Sage 5.2 released  Jeroen Demeyer  7/30/12 11:29 PM  Sage 5.2 was released on 25 July 2012. It is available in
source and binary form from: * http://www.sagemath.org/download.html Sage (http://www.sagemath.org/) is developed by volunteers and combines over 90 open source packages. For instructions about installing Sage, see * http://www.sagemath.org/doc/installation The following page lists the platforms on which Sage should work: * http://wiki.sagemath.org/SupportedPlatforms If you have any questions and/or problems, please report them to any of these Google groups: * sagesupport: http://groups.google.com/group/sagesupport * sagedevel: http://groups.google.com/group/sagedevel You can also drop by in #sagemath on freenode or post your questions at http://ask.sagemath.org/ The following 54 people contributed to this release. Of those, 5 made their first contribution to Sage:  Alexander Dreyer  Andrey Novoseltsev  André Apitzsch  Anne Schilling  Armin Straub  Benjamin Jones  Birk Eisermann [first contribution]  Burcin Erocal  Charles Bouillaguet  Chris Berg  Dan Drake  Daniel Krenn  David Coudert  David Roe  Dima Pasechnik  Dmitrii Pasechnik  Douglas McNeil  Franco Saliola  François Bissey  Frédéric Chapoton  Hugh Thomas  Ivan Andrus  Jason Grout  Javier López Peña  Jeroen Demeyer  Johan Bosman  John Palmieri  Jonathan Gutow  KarlDieter Crisman  Keshav Kini  Leif Leonhardy  Luis Felipe Tabera Alonso  Marshall Hampton  Martin Albrecht  Martin Raum  Mike Hansen  Nathann Cohen  Nicolas M. Thiéry  Niels Ranosch  Paul Ivanov [first contribution]  Paulo César Pereira de Andrade  Punarbasu Purkayastha  R. Andrew Ohana  Rado Kirov [first contribution]  Rob Beezer  Robert Bradshaw  Samuel Gonshaw [first contribution]  Simon King  Stephen MontgomerySmith  Timothy Walsh [first contribution]  Titus Nicolae  Volker Braun  Wai Yan Pong  William Stein * Release manager: Jeroen Demeyer. * We closed 87 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage5.2/tickets.html Closed tickets: #1861: Ivan Andrus: better document sage.el [Reviewed by KarlDieter Crisman] #5873: Fix matplotlib build on FreeBSD [Reviewed by Stephen MontgomerySmith, Paul Ivanov] #6582: Potential issue in polybori  0.5rc.p8 and/or 0.5rc.p9 [Reviewed by Alexander Dreyer] #6880: docstrings and @cached_method  if you used cached_method then docstring displays wrong file, etc. [Reviewed by Simon King] #7003: Update jmol [Reviewed by Jason Grout] #7831: numpy1.5.0 fixes for FreeBSD [Reviewed by Stephen MontgomerySmith] #9547: x * Infinity assumes that x is positive [Reviewed by Burcin Erocal, Volker Braun] #10340: Strange error in groebner_basis() [Reviewed by Alexander Dreyer] #11423: Make atan2(0,0) consistent [Reviewed by Volker Braun, Titus Nicolae, Burcin Erocal] #12059: Make R work on FreeBSD [Reviewed by Stephen MontgomerySmith] #12303: leave beta symbolic for exact complex inputs [Reviewed by Burcin Erocal] #12654: polybori crash (Linux) [Reviewed by Alexander Dreyer] #12984: Possible future issues with ECL build with unicode enabled [Reviewed by KarlDieter Crisman, Paulo César Pereira de Andrade] #13126: John Palmieri, Jeroen Demeyer: Update and clean up openssl [Reviewed by Jeroen Demeyer, John Palmieri, KarlDieter Crisman, Benjamin Jones] #13144: Fix Sympow on FreeBSD [Reviewed by Stephen MontgomerySmith] #3766: move sage_fortran from fortran spkg to sage_scripts spkg [Reviewed by KarlDieter Crisman] #12818: Building polybori under FreeBSD [Reviewed by Stephen MontgomerySmith, Alexander Dreyer, KarlDieter Crisman] #13040: Polybori spkg: allow CC to contain multiple words [Reviewed by R. Andrew Ohana] #876: Implement or wrap Braid Groups [Reviewed by KarlDieter Crisman] #8393: bring plot3d.py to 100% coverage [Reviewed by KarlDieter Crisman] #10144: Update plot.py to 100% coverage [Reviewed by KarlDieter Crisman] #10694: bug with plot [Reviewed by KarlDieter Crisman] #11953: Marshall Hampton, John Palmieri: Upgrade optional package biopython to version 1.60 [Reviewed by Marshall Hampton, John Palmieri] #13205: make LP return bounds on variables [Reviewed by Dmitrii Pasechnik] #13207: Please consider updating to gfan 0.5 [Reviewed by Marshall Hampton] #13270: Jason Grout, Keshav Kini: Restarted notebook server allows user registration [Reviewed by Punarbasu Purkayastha] Merged in sage5.2.beta0: #10764: François Bissey, André Apitzsch: Cleanup a few Cython warnings [Reviewed by François Bissey, André Apitzsch] #11078: William Stein, Jonathan Gutow: jmol in the flask notebook [Reviewed by Jason Grout] #11080: Mike Hansen, Rado Kirov, William Stein, Jason Grout, Jeroen Demeyer: move notebook to flask/wsgibased notebook [Reviewed by Rado Kirov, Dan Drake, Jason Grout, Simon King, Dmitrii Pasechnik, John Palmieri, Punarbasu Purkayastha] #11503: Jonathan Gutow: Make new spkg to install Jmol in SAGE_LOCAL/share [Reviewed by Dan Drake, Jason Grout, Punarbasu Purkayastha] #11528: Wai Yan Pong: Allow deleting row or column from matrix [Reviewed by Rob Beezer] #11851: Niels Ranosch, Burcin Erocal: make pybtex an optional spkg [Reviewed by John Palmieri] #11874: Rado Kirov, Jason Grout: Remove twisted spkg [Reviewed by Dmitrii Pasechnik, Jason Grout] #12229: Jason Grout, KarlDieter Crisman: Add section in the developers manual about sagenb development [Reviewed by William Stein, Jeroen Demeyer, Punarbasu Purkayastha, KarlDieter Crisman, Keshav Kini] #12327: Ivan Andrus: Improve loading page of Mac App [Reviewed by KarlDieter Crisman] #12917: Nathann Cohen: is_cartesian_product [Reviewed by David Coudert] #12974: Punarbasu Purkayastha: make Graphics class inheritable and some clean ups [Reviewed by KarlDieter Crisman, Jeroen Demeyer] #12989: Nathann Cohen: Ellingham–Horton graphs [Reviewed by Keshav Kini] #13014: Douglas McNeil: lcm for SR rationals [Reviewed by Dan Drake, William Stein] #13038: Nathann Cohen: ClebschGraph, CoxeterGraph, HoffmanGraph [Reviewed by Keshav Kini] #13052: Rob Beezer: Positive definite check for matrices over RDF/CDF [Reviewed by Dan Drake, Andrey Novoseltsev] #13090: Punarbasu Purkayastha: Make LinearCode take minimum distance as a parameter [Reviewed by Dmitrii Pasechnik] #13103: Charles Bouillaguet: Makes BooleanPolynomial more compatible with MPolynomial [Reviewed by Martin Albrecht] #13113: Keshav Kini: sage pkg can't handle its own options [Reviewed by John Palmieri] #13139: André Apitzsch: Bug in IntegerFactorization [Reviewed by R. Andrew Ohana] #13148: Dima Pasechnik: make LP return the number of variables [Reviewed by Nathann Cohen] #13167: Jeroen Demeyer: Clarify some comments concerning the matplotlib Delaunay code in list_plot3d.py [Reviewed by KarlDieter Crisman] #13168: Anne Schilling: Fixing typos in latex options documentation [Reviewed by Nicolas M. Thiéry] #13172: David Roe: Bug in mod(a, p^k).nth_root() for p>62, k>1 [Reviewed by Robert Bradshaw] Merged in sage5.2.beta1: #4529: Punarbasu Purkayastha, KarlDieter Crisman: Implement plots with logarithmic scale [Reviewed by KarlDieter Crisman, Punarbasu Purkayastha] #5043: Ivan Andrus: gap_console help broken [Reviewed by KarlDieter Crisman] #10795: Rob Beezer: Fix and upgrade double dense matrix QR decomposition [Reviewed by Martin Raum, Dan Drake] #12433: R. Andrew Ohana, Leif Leonhardy: Make zn_poly respect the CC environment variable, work around GCC 4.7.0 bug on ia64 (and clean up the spkg) [Reviewed by Leif Leonhardy, Jeroen Demeyer] #12544: Andrey Novoseltsev: Switch cones to `PointCollection` [Reviewed by Volker Braun] #12706: Frédéric Chapoton: monomials of 0 [Reviewed by Keshav Kini] #12751: Jeroen Demeyer: Allow building Sage with GCC4.7.x [Reviewed by Volker Braun] #12806: Daniel Krenn, Javier López Peña: upgrade of spkg networkx1.2.p2 to 1.6 [Reviewed by Keshav Kini, KarlDieter Crisman] #12965: Andrey Novoseltsev: X.Kaehler_cone().lattice() is not a lattice [Reviewed by Volker Braun] #13029: Robert Bradshaw: Upgrade Cython to 0.17 [Reviewed by R. Andrew Ohana] #13058: Nathann Cohen, Dima Pasechnik: HallJanko Graph [Reviewed by Keshav Kini, Dima Pasechnik] #13124: Alexander Dreyer: Updating PolyBoRi to release 0.8.2 [Reviewed by Martin Albrecht] #13140: John Palmieri, Rob Beezer: OS X Lion doctest failures for double dense QR decomposition [Reviewed by Rob Beezer, John Palmieri] #13155: Charles Bouillaguet: Boolean Multivariate Ideals should not have negative dimension.... [Reviewed by Martin Albrecht] #13166: Armin Straub: Compute qbinomial coefficients more efficiently [Reviewed by Javier López Peña] #13169: Nicolas M. Thiéry: Little doctest improvements in permutation groups [Reviewed by Frédéric Chapoton] #13170: Simon King: Speedup the default nonzero test for matrices [Reviewed by Javier López Peña] #13175: Jeroen Demeyer: Upgrade Mercurial [Reviewed by Volker Braun] #13187: André Apitzsch: Minpoly and charpoly don't check their arguments correctly [Reviewed by Robert Bradshaw] #13191: Volker Braun: Construct a 2d fan from rays only [Reviewed by Andrey Novoseltsev] #13196: Charles Bouillaguet, Javier López Peña: GL(n, GF(q)).random_element() is way too slow for what it does [Reviewed by Dima Pasechnik, Charles Bouillaguet] #13206: André Apitzsch: Remove from __future__ import with_statement [Reviewed by Volker Braun] #13208: Franco Saliola: Move the basis method from CombinatorialFreeModule to ModulesWithBasis.ParentMethods [Reviewed by Chris Berg] #13216: Frédéric Chapoton: one test in lattice polytope should be tagged # random [Reviewed by Volker Braun] #13217: Armin Straub: Expand the Dedekind eta function more efficiently [Reviewed by Frédéric Chapoton] #13219: John Palmieri: Document 'make' targets [Reviewed by Keshav Kini] #13222: Franco Saliola: Fix is_graded for Posets to use appropriate definition [Reviewed by Anne Schilling] Merged in sage5.2.rc0: #10607: Marshall Hampton, John Palmieri: Update phcpack to latest verson [Reviewed by Marshall Hampton, John Palmieri] #11563: Nicolas M. Thiéry: Make lrcalc a standard package [Reviewed by Anne Schilling, Jeroen Demeyer, John Palmieri] #11996: Johan Bosman: Bug in LaTeX representation of subgroups of permutation groups [Reviewed by Samuel Gonshaw] #12343: Luis Felipe Tabera Alonso: Cleanup unexisting methods after #10263 [Reviewed by André Apitzsch] #12925: Nicolas M. Thiéry, Hugh Thomas: Thematic tutorial on combinatorics [Reviewed by Hugh Thomas, Nicolas M. Thiéry, Timothy Walsh] #13073: Birk Eisermann: recognition of weakly chordal graphs [Reviewed by Nathann Cohen,Birk Eisermann] #13088: Frédéric Chapoton: implement the Paley graphs [Reviewed by Nathann Cohen] #13109: Volker Braun: Rewrite deprecation to use trac ticket numbers [Reviewed by John Palmieri, KarlDieter Crisman] #13146: David Roe: Removing tabs in .rst, .tex and .pxi files [Reviewed by Keshav Kini, André Apitzsch, Jeroen Demeyer] #13193: Benjamin Jones: erf evaluation is wrong along imaginary axis [Reviewed by KarlDieter Crisman] #13220: John Palmieri: bug in morphisms of chain complexes [Reviewed by Marshall Hampton] 
Re: Sage 5.2 released  kcrisman  7/31/12 6:31 AM  I'm pretty sure this isn't his first contribution :) Not just the (sadly now moribund) graph editor, even? I guess sagenb things don't count in the same way any more... 
Re: [sagerelease] Re: Sage 5.2 released  Jeroen Demeyer  7/31/12 6:44 AM  Okay, there were contributions of "Radoslav Kirov" in sage4.7.2, but
nothing since then. 
Sage release goals  Jeroen Demeyer  7/31/12 1:05 PM  I copy a question by Roland van den Brink:
On 20120731 13:41, Roland van den Brink wrote: > Dear Jeroen, > > Thank you so much for all the good work! > > Will version 5.3 be the version which meets the benchmark originally set > for 5.0? > (amongst other 90% coverage) > > Maybe an idea to mention this as release remark to 'close the subject', > and to create the opportunity for a recognizable new set of goals. > > Roland Personally, I don't know whether it really makes sense to put such goals, especially when we don't guarantee they will be met. On the other, we are "virtually" at 90% coverage if we would delete the old notebook: http://trac.sagemath.org/sage_trac/ticket/11409 
Re: Sage release goals  kcrisman  7/31/12 1:27 PM  Heh, not to mention Cygwin support ;) although jpflori has made remarkable progress on that as of late. 
Re: Sage 5.2 released  Volker Braun  7/31/12 3:12 PM  I get not 100% reproducible test failures with sage/interfaces/expect.py, see for example http://patchbot.sagemath.org/log/0/Fedora/17/x86_64/3.4.45.fc17.x86_64/volkerdesktop.stp.dias.ie/20120731%2002:38:03%20+0100?short sage t force_lib devel/sage0/sage/interfaces/expect.py ********************************************************************** File "/mnt/storage2TB/patchbot/Sage/sage5.2/devel/sage0/sage/interfaces/expect.py", line 826: sage: singular.interrupt(timeout=3) # sometimes very slow (up to 60s on sage.math, 2012) Expected: False Got: True This is probably going to be fixed by your work on making singular more interruptable, but I just wanted to mention things. 
Re: [sagerelease] Sage 5.2 released  Justin C. Walker  7/31/12 4:09 PM  For the record, this release built from source on Mac OS X, both 10.6.8 and 10.7.4, without problems, and passed all tests ('ptestlong')! Justin  Justin C. Walker, CurmudgeonAtLarge Director Institute for the Enhancement of the Director's Income  "Weaseling out of things is what separates us from the animals. Well, except the weasel."  Homer J Simpson  
Re: Sage 5.2 released  Simon King  8/13/12 6:34 AM  Hi Jeroen, Am Dienstag, 31. Juli 2012 08:29:32 UTC+2 schrieb Jeroen Demeyer: Sage 5.2 was released on 25 July 2012. I get an error when building it from sources with four parallel threads. Setting: $ uname a Linux mpc622 2.6.34.linuxpool #0 SMP PREEMPT Wed May 19 16:32:19 CEST 2010 x86_64 GNU/Linux $ cat /etc/issue Debian GNU/Linux 6.0 \n \l The machine has three Intel(R) Core(TM) i3 CPU 530 @ 2.93GHz I posted the install.log at http://sage.math.washington.edu/home/SimonKing/logs/install5.2.log What went wrong? Best regards, Simon 
Re: [sagerelease] Re: Sage 5.2 released  leif  8/13/12 9:22 AM  Error installing pyOpenSSL0.12.tar.gz.
real 0m23.205s user 0m19.121s sys 0m2.948s ************************************************************************ Error installing package sagenb0.9.1 ************************************************************************ Please email sagedevel (http://groups.google.com/group/sagedevel) explaining the problem and including the relevant part of the log file /mnt/local/king/SAGE/stable/sage5.2/spkg/logs/sagenb0.9.1.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /mnt/local/king/SAGE/stable/sage5.2/spkg/build/sagenb0.9.1 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/mnt/local/king/SAGE/stable/sage5.2/spkg/build/sagenb0.9.1' && '/mnt/local/king/SAGE/stable/sage5.2/sage' sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************ make[1]: *** [installed/sagenb0.9.1] Fehler 1 make[1]: *** Warte auf noch nicht beendete Prozesse... $ ï¿½berbenutzermache einpaketwerkzeughole install bibliothekoffenessicherebuchsenebeneentwickler In case you don't have ï¿½berbenutzer privileges, try $ ./sage i openssl && make leif  () The ASCII Ribbon Campaign /\ Help Cure HTML EMail 
Re: [sagerelease] Re: Sage 5.2 released  Benjamin Jones  8/13/12 10:17 AM  On Mon, Aug 13, 2012 at 11:22 AM, leif <not.r...@online.de> wrote:> $ überbenutzermache einpaketwerkzeughole install > bibliothekoffenessicherebuchsenebeneentwickler > > In case you don't have überbenutzer privileges, try >Wow, the German localization of your distribution is awesome, leif :)  Benjamin Jones 
Re: [sagerelease] Re: Sage 5.2 released  Alexander Dreyer  8/13/12 12:16 PM  > $ ï¿½berbenutzermache einpaketwerkzeughole installYMMD! My best, Alexander  Dr. rer. nat. Dipl.Math. Alexander Dreyer Abteilung "Systemanalyse, Prognose und Regelung" Fraunhofer Institut fï¿½r Techno und Wirtschaftsmathematik (ITWM) FraunhoferPlatz 1 67663 Kaiserslautern Telefon +49 (0) 631316004318 Fax +49 (0) 631316005318 EMail alexande...@itwm.fraunhofer.de Internet http://www.itwm.fraunhofer.de/sys/dreyer.html 
Re: Sage 5.2 released  Simon King  8/14/12 2:01 AM  Hi Leif,
$ überbenutzermache einpaketwerkzeughole install > bibliothekoffenessicherebuchsenebeneentwickler > > In case you don't have überbenutzer privileges, try >As I wrote in my previous post, this is what I tried. Slight problem was: Since Python has not been available, ./sage i openssl could not download the openssl spkg. But I downloaded it manually, installed it, and did make. And 5 minutes ago, I found that it indeed worked. The question arises whether openssl should be a standard spkg that is installed if the openssl headers can not be found on the system. That would be similar to the gcc spkg, which is standard but is only installed if the gcc found on the machine is the wrong version (or the user asks for its installation). Cheers, Simon 
Re: [sagerelease] Re: Sage 5.2 released  Jeroen Demeyer  8/14/12 3:16 AM  On 20120814 11:01, Simon King wrote:The problem is licensing. OpenSSL is not GPLcompatibile. If we ship OpenSSL with Sage, we *certainly* violate the GPL. IMHO, we might still be violating the GPL with the optional package, but that's not so clear. 
Re: Sage 5.2 released  Volker Braun  8/15/12 6:49 AM  Really we should get sage i to work without ssl as long as you don't download from a https url. In fact, nothing in Sage should depend on ssl except for the notebook. For the record, the next Sage version checks for ssl headers/libraries in prereq and will recommend that you install it via your package manager before the compilation starts. 

Re: Sage 5.2 released  Volker Braun  8/15/12 6:52 AM  Nice, now my post has a "do you want to translate to english" button. If you press it, the following appears:
Translated by Google  German ≫ English Over $ userget install make einpaketwerkzeug library open secure socket flush with developers 
Re: [sagerelease] Re: Sage 5.2 released  leif  8/15/12 8:01 AM  Flush with developers?
Salbei! 
Re: [sagerelease] Re: Sage 5.2 released  Jeroen Demeyer  8/15/12 11:25 AM  On 20120815 15:49, Volker Braun wrote:Yes, we should: http://trac.sagemath.org/sage_trac/ticket/13373 