Hello folks, Sage 3.3 was released on February 21st, 2009. It is available at http://www.sagemath.org/download.html * About Sage (http://www.sagemath.org) Sage is developed by volunteers and combines 83 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 57 people contributed to this release. Of those 11 made their first contribution to Sage: * Michael Abshoff * Martin Albrecht * Nick Alexander * Ivan Andrus [first contribution] * Maite Aranes [first contribution] * Jason Bandlow * Sebastien Barthelemy * Rob Beezer [first contribution] * Arnaud Bergeron * Tom Boothby * Robert Bradshaw * Paul Butler * Craig Citro * Timothy Clemans * John Cremona * Karl-Dieter Crisman * Dan Drake * Burcin Erocal * Alex Ghitza * Dan Gordon [first contribution] * Jason Grout * Bill Hart * Marshall Hampton * Florent Hivert [first contribution] * David Moller Hansen [first contribution] * Mike Hansen * Alexander Hupfer * Wilfried Huss * David Joyner * Kiran Kedlaya * Simon King * Emily Kirkman * Sebastien Labbe * Yann Laigle-Chapuy [first contribution] * David Loeffler * Mark McLure [first contribution] * Matthias Meulien [first contribution] * Robert Miller * Tobias Nagel * Minh Van Nguyen * John Palmieri * David Perkinson [first contribution] * John Perry * David Roe * Harald Schilly * Dan Shumow * Jaap Spies * William Stein * Blair Sutton [first contribution] * Glenn Tarbox * Nicolas Thiery * Gonzalo Tornaria * Minh Van Nguyen * Georg Weber * Carl Witty * Mike Zabrocki * Paul Zimmermann Cheers, Michael Abshoff (release chair), William Stein * Major Features, New Spkgs and Bugfixes The focus of Sage Days 12 in San Diego sponsored by CCR West was to fix as many open bugs in Sage as possible and it proved to be a great success by closing about a third of the known defects in Sage within a five day period. The final status report can be found at http://wiki.sagemath.org/days12/statusreports?action=AttachFile&do=view&target=report.pdf We also updated various Sage components with known security issues, so please update if you run a Sage server, especially if it is exposed to the public net. Aside from the above there a are very large number of improvements as well as updates to the components of Sage. One of the new major usability improvements to the notebook is the addition and integration of the TinyMCE editor which now allows to add inline text cells to the notebook via a very nice WYSIWYG editor. This was made possible by Jason Grout who while working on this ticket did also clean up the way Sage's other Javascript based components were installed and used. For all the details of what else changed in Sage 3.3 please see the release tour in the Sage wiki at http://wiki.sagemath.org/sage-3.3 * Known Issues with 3.3: * RHEL 5 clisp build issue: the latest clisp.spkg does not build so please use the clisp.spkg from Sage 3.0.3. * On Fedora Core 9 and 10 system Sage can fail at startup due to "out of memory" conditions related to libSingular. These failures are due to a bug in the Fedora kernel's new security features that interacts poorly with libSingular's memory allocation system. It also seems to be much more easily triggered on 64 bit platforms. The bug indeed was first detected about 9 months ago, but we hoped that the kernel would be fixed; we have decided to fix the problem on the Singular side, instead, but have not yet completed the fix. * If you upgrade please delete the old matplotlibrc from $DOT_SAGE, $SAGE_ROOT, and $SAGE_ROOT/tmp since they cause deprecation warnings when doctesting or using certain functionality. These are false positives and caused by the outdated matplotlibrc we used to ship. * Bug Statistics We closed a record 385 tickets. For details see http://trac.sagemath.org/sage_trac/milestone/sage-3.3 or check out the closed ticket section at the end of the announcement. * Upcoming Releases * Sage 3.4 will focus on two major features: The ReST transition of the documentation in Sage spearheaded by Mike Hansen and the merging of Jon Hanke's quadratic forms library code into the main Sage library. This code will play a central role at Sage Days 13 that will take place from February 28th until March 2nd 2009 at the University of Georgia, Athens. This implies that this release will be made in the next 4 days. * Sage 3.4.1 will merge code from the coding sprint of SD 13 as well as fixes for the usual bugs that will crop up. This release ought to be out two or three days after the end of SD 13 and is meant to stabilize the 3.4 series due to the large amount of code that went into the 3.3 and 3.4 release cycles. * Sage 3.4.2 should contain additional bug fixes and maybe even more code for quadratic forms to get ready for the Arizona Winterschool 2009 which takes place during the middle of March. There will be many Sage developers and users there, so this ought to be an interesting workshop. * Doctesting Coverage For 3.2.3 we had: Overall weighted coverage score: 64.3% Total number of functions: 21982 We increased coverage by 0.7% in 3.3 while adding 247 functions: Overall weighted coverage score: 65.0% Total number of functions: 22229 * Closed Tickets: Merged in Sage 3.3.final: #1641: William Stein: Make ATLAS restart build on tolerance error [Reviewed by Michael Abshoff] #5329: William Stein: sage-3.3.rc3 -- latex mistake [Reviewed by Michael Abshoff] #5327: Robert Miller: multiple edge plots use symbolic computations [Reviewed William Stein] Merged in Sage 3.3.rc3: #4440: Alexander Hupfer, Tom Boothby: Automatic Indentation [Reviewed by Jason Grout] #4746: Robert Bradshaw: Bug in srange [Reviewed by Carl Witty, William Stein] #4688: Maite Aranes, Alex Ghitza: wrap pari functions idealstar and ideallog [Reviewed by John Cremona] #4779: William Stein: make function for creating random rings and running automated testing on them [Reviewed by Martin Albrecht, Michael Abshoff] #5104: Robert Bradshaw: setup.py dependency checking issues [Reviewed by Michael Abshoff] #5216: Mike Hansen: Update bzip2 to 1.0.5 release [Reviewed by Michael Abshoff] #5251: Robert Bradshaw: preparser bug in parsing the backslash "solve right" notation [Reviewed by Mike Hansen] #5257: Mike Hansen: Clicking on "Log" in the notebook (bringing you to the /history page) gives errors [Reviewed by Michael Abshoff] #5287: Martin Albrecht: improve mq.SR usability and performance [Reviewed by William Stein] #5293: Tom Boothby: tab-completion menu creates two copies of the choice made [Reviewed by Marshall Hampton, Jason Grout] #5301: William Stein: In sage-3.3.rc2, doing sage -t -long "devel/sage/sage/plot/plot.py" causing a matplotlib GUI window to popup [Reviewed by Michael Abshoff] #5302: Robert Miller: Numerical noise in graph.py get_pos() and graph_plot.py [Reviewed by Jaap Spies, Michael Abshoff] #5303: Michael Abshoff: Sage 3.3.rc2: numerical noise in sage/schemes/elliptic_curves/sha_tate.py [Reviewed by William Stein, John Cremona] #5304: Michael Abshoff: Sage 3.3.rc2: Fix documentation build [Reviewed by Mike Hansen] #5309: William Stein: mark some doctests in misc/package.py #optional - internet [Reviewed by Michael Abshoff] #5311: Michael Abshoff: Update to ATLAS 3.8.3 (latest upstream release) [Reviewed by Glenn Tarbox] #5314: Florent Hivert: The empty permutations exists! [Reviewed by Mike Hansen] #5315: Michael Abshoff: Fix MPIR.spkg build on more OSX MacIntel boxen [Reviewed by Mark McLure] #5316: Carl Witty: some elements of NumberField_quadratic are NumberFieldElement_absolute --> segfault [Reviewed by William Stein] #5320: Mike Hansen: update Sphinx to 0.5.1, setuptools to 0.6c9 [Reviewed by Michael Abshoff] Merged in Sage 3.3.rc2: #5106: Robert Bradshaw: preparse bug with time and generator assignment naming [Reviewed by Marshall Hampton] #5171: Robert Miller: Overhaul the Graph and DiGraph initialization functions [Reviewed by William Stein] #5227: Minh Van Nguyen: add next batch of 14 people to devmap [Reviewed by Harald Schilly, Michael Abshoff] #5285: Mike Zabrocki, Jason Bandlow: Dyck Paths documentation problem [Reviewed by Mike Hansen] #5289: Michael Abshoff: gdmodule fails to build on Linux/Solaris systems without a system wide libpng [Reviewed by Mike Hansen] #5290: Michael Abshoff: Sage 3.3.rc1: Sage fails to start due to dangling missed import in plot.py [Reviewed by Jason Grout, Emily Kirkman] #5291: Timothy Clemans: notebook - Do not save snapshots if nothing has changed [Reviewed by William Stein] #5292: Robert Bradshaw: Error in FractionField conversion [Reviewed by William Stein, Mike Hansen] #5297: John Palmieri: sparse vectors and free module elements: pairwise_product is broken [Reviewed by Mike Hansen] #5298: Mike Hansen: hg_sage.apply($URL) broken due to swith to trac 0.11.3 [Reviewed by William Stein] Merged in Sage 3.3.rc1: #1777: Jason Grout: jmol up/down metaphor confusing in the "View" right-click menu [Reviewed by Timothy Clemans] #2522: William Stein: modify "sage -pkg" to not include OSX junk in spkgs [Reviewed by Michael Abshoff] #2873: Jason Grout: Customize JMOL menu [Reviewed by Timothy Clemans] #3106: Jason Grout: Add an "image" link for a screenshot of the JMOL applet in the notebook [Reviewed by Timothy Clemans] #3337: David Joyner, Michael Abshoff: Upgrade gap-guava to new 4.4.12/3.9 release [Reviewed by Michael Abshoff, Carl Witty, William Stein] #3541: Emily Kirkman: graph multiedge plotting [Reviewed by Robert Miller] #4274: William Stein: assertion failure in rank for elliptic curves [Reviewed by John Cremona, Michael Abshoff] #4354: Arnaud Bergeron: loading a file with spaces in the filename doesn't work [Reviewed by Georg Weber] #4371: Nicolas Thiery: Add support for lazy attributes via a decorator [Reviewed by Robert Miller] #4752: Josh Kantor: list_plot3d crashes sage with some exact input [Reviewed by William Stein, John Palmieri, Michael Abshoff] #4774: Jason Grout, Michael Abshoff: Upgrade matplotlib to 0.98.5.3-svn6910 [Reviewed by Michael Abshoff, Jason GRout] #5213: Nick Alexander, Alex Ghitza: make charpoly/minpoly of number field elements use matrix() [Reviewed by Alex Ghitza, Michael Abshoff] #5217: Michael Abshoff: update libpng to 1.2.34 [Reviewed by Marshall Hampton] #5228: Nick Alexander: make composite_fields and galois_closure return maps and preserve embeddings [Reviewed by Alex Ghitza] #5239: Michael Abshoff: Sage 3.3.rc0: even more numerical noise in sage/sage/plot/plot.py [Reviewed by Jason Grout] #5242: Florent Hivert: generic_power can now handle semi-groups [Reviewed by John Cremona, Martin Albrecht] #5244: Florent Hivert: is_unit for symbolic ring [Reviewed by Martin Albrecht] #5252: John Cremona: elliptic curves: P.height() lies about its precision [Reviewed by Alex Ghitza] #5253: Jason Grout: Make a jacobian function which computes the jacobian matrix [Reviewed by Carl Witty] #5255: Florent Hivert: Deprecating the use of iterator in CombinatorialClass [Reviewed by Mike Hansen] #5256: Florent Hivert: coherent handling of trivial matrices [Reviewed by Martin Albrecht, Mike Hansen] #5258: Jason Grout: escape html strings with cgi.escape instead of custom (and lacking) regexp [Reviewed by William Stein] #5259: Jason Grout: invalid array elements sent to matplotlib quiver, causing blank plot [Reviewed by Florent Hivert] #5265: Michael Abshoff: Link the matrix_mod2_dense extension against png12 [Reviewed by Jason Grout] #5266: Jason Grout: plot_vector_field does not plot the end of the range when given plot_points argument [Reviewed by Mike Hansen] #5267: Alex Ghitza: bug in changing a constant multivariate polynomial into a univariate one [Reviewed by Martin Albrecht] #5269: Alex Ghitza: coordinate ring of an affine patch on a hyperelliptic curve is broken [Reviewed by Martin Albrecht] #5271: Michael Abshoff: clean up jmol-11.6.16.spkg from #2873 [Reviewed by Mike Hansen] #5272: Carl Witty: extend sage_input to work with RIF, CIF, AA, and QQbar [Reviewed by Marshall Hampton] #5273: John Palmieri: change error message for integer matrices which are too large [Reviewed by Mike Hansen] #5277: Michael Abshoff: tachyon.spkg: link against libpng12 instead of libpng [Reviewed by Marshall Hampton] #5282: William Stein: In %python mode in the notebook, tracebacks are not properly reported [Reviewed by Michael Abshoff] Merged in Sage 3.3.rc0: #2898: Jason Grout, Nick Alexander, Carl Witty: Coerce integral float and RDF to Integers [Reviewed by Robert Bradshaw, Mike Hansen] #3214: Alex Ghitza, Burcin Erocal: uniformise the behaviour of gcd for rational numbers [Reviewed by John Cremona, Robert Bradshaw] #4721: Paul Butler: Indefinite integration for piecewise functions [Reviewed by David Joyner] #5101: Carl Witty: more types for sage_input: vectors, matrices, etc. [Reviewed by Jason Grout] #5142: John Palmieri: speed up elementary_divisors for sparse integer matrices [Reviewed by Alex Ghitza] #5185: John Palmieri: is_zero is broken for sparse vectors [Reviewed by Carl Witty] #5194: Mike Hansen: add option to turn off automatic updates for an interact [Reviewed by John Perry] #5199: Carl Witty: new symbolics can treat floats as integers inappropriately [Reviewed by Burcin Erocal] #5205: Michael Abshoff: Set "# -*- coding: utf-8 -*-" encoding for sage/server/notebook/template.py [Reviewed by Mike Hansen] #5207: Alex Ghitza: remove unnecessary use of symbolics in doctests in weierstrass_morphism.py [Reviewed by John Cremona] #5208: Rob Beezer: Differing behavior for matrix left_kernel vs. right_kernel [Reviewed by Mike Hansen, Michael Abshoff] #5209: Michael Abshoff: Sage 3.3.a6: numerical noise in sage/plot/plot.py on OpenSUSE 11.1 64 bit [Reviewed by Marshall Hampton] #5210: Bill Hart, Gonzalo Tornaria, Michael Abshoff: gmp-mpir-0.9.rc3: make check failure on various OSX boxen [Reviewed by Nick Alexander] #5215: Michael Abshoff: Remove ipython1-20070130.spkg from Sage [Reviewed by Mike Hansen] #5212: Nick Alexander: bug with numbers in names in sage.structure.parent_gens.normalize_names [Reviewed by David Roe] #5222: William Stein: wrap FLINTs pseudo-division algorithm for univariate polynomials over ZZ [Reviewed by Burcin Erocal] #5224: Robert Miller: speed up isomorphism testing for graphs which are c_graphs [Reviewed by Michael Abshoff] #5231: Nick Alexander: make relative number fields lazy [Reviewed by David Roe] #5232: William Stein: interact -- major bug in interact ranges due to str versus repr [Reviewed by Mike Hansen] #5233: Mike Hansen: improve timings for adjacency_matrix, weighted_adjacency_matrix, and kirchoff_matrix [Reviewed by Jason Grout] Merged in Sage 3.3.alpha6: #2113: Jason Grout: twisted.web2 should be gzip compressing things it sends out to the notebook [Reviewed by William Stein] #4245: Jason Grout: notebook -- error clicking editing when there is a < in the html [Reviewed by Karl-Dieter Crisman] #4280: Mike Hansen: Syntax error for a comment line, then help query in a notebook cell [Reviewed by Jason Grout] #4805: John Cremona: fix S-Integral precision issue (possible p-adic precision problem) [Reviewed by David Roe, William Stein] #4964: David Moller Hansen: Add Weil pairing to Sage [Reviewed by John Cremona] #4972: Jason Grout: matrix setitem should deal with slicing [Reviewed by Carl Witty] #4976: Wilfried Huss: fill option for plot, polar_plot and parametric_plot [Reviewed by Karl-Dieter Crisman, Jason Grout, Michael Abshoff] #5023: Paul Zimmermann: typo in calculus.py [Reviewed by Jaap Spies] #5027: Michael Abshoff: doctest failure for rings/polynomial/toy_d_basis.py [Reviewed by Jaap Spies] #5071: Robert Bradsahw: unit of least precision for RR and RDF [Reviewed by David Roe, Carl Witty] #5137: Martin Albrecht: create variables 's' only once in sr if multiple plaintexts are considered [Reviewed by Carl Witty] #5144: John Palmieri: speed up right_nullity for matrices [Reviewed by Jason Grout] #5151: David Joyner: linear codes decoding algorithms in Sage [Reviewed by Robert Miller] #5158: Wilfried Huss: bug in symbolic factorial [Reviewed by Carl Witty] #5163: Jason Grout: jsmath extensions for published webpages [Reviewed by John Palmieri] #5166: Burcin Erocal: Sage 3.3.a4: sage/symbolic/function.pyx doctest failure on OSX [Reviewed by Carl Witty] #5168: John Palmieri: matrix0.pyx: fix doctest for commutator [Reviewed by Carl Witty] #5172: Michael Abshoff: Sage 3.3.a5: more numerical noise in sage/calculus/calculus.py [Reviewed by Jaap Spies] #5173: Carl Witty: Sage 3.3.a5: doctest failure in sage/rings/polynomial/polynomial_element.pyx due to print order of roots [Reviewed by Michael Abshoff] #5176: Martin Albrecht: notebook chokes horribly on Umlautes [Reviewed by Jason Grout] #5179: Jason Grout: Replace __getslice__ with functionality in __getitem__ in matrices [Reviewed by Carl Witty] #5181: John Palmieri: arith.py: some docstrings with backslashes in them don't start with r""" [Reviewed by Carl Witty] #5189: Jason Grout: notebook -- now possible to delete all computation cells [Reviewed by Timothy Clemans] #5192: Karl-Dieter Crisman: Improve factor documentation [Reviewed by Timothy Clemans] #5193: Carl Witty: maximum allowed matrix size is too big [Reviewed by Jason Grout] #5198: Carl Witty: apply_map skips zeroes in sparse vectors and matrices [Reviewed by Robert Bradshaw] #5202: Michael Abshoff: Update MPFR to 2.4.0 (latest upstream) [Reviewed by Mike Hansen] #5203: Michael Abshoff: Update mpir to 0.9.rc3 release (latest upstream) [Reviewed by Mike Hansen] Merged in Sage 3.3.alpha5: #4544: Carl Witty: comparison of CDF (or any inexact) elements needs fixing [Reviewed by Michael Abshoff] #4593: Martin Albrecht: do not unconditionally use M2 for Gbasis computations over ZZ if it is installed [Reviewed by Michael Abshoff] #4817: Ivan Andrus, Karl-Dieter Crisman: make an os x clickable .app launcher thing for sage automatically when one does -bdist on osx [Reviewed by Michael Abshoff] #5116: Martin Albrecht: update M4RI to newest upstream release [Reviewed by Michael Abshoff] #5129: Michael Abshoff: numerical noise in roots calculus/calculus.py [Reviewed by Jaap Spies] #5141: Jason Grout: tinymce should be disabled on published worksheets [Reviewed by Timothy Clemans, Michael Abshoff] #5143: Jason Grout: shift-enter should save and exit tinyMCE; new font formatting buttons [Reviewed by Timothy Clemans] #5164: Michael Abshoff: NTL.spkg: Set SHAREDFALGS to -fnocommon on Darwin [Reviewed by Jaap Spies] #5170: Jason Grout: Get rid of the tooltip for Tinymce saying to doubleclick - it's annoying after a while. [Reviewed by Timothy Clemans, William Stein] Merged in Sage 3.3.alpha4: #2159: John Perry: Gröbner bases over any field (cont'd) [Reviewed by Martin Albrecht] #4734: William Stein: sage -notebook option now broken [Reviewed by Michael Abshoff] #4946: Michael Abshoff: readline on opensuse11 64-bit still doesn't work [Reviewed by Mike Hansen] #5018: Marshall Hampton: lrs optional package improvements [Reviewed by Michael Abshoff] #5094: Karl-Dieter Crisman: Delete/Change SageX references to Cython [Reviewed by Michael Abshoff] #5096: Burcin Erocal: pynac interface enhancements [Reviewed by Mike Hansen, William Stein, Michael Abshoff] #5102: Alex Ghitza: eisenstein_series_qexp broken over finite fields [Reviewed by William Stein] #5118: Robert Miller: Improve elliptic curve printing [Reviewed by Michael Abshoff] #5125: John Perry: Ideal.basis_is_groebner() may return wrong results [Reviewed by Martin Albrecht] #5132: Burcin Erocal: real numbers don't support __mod__ [Reviewed by Mike Hansen] #5138: William Stein: implement computing manin constants of elliptic curves [Reviewed by John Cremona] #5139: William Stein: add computation of Bach bound of number fields to Sage [Reviewed by Dan Dan Shumow] #5147: Nick Alexander: make plot output file in DOCTEST_MODE changeable for sage-mode.el [Reviewed by Mike Hansen] #5148: Minh Van Nguyen, Harald Schilly: corrections to Andrey Novoseltsev's devmap entry [Reviewed by Michael Abshoff] #5149: William Stein: Cremona database -- fix a bug in handling of 990h [Reviewed by John Cremona] #5150: Minh Van Nguyen, Harald Schilly: update Nils-Peter Skoruppa's contributions [Reviewed by Michael Abshoff] #5152: David Joyner: order of abelian group element is a rational number, but should be an integer [Reviewed by William Stein] #5154: Paul Zimmermann: bug in modular composition over GF(2) [Reviewed by Martin Albrecht] #5157: William Stein: if the mwrank interface is interrupted from the notebook (!) it stays broken for the rest of the sage session [Reviewed by Mike Hansen] #5161: Michael Abshoff: Remove outdated SHAREDFLAGS and Solaris specific injected flags from sage-env [Reviewed by Mike Hansen] #5162: Michael Abshoff: atlas.spkg: Fix mistake introduced in atlas-3.8.2.p1 and actually correct the bug [Reviewed by Mike Hansen] Merged in Sage 3.3.alpha3: #773: William Stein: SAGE drops . from path [Reviewed by Robert Miller, Michael Abshoff] #791: David Roe: ugly absprec parameter in Polynomial constructor [Reviewed by Alex Ghitza] #1367: Nick Alexander: weird bug creating fractional ideal in relative number field [Reviewed by David Roe] #1619: Sebastien Barthelemy: update cddlib to 0.94f [Reviewed by Michael Abshoff] #1847: Robert Miller: add nice print method for Sha(Elliptic curve) [Reviewed by Alex Ghitza] #1867: William Stein: factoring multivariate polynomials over finite fields is broken in Singular [Reviewed by Kiran Kedlaya] #2404: Alex Ghitza: subs_expr claims to take a dictionary, but doesn't [Reviewed by Mike Hansen] #2601: William Stein: problem with _mpoly_dict_recursive() [Reviewed by Alex Ghitza] #2858: William Stein: parametric_plot3d throws an error when the sum of the components cancels a variable [Reviewed by Mike Hansen] #2950: Dan Shumow: point3d misinterpret arguments [Reviewed by Mike Hansen] #2957: Martin Albrecht: Singular multivariate polynomials are buggy on exponent overflow [Reviewed by Burcin Erocal] #3201: Mike Hansen: notebook -- bug in parsing \ at end of line in %latex mode [Reviewed by Jason Grout] #3326: Mike Hansen: trailing question marks in %html blocks are mistreated [Reviewed by John Palmieri] #3547: Arnaud Bergeron: create a polygon3d function [Reviewed by Dan Shumow] #3704: Robert Miller: make diagonal_matrix accept much more general arguments [Reviewed by Jason Grout] #3762: Robert Bradshaw: deprecate quaddouble, switch the number of partitions code to use MPFR all the way [Reviewed by William Stein] #3890: David Roe: exact division syntax in finite fields of prime order [Reviewed by Kiran Kedlaya] #3933: Robert Miller: Set iteration is broken over sets created with iterators [Reviewed by Arnaud Bergeron] #3938: Robert Bradshaw, David Roe, Carl Witty: coercion framework converts built-in types to Sage types when it should not [Reviewed by Craig Citro] #4364: Martin Albrecht: major bug in singular polynomial GCD [Reviewed by William Stein] #4560: David Roe: SR and containment broken [Reviewed by Burcin Erocal] #4697: Karl-Dieter Crisman: change integration error message [Reviewed by Michael Abshoff] #4727: Nick Alexander: list method on relative number field elements is broken -- it doesn't satisfy the most basic consistency check [Reviewed by David Roe] #4728: Nick Alexander: .roots() is inconsistent between polynomials and symbolic polynomials [Reviewed by Martin Albrecht, Jason Grout] #4770: Martin Albrecht: implement maxima.cputime() [Reviewed by Simon King] #4813: Dan Drake: add code from arxiv_0812_2725 to the tests/ directory [Reviewed by Mike Hansen] #4827: Harald Schilly: add L-BFGS-B bound constraint solver to minimize_constraint [Reviewed by Jason Grout] #4859: Dan Gordon: basic covering design module [Reviewed by William Stein, David Joyner] #4860: Robert Miller: upgrade networkx to 0.99 upstream release [Reviewed by Michael Abshoff, Minh Van Nguyen] #4869: Nick Alexander: make element of relative number field from polynomial [Reviewed by David Roe] #4891: William Stein: make a command that installs all optional spkg's and reports the ones that don't work [Reviewed by Martin Albrecht] #4892: Robert Miller: Changing precision of a Complex can convert it to a real [Reviewed by Alex Ghitza] #4937: John Cremona: bug in _p_primary_torsion_basis() for elliptic curves [Reviewed by David Roe] #4957: Craig Citro: inconsistent integer hashing [Reviewed by Robert Bradshaw] #4978: Michael Abshoff: fix NTL tuning issue on Linux/ppc64 [Reviewed by Carl Witty] #5009: Robert Miller: elementary_divisors for integer matrices: fix doc string [Reviewed by Mike Hansen] #5021: John Palmieri: add some jsMath extensions [Reviewed by Jason Grout] #5025: Jason Grout: tinymce: tinymce: fix creation of text cells to not cause duplicate ids and not be considered compute cells [Reviewed by Mike Hansen, Tom Boothby, Karl-Dieter Crisman] #5040: Michael Abshoff: NTL's DoConfig errors out when NTL is build with dependencies in a directory containing [-h|help|-help|--help] [Reviewed by Carl Witty] #5044: William Stein: on some systems mwrank dumps core and crashes on exit when run under pexpect [Reviewed by Michael Abshoff] #5052: Dan Drake: preparser does not respect leading space in front of "load foo.sage" [Reviewed by Tom Boothby] #5053: Simon King: If the hostname of the computer has a "-" in it, then no tempfiles will ever be deleted from $DOT_SAGE/temp [Reviewed by Michael Abshoff] #5055: Karl-Dieter Crisman: Trivial typo in interact documentation [Reviewed by Martin Albrecht] #5066: Nick Alexander: break out relative number fields into separate file [Reviewed by David Roe] #5095: Mike Hansen: AJAX requests don't work from the worksheet listing page [Reviewed by John Palmieri] #5097: Alex Ghitza: doctest failures in 3.3.alpha2 due to lack of #optional tag [Reviewed by Michael Abshoff] #5109: Blair Sutton, Mike Hansen: add support for Bell polynomials in Sage [Reviewed by David Joyner] #5113: Robert Bradshaw: elliptic curve construction from weierstrass equation [Reviewed by Jason Grout] #5115: Dan Drake: documentation for IterableFunctionCall is poor [Reviewed by Michael Abshoff] #5121: Jason Grout: major bug in plot command [Reviewed by William Stein] Merged in Sage 3.3.alpha2: #1127: Alex Ghitza: modularSymbol complement fails for E=128a [Reviewed by Robert Bradshaw] #1587: Simon King: M.kernel() gives the kernel when M acts on row vectors from the right -- Document this; add better examples [Reviewed by John Palmieri] #2020: William Stein: change an error message when running a certain command and the elliptic curve database is too small [Reviewed by Craig Citro] #2360: Martin Albrecht: Strange Polynomial substitution problem [Reviewed by Robert Bradshaw] #2402: Mike Hansen: there should be a hg_examples mercurial wrapper for the examples repository [Reviewed by Michael Abshoff] #2535: Craig Citro: Problem with cuspidal_subspace and new_subspace for modular symbols [Reviewed by Nick Alexander, William Stein, David Roe] #2638: Mike Hansen: complex QQbar expressions exceed maximum recursion depth when exact computation is triggered [Reviewed by Tom Boothby] #2861: William Stein: scripts do not exit with correct exit code when sys.exit() is used [Reviewed by Robert Miller] #2697: Karl-Dieter Crisman, Robert Bradshaw: allow integration without explicit variable declaration [Reviewed by Robert Miller, Karl-Dieter Crisman] #3045: Alex Ghitza: K.gen() where K = GF(p) returns 1, not a primitive element [Reviewed by David Roe] #3056: Tom Boothby: bug with polynomials over power series [Reviewed by Craig Citro] #3268: Mike Hansen: Fix GAP interface printing [Reviewed by Robert Bradshaw] #3294: Mike Hansen: GAP interface broken after CTRL-C [Reviewed by Martin Albrecht] #3298: Burcin Erocal: Cython warnings for PolyBoRi [Reviewed by Michael Abshoff] #3610: Carl Witty: __contains__ for RealIntervalFields does not work correctly [Reviewed by Robert Bradshaw] #3658: Craig Citro: A PARI bug results in an unreliable prime_pi [Reviewed by Tom Boothby] #3752: Mike Hansen: gap.eval -- oddity in parsing multiline input and comments [Reviewed by Martin Albrecht] #3758: Dan Shumow: crypto -- sage -t -long devel/sage/sage/crypto/mq/sr.py fails on many machines [Reviewed by Martin Albrecht] #3871: William Stein: do not save pngs in SAGE_ROOT; extending #3759 [Reviewed by Michael Abshoff] #4048: Alex Ghitza: missing minpoly for GF(p) [Reviewed by Mike Hansen] #4322: Alex Ghitza: modular polynomials database is broken [Reviewed by Craig Citro] #4405: Mike Hansen: double/single quotation marks in docstring [Reviewed by Martin Albrecht] #4524: Mike Hansen: interact -- incomplete default string in the input box [Reviewed by Sebastien Labbe] #4588: William Stein: doctest -- get rid of the "feature" where docstrings with require, optional, and package all in them are automatically marked optional [Reviewed by Robert Miller] #4611: David Roe: deprecate sqrt_approx [Reviewed by Martin Albrecht] #4623: Paul Zimmermann: x^2 is wrong in RealIntervalField [Reviewed by Alex Ghitza] #4648: Robert Miller: sparse linear algebra: nonzero_positions is slow [Reviewed by Craig Citro] #4665: William Stein: sage/misc/cython.py creates file sage/misc/hello.spyx in tree while doctesting [Reviewed by Michael Abshoff] #4755: Alex Ghitza: CremonaDatabase().number_of_curves() should work when the optional database isn't installed. [Reviewed by Robert Bradshaw] #4840: Burcin Erocal: FLINT: call the stack cleanup function at exit [Reviewed by Mike Hansen] #4850: William Stein: bug in power_mod [Reviewed by Burcin Erocal] #4892: Robert Miller: Changing precision of a Complex can convert it to a real [Reviewed by Alex Ghitza] #4895: Jason Bandlow: bug in pattern avoiding permutations [Reviewed by Mike Hansen] #4900: John Cremona: New BSGS point counting on elliptic curves over finite fields [Reviewed by David Roe] #4936: William Stein: massive bloat: make something delete everything in ~/.sage/gap > 1 week old and untouched [Reviewed by Mike Hansen] #4961: Robert Miller: sage/modules/vector_modn_sparse_c.pxi: allocate_c_vector_modint can leak memory in case of failure [Reviewed by Michael Abshoff] #4962: Robert Miller: sage/modules/vector_modn_sparse_c.pxi: init_c_vector_modint leaks leak memory in case of OverflowError [Reviewed by Michael Abshoff] #4971: William Stein: make get_memory_usage() return a float on all platforms [Reviewed by Michael Abshoff] #4981: Burcin Erocal: clean up polynomial_ring.py [Reviewed by John Cremona] #5001: William Stein: kernels of integer matrices [Reviewed by John Palmieri] #5003: Robert Miller: equality testing in graphs should check "weighted" property [Reviewed by Dan Shumow, Mike Hansen] #5026: Craig Citro: numerical noise doctest failure in rings/polynomial/complex_roots.py [Reviewed by Michael Abshoff] #5029: Robert Bradshaw: Better diffs for trac [Reviewed by Mike Hansen, William Stein] #5032: Robert Bradshaw: dividing a sparse matrix by a scalar gives a dense matrix, but multiplying gives a sparse one [Reviewed by Robert Miller] #5047: Simon King: comparing complex i raises error [Reviewed by Burcin Erocal] #5056: John Perry: rename Ideal.reduced_basis to Ideal.interreduced_basis [Reviewed by Simon King] #5060: Robert Bradshaw: setup.py dependency checking detects unexpected dependencies [Reviewed by Craig Citro] #5064: Tom Boothby: Steenrod algebras are non-unique [Reviewed by Dan Shumow] #5067: Robert Miller: linear_code -- four doctest failures in spectrum method='leon' exposed by #4588 [Reviewed by David Joyner] #5068: William Stein: change_ring fails for polynomials over finite fields in many cases [Reviewed by Martin Albrecht] #5069: Robert Bradshaw: Move univariate polynomial rings to new coercion model [Reviewed by David Roe] #5072: Martin Albrecht: segfault in libsingular gcd when base rings aren't identical [Reviewed by William Stein] #5073: Mike Hansen: Update IPython to 0.9.1 [Reviewed by Tom Boothby, Michael Abshoff] #5077: Alex Ghitza: bug in fibonacci function [Reviewed by Mike Hansen] #5078: Robert Bradshaw: bug in factoring out constant literal [Reviewed by Tom Boothby] #5079: Robert Bradshaw: overly greedy RealNumber handling in preparser [Reviewed by Tom Boothby, Mike Hansen] #5087: Alex Ghitza: purge "cannonical" typos [Reviewed by Michael Abshoff] #5088: Yann Laigle-Chapuy: use Pohlig-Hellman for generic discrete logarithm [Reviewed by William Stein] #5089: John Palmieri: add kernel method for sparse integer matrices [Reviewed by William Stein] Merged in Sage 3.3.alpha1: #22: Michael Abshoff: add persistent SAGE64 building switch on OSX and Solaris [Reviewed by Robert Miller] #313: Mike Hansen: Slideshow doesn't update correctly when first cell deleted. [Reviewed by Jason Grout] #1019: Mike Hansen: strange behavior in notebook with %octave [Reviewed by Jason Grout] #1234: William Stein: analytic_rank crashes [Reviewed by John Cremona] #1897: Mike Hansen: %latex -- bug in passing in predefined sage variables [Reviewed by Jason Grout] #2578: Craig Citro: make bernoulli_polynomial independent of maxima [Reviewed by William Stein] #2789: Nick Alexander: multivariate polynomials over residue fields of number fields are broken [Reviewed by Martin Albrecht] #3124: Mike Hansen: bug in solve_mod [Reviewed by Alex Ghitza] #3185: Michael Abshoff: fix 64 bit OSX build support for f2c [Reviewed by Robert Miller] #3227: Michael Abshoff: add 64 bit OSX build support for tachyon [Reviewed by Robert Miller] #3229: Michael Abshoff: add 64 bit OSX build support to flintqs [Reviewed by Robert Miller] #3321: Martin Albrecht: Matrix.visualize_structure is too dark/messed up [Reviewed by Dan Drake] #3544: William Stein: PermutationGroup.is_transitive is broken [Reviewed by Robert Miller] #3571: Craig Citro: ivalue field in integer_mod.pyx shouldn't be public [Reviewed by Robert Bradshaw] #3830: Robert Miller: plot(sin(1/x), (x,-1,3), foo=10) yields an error message about line, but should yield one about plot. [Reviewed by Dan Drake] #4010: Mike Hansen: notebook -- Renaming worksheet: clicking OK with a blank text box should revert to worksheet's old name not name it to "null" [Reviewed by Jason Grout] #4152: Mike Hansen, Jason Grout: parametric_plot should take the variable range as (var, min, max) like plot [Reviewed by Jason Grout, Mike Hansen] #4523: Mike Hansen: browser cache not cleared when restarting the worksheet [Reviewed by Dan Drake] #4563: Jason Grout: polar plot does not accept (t, 0, 2*pi) syntax for the interval [Reviewed by Robert Bradshaw] #4590: Mike Hansen: sage/interfaces/phc.py writes tmp files into cwd [Reviewed by Jason Grout] #4616: Robert Miller: cosine_series_coefficient hangs [Reviewed by David Joyner] #4626: Robert Miller: error in bessel_J(0,0) [Reviewed by Paul Zimmermann] #4733: Jason Grout: matrix exponential for general matrices [Reviewed by Alex Ghitza] #4757: Mike Hansen, Jason Grout: eigenspaces_right over CDF gives total nonsense [Reviewed by Nick Alexander] #4762: Alex Ghitza: Odd error message for congruence subgroups [Reviewed by Nick Alexander] #4818: William Stein: bug in list_plot3d -- invalid index? [Reviewed by Robert Bradshaw] #4820: John Cremona: Type inconsistency in rational points on elliptic curves [Reviewed by Nick Alexander] #4832: John Palmieri: prevent search_src and search_doc from printing the sage banner [Reviewed by Nick Alexander] #4963: Jason Grout: Make a screen-full of whitespace at the bottom of the notebook cells [Reviewed by Tom Boothby] #4965: Martin Albrecht, Burcin Erocal: Z/nZ[x] via FLINT's zmod_poly [Reviewed by Robert Bradshaw] #4977: Nick Alexander: vector(RR vector) doesn't create a new vector [Reviewed by Alex Ghitza] #4988: John Cremona: major easy-to-fix but STUPID bug in gcd [Reviewed by Nick Alexander] #4992: Michael Abshoff: OSX 64 bit: add 64 bit build support for pynac [Reviewed by Robert Miller] #4993: Michael Abshoff: OSX 64 bit: add 64 bit build support for r [Reviewed by Robert Miller] #4994: Michael Abshoff: OSX 64 bit: add 64 bit build support for ghmm [Reviewed by Robert Miller] #4995: Michael Abshoff: OSX 64 bit: add 64 bit build support for boehm_gc [Reviewed by Robert Miller] #4996: Michael Abshoff: OSX64: add proper libcsage build support [Reviewed by Robert Miller] #4998: Michael Abshoff: OSX64: build Singular with "--with-malloc=system" [Reviewed by Robert Miller] #5028: Sebastien Labbe: point2d? says point.options instead of point2d.options [Reviewed by Mike Hansen] #5030: William Stein: get matrix/constructor.py up to 100% coverage [Reviewed by Mike Hansen] #5031: William Stein: get doctesting of matrix/misc.pyx up to 100%; also make A.lift() 20 times faster by moving it [Reviewed by Robert Bradshaw] #5033: William Stein: matrix lift function bad in two ways [Reviewed by Dan Drake] #5034: William Stein: stupid output of sage -br: "using n cpus" [Reviewed by Robert Miller] #5035: William Stein: get doctest coverage of matrix_generic_dense.pyx up to 100% [Reviewed by Dan Drake] #5041: William Stein: make it so the magma .sig files in extcode don't get written there by magma [Reviewed by Martin Albrecht] #5045: William Stein: sage's "make check" should check that the sage build flags (in sage-flags.txt) are right [Reviewed by Michael Abshoff] #5050: Mike Hansen: clean up how the percent directives at the top of cells are processed [Review by Robert Miller] #5057: Michael Abshoff: Add fortran-OSX64-20090120.spkg: to the experimental spkg repo [Reviewed by Robert Miller] #5058: Robert Miller: sage -f and sage -i is broken for local files with ".spkg" elsewhere in the path [Reviewed by Tom Boothby] #5059: Craig Citro: Fix a bunch of broken pickles [Reviewed by Robert Bradshaw] Merged in Sage 3.3.alpha0: #508: Arnaud Bergeron: problem with "sage -c" [Reviewed by Georg Weber] #2770: Arnaud Bergeron: plot_region function [Reviewed by David Joyner] #3749: David Joyner: Request for a method "is_cyclic" for groups in SAGE [Reviewed by John Cremona] #3767: Jason Grout: move jquery into its own spkg [Reviewed by Timothy Clemans, Michael Abshoff] #4184: Jason Grout: Upgrade jQueryUI [Reviewed by Timothy Clemans, Michael Abshoff] #4185: Michael Abshoff: Solaris 10: fix spkg-install for jmol to not use GNUisms [Reviewed by Mike Hansen] #4267: Jason Grout: remove javascript code from extcode repository [Reviewed by Michael Abshoff] #4674: Jason Grout, Michael Abshoff: update to latest upstream jsmath 3.6a [Reviewed by Michael Abshoff, Jason Grout] #4296: Alex Ghitza: univariate polynomial power ignores 2nd argument [Reviewed by John Cremona] #4363: Mike Hansen: Do not automatically evaluate interact cells in notebook [Reviewed by Marshall Hampton] #4495: Robert Miller: weight distribution for binary codes [Reviewed by David Joyner] #4612: Craig Citro, Robert Bradshaw: is_perfect_power for rationals [Reviewed by John Cremona] #4650: Craig Citro: make density() in matrix_modn_sparse much faster [Reviewed by Michael Abshoff] #4676: Marshall Hampton: Polyhedral improvements [Reviewed by Dan Drake, Arnaud Bergeron, David Joyner] #4704: Jason Grout: Use jquery to make the javascript code nicer [Reviewed by Tom Boothby] #4705: Jason Grout: Make in-line wysiwyg editor for text cells using TinyMCE [Reviewed by Marshall Hampton, Dan Drake, Karl-Dieter Crisman] #4718: Timothy Clemans: notebook -- move source code, upload, and help window html to template [Reviewed by Mike Hansen] #4723: Carl Witty: Infinite precision increase finding roots over QQbar [Reviewed by Nick Alexander] #4753: William Stein, Craig Citro: make sparse * sparse = dense mod p like 50 frickin' times faster [Reviewed by Craig Citro, William Stein] #4804: Mike Hansen: add latex output for ceiling, floor, and derivative functions [Reviewed by Wilfried Huss] #4831: John Cremona, Maite Aranes: More number field ideal utilities [Reviewed by David Loeffler] #4837: Alex Ghitza: implement random_element for number fields [Reviewed by John Cremona] #4851: Mike Hansen: infinite recursion with encoding entities for worksheet titles with apostrophes, etc [Reviewed by Dan Drake] #4874: Yann Laigle-Chapuy: performance issue for generic polynomial rings [Reviewed by John Cremona] #4878: Arnaud Bergeron: Add a density_plot() function [Reviewed by William Stein, David Joyner] #4884: Arnaud Bergeron: Make colormap handling better [Reviewed by David Joyner, William Stein] #4888: David Perkinson: laplacian_matrix() broken for DiGraphs [Reviewed by Robert Miller, Michael Abshoff] #4893: John Cremona: srange docstring is misleading [Reviewed by Alex Ghitza] #4897: John Cremona: integral_points() misses some points [Reviewed by Tobias Nagel] #4901: John Cremona: bug in elliptic logarithm [Reviewed by Alex Ghitza] #4945: John Palmieri: LaTeX for gp elements shouldn't use verbatim environment [Reviewed by Martin Albrecht] #4947: Mike Hansen: worksheets with interact cells auto-launch [Reviewed by Marshall Hampton] #4967: Matthias Meulien, William Stein: Trouble with .gaprc file when compiling from source [Reviewed by Michael Abshoff] #4969: Mike Hansen: upgrade mercurial to version 1.1.2 [Reviewed by Michael Abshoff] #4973: Craig Citro, Jason Grout: rewrite the function __getitem__ in matrix0.pyx to support slices better, negative indices, and be faster [Reviewed by Jason Grout, Craig Citro] #4974: Craig Citro, Jason Grout, Yann Laigle-Chapuy: eliminate normalize_slice in favor of a standard Python idiom [Reviewed by Jason Grout, Yann Laigle-Chapuy, Craig Citro] #4975: Mike Hansen: Sage 3.2.2 chokes on utf-8 encoded files [Reviewed by Michael Abshoff] #4991: Michael Abshoff: GDB is broken on OSX due to ipython's readline detection [Reviewed by William Stein] #4966: Michael Abshoff: Switch gmp to eMPIRe svn1555 [Reviewed by William Stein] #4999: Michael Abshoff: Solaris 10/Sparc: numerical noise doctest failure in sage/gsl/integration.pyx [Reviewed by Craig Citro] #5000: Michael Abshoff: Solaris 10/x86: fix numerical noise in schemes/elliptic_curves/ell_rational_field.py [Reviewed by Craig Citro] #5004: Mike Hansen: bug in latexing of powers of negative numbers [Reviewed by William Stein] #5007: Michael Abshoff: sage-native-execute uses bashism [Reviewed by Craig Citro] #5008: Michael Abshoff: Solaris/gcc 4.3.2: fix matplotlib build [Reviewed by Mike Hansen] #5010: Michael Abshoff: Solaris 10: rings/real_double.pyx doctests failure: nan vs. NaN [Reviewed by Craig Citro] #5011: Michael Abshoff: Solaris: fix get_memory_usage() to use top [Reviewed by Craig Citro] #5012: Michael Abshoff, Carl Witty: Solaris 10/x86: Numerical noise in sage/rings/qqbar.py [Reviewed by Craig Citro] #5013: Michael Abshoff: Solaris 10/x86: Fix numerical noise failure in sage/ext/fast_eval.py [Reviewed by Marshall Hampton] #5015: Mike Hansen: Horrible bug in old (and new) symbolic calculus: f(x)=1; f*e --> BOOM! [Reviewed by William Stein] #5016: Michael Abshoff: bump ecmgmp [Reviewed by Mike Hansen] #5017: Robert Miller: graph.automorphism_group(translation=True) gives error in 3.2.3 [Reviewed by Jaap Spies] #5020: Mike Hansen: auto-cells do not automaticall evaluate (or at least update) [Reviewed by Dan Drake] #5022: Michael Abshoff: Solaris 10: update libgcrypt to 1.4.3 [Reviewed by Mike Hansen] #5024: Michael Abshoff: Solaris 10: Do not create dynamic liblpack on non-Linux [Reviewed by Mike Hansen]