans: notebook -- allow admin user to view any worksheet [Reviewed by William Stein]
> #3751: John Cremona: Type of output returned by QuadraticField(-1).class_number() [Reviewed by Nick Alexander]
> #3755: William Stein: finance -- improve implementation of hurst exponent [Reviewed by Brett Nakashima]
> #3756: William Stein: finance -- fix a bug in fractional brownian motion random walks [Reviewed by Igor Tolkov]
> #3757: Carl Witty: change printing for intervals (and AA/QQbar) [Reviewed by Jason Grout and William Stein]
> #3763: Carl Witty: add conversions from AA/QQbar to standard types [Reviewed by John Cremona]
> #3764: Timothy Clemans: notebook -- notebook.py coverage to 17% [Reviewed by William Stein]
> #3771: William Stein: make it so typing "sage -br" for new binary sage installs doesn't require rebuilding everything [Reviewed by Craig Citro]
> #3779: Mike Hansen: inconsistency for variables method, leads to errors in differentiation [Reviewed by Robert Bradshaw]
> #3781: Mike Hansen: add a cached_method decorator [Reviewed by Nick Alexander]
> #3782: Tom Denton: add support for non-symmetric Macdonald polynomials with permuted basement [Reviewed by Mike Hansen]
> #3788: Robert Bradshaw: many matrix_dense_modn operations are unreasonably slow [Reviewed by Mike Hansen]
> #3789: Robert Miller: graphs(<tab>) [Reviewed by Mike Hansen]
> #3790: Mike Hansen: limit gets stuck without computing anything [Reviewed by Michael Abshoff]
> #3793: John Cremona: Some elliptic curve doctests fail when the optional database is installed [Nick Alexander]
> #3795: Mike Hansen: increase coverage of sage/server/notebook/cell.py [Reviewed by Nick Alexander]
> #3797: Robert Miller: several improvements to graph generation [Reviewed by Carl Witty]
> #3798: Robert Miller: some docstrings for sage.graphs [Reviewed by Emily Kirkman]
> #3800: Craig Citro: Problem with Cusp constructor [Reviewed by William Stein]
> #3801: Robert Miller, Franco Saliola: Spring layout for posets [Reviewed by Franco Saliola, Robert Miller]
> 
> Merged in Sage 3.1.alpha0:
> 
> #3361: Waldek Hebish, Bill Page: Update optional fricas.spkg to 1.0.3 release - make it use clisp again [Reviewed by Michael Abshoff]
> #3497: Glenn Tarbox: ignore git repo info in main sage repo [Reviewed by Michael Abshoff]
> #3558: Mike Hansen: make "% cells" work in the notebook when the mode is not set to "sage [Reviewed by William Stein]
> #3599: Igor Tolkov: Longer slider and labels on sliders [Reviewed by William Stein]
> #3609: John Cremona: Update eclib to eclib-20080310.p5.spkg [Reviewed by Michael Abshoff]
> #3636: Igor Tolkov: Text control, no label [Reviewed by William Stein]
> #3645: John Palmieri: tutorial: make documentation for .n() more prominent [Reviewed by William Stein]
> #3679: Igor Tolkov: Range Slider Control [Reviewed by William Stein]
> #3697: Tom Draper: Adds is_primitive() method to polynomials over Finite Fields [Reviewed by Robert Bradshaw]
> #3698: William Stein: add multinomial_coefficients and binomial_coefficients to sage [Reviewed by Pearu Peterson]
> #3703: Robert Miller: fix bug in set_edge_label [Reviewed by Jason Grout]
> #3705: Mike Hansen: upgrade Mercurial to 1.01 [Reviewed by Michael Abshoff]
> #3708: David Joyner: something screwy in the reference manual [Reviewed by Michael Abshoff]
> #3721: Yi Qiang: Use SAGE_TESTDIR for dsage unit tests [Reviewed by Michael Abshoff]
> #3725: Martin Albrecht: tiny doc improvement for mq.SR [Reviewed by Michael Abshoff]
> #3729: Tim Abbott: Only overwrite RHOME environment variable when it is unset [Reviewed by Michael Abshoff]
> #3734: John Cremona: inverse() fails for 0 by 0 matrices [Reviewed by Didier Deshommes]
> #3739: Timothy Clemans: notebook -- new user default [Reviewed by William Stein]
> #3747: David Harvey: incorrect power in modular arithmetic [Reviewed by William Stein, John Cremona]
> 
> ===================================================================
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