Sage 5.2 released

[Jeroen Demeyer]

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:

* sage-support: http://groups.google.com/group/sage-support
* sage-devel: http://groups.google.com/group/sage-devel

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
- Karl-Dieter 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 Montgomery-Smith
- 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/sage-5.2/tickets.html

Closed tickets:

#1861: Ivan Andrus: better document sage.el [Reviewed by Karl-Dieter
Crisman]
#5873: Fix matplotlib build on FreeBSD [Reviewed by Stephen
Montgomery-Smith, 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: numpy-1.5.0 fixes for FreeBSD [Reviewed by Stephen Montgomery-Smith]
#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 Montgomery-Smith]
#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 Karl-Dieter Crisman, Paulo César Pereira de Andrade]
#13126: John Palmieri, Jeroen Demeyer: Update and clean up openssl
[Reviewed by Jeroen Demeyer, John Palmieri, Karl-Dieter Crisman,
Benjamin Jones]
#13144: Fix Sympow on FreeBSD [Reviewed by Stephen Montgomery-Smith]
#3766: move sage_fortran from fortran spkg to sage_scripts spkg
[Reviewed by Karl-Dieter Crisman]
#12818: Building polybori under FreeBSD [Reviewed by Stephen
Montgomery-Smith, Alexander Dreyer, Karl-Dieter Crisman]
#13040: Polybori spkg: allow CC to contain multiple words [Reviewed by
R. Andrew Ohana]
#876: Implement or wrap Braid Groups [Reviewed by Karl-Dieter Crisman]
#8393: bring plot3d.py to 100% coverage [Reviewed by Karl-Dieter Crisman]
#10144: Update plot.py to 100% coverage [Reviewed by Karl-Dieter Crisman]
#10694: bug with plot [Reviewed by Karl-Dieter 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 sage-5.2.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/wsgi-based 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, Karl-Dieter Crisman: Add section in the developers
manual about sagenb development [Reviewed by William Stein, Jeroen
Demeyer, Punarbasu Purkayastha, Karl-Dieter Crisman, Keshav Kini]
#12327: Ivan Andrus: Improve loading page of Mac App [Reviewed by
Karl-Dieter Crisman]
#12917: Nathann Cohen: is_cartesian_product [Reviewed by David Coudert]
#12974: Punarbasu Purkayastha: make Graphics class inheritable and some
clean ups [Reviewed by Karl-Dieter 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 Karl-Dieter 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 sage-5.2.beta1:

#4529: Punarbasu Purkayastha, Karl-Dieter Crisman: Implement plots with
logarithmic scale [Reviewed by Karl-Dieter Crisman, Punarbasu Purkayastha]
#5043: Ivan Andrus: gap_console help broken [Reviewed by Karl-Dieter
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 GCC-4.7.x [Reviewed by
Volker Braun]
#12806: Daniel Krenn, Javier López Peña: upgrade of spkg networkx-1.2.p2
to 1.6 [Reviewed by Keshav Kini, Karl-Dieter 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: Hall-Janko 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 q-binomial 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 2-d 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 sage-5.2.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, Karl-Dieter 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 Karl-Dieter Crisman]
#13220: John Palmieri: bug in morphisms of chain complexes [Reviewed by
Marshall Hampton]

[kcrisman]

>   - Rado Kirov [first contribution]

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...

[Jeroen Demeyer]

Okay, there were contributions of "Radoslav Kirov" in sage-4.7.2, but
nothing since then.

[Jeroen Demeyer]

I copy a question by Roland van den Brink:

On 2012-07-31 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

[kcrisman]

> > 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)
>

Heh, not to mention Cygwin support ;-) although jpflori has made
remarkable progress on that as of late.

[Volker Braun]

I get not 100% reproducible test failures with sage/interfaces/expect.py, see for example http://patchbot.sagemath.org/log/0/Fedora/17/x86_64/3.4.4-5.fc17.x86_64/volker-desktop.stp.dias.ie/2012-07-31%2002:38:03%20+0100?short

sage -t  -force_lib devel/sage-0/sage/interfaces/expect.py

**********************************************************************

File "/mnt/storage2TB/patchbot/Sage/sage-5.2/devel/sage-0/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.

[Justin C. Walker]

On Jul 30, 2012, at 23:29 , Jeroen Demeyer wrote:

> 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

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, Curmudgeon-At-Large
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
--------

[Simon King]

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/install-5.2.log

What went wrong?

Best regards,
Simon

[leif]

Error installing pyOpenSSL-0.12.tar.gz.

real 0m23.205s
user 0m19.121s
sys 0m2.948s
************************************************************************
Error installing package sagenb-0.9.1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/mnt/local/king/SAGE/stable/sage-5.2/spkg/logs/sagenb-0.9.1.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/sage-5.2/spkg/build/sagenb-0.9.1 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/sage-5.2/spkg/build/sagenb-0.9.1' &&
'/mnt/local/king/SAGE/stable/sage-5.2/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/sagenb-0.9.1] Fehler 1
make[1]: *** Warte auf noch nicht beendete Prozesse...


$ �berbenutzermache einpaketwerkzeug-hole install
bibliothekoffenessicherebuchsenebene-entwickler

In case you don't have �berbenutzer privileges, try

$ ./sage -i openssl && make


-leif


--
() The ASCII Ribbon Campaign
/\ Help Cure HTML E-Mail

[Benjamin Jones]

On Mon, Aug 13, 2012 at 11:22 AM, leif <not.r...@online.de> wrote:
>
>
>
> Error installing pyOpenSSL-0.12.tar.gz.
>
> real 0m23.205s
> user 0m19.121s
> sys 0m2.948s
> ************************************************************************
> Error installing package sagenb-0.9.1
> ************************************************************************
> Please email sage-devel (http://groups.google.com/group/sage-devel)
> explaining the problem and including the relevant part of the log file
> /mnt/local/king/SAGE/stable/sage-5.2/spkg/logs/sagenb-0.9.1.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/sage-5.2/spkg/build/sagenb-0.9.1 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/sage-5.2/spkg/build/sagenb-0.9.1' &&
> '/mnt/local/king/SAGE/stable/sage-5.2/sage' -sh)
> When you are done debugging, you can type "exit" to leave the subshell.
> ************************************************************************
> make[1]: *** [installed/sagenb-0.9.1] Fehler 1
> make[1]: *** Warte auf noch nicht beendete Prozesse...
>
>

> $ überbenutzermache einpaketwerkzeug-hole install
> bibliothekoffenessicherebuchsenebene-entwickler
>
> In case you don't have überbenutzer privileges, try

>
> $ ./sage -i openssl && make
>
>
> -leif
>

Wow, the German localization of your distribution is awesome, leif :)

--
Benjamin Jones

[Alexander Dreyer]

> $ �berbenutzermache einpaketwerkzeug-hole install
> bibliothekoffenessicherebuchsenebene-entwickler
>
> In case you don't have �berbenutzer privileges, try
>
> $ ./sage -i openssl && make

YMMD!

My best,
Alexander


--
Dr. rer. nat. Dipl.-Math. Alexander Dreyer

Abteilung "Systemanalyse, Prognose und Regelung"
Fraunhofer Institut f�r Techno- und Wirtschaftsmathematik (ITWM)
Fraunhofer-Platz 1
67663 Kaiserslautern

Telefon +49 (0) 631-31600-4318
Fax +49 (0) 631-31600-5318
E-Mail alexande...@itwm.fraunhofer.de
Internet http://www.itwm.fraunhofer.de/sys/dreyer.html

[Simon King]

Hi Leif,

$ überbenutzermache einpaketwerkzeug-hole install
> bibliothekoffenessicherebuchsenebene-entwickler
>
> In case you don't have überbenutzer privileges, try

>
> $ ./sage -i openssl && make

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

[Jeroen Demeyer]

On 2012-08-14 11:01, Simon King wrote:
> 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).

The problem is licensing. OpenSSL is not GPL-compatibile.

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.

[Volker Braun]

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.

--

[Volker Braun]

Nice, now my post has a "do you want to translate to english" button. If you press it, the following appears:

On Wednesday, August 15, 2012 9:49:24 AM UTC-4, Volker Braun wrote:

 $ überbenutzermache einpaketwerkzeug-hole install  bibliothekoffenessicherebuchsenebene-entwickler

Translated by Google - German ≫ English

Over $ user-get install make einpaketwerkzeug library open secure socket flush with developers

[leif]

Flush with developers?

Salbei!

[Jeroen Demeyer]

On 2012-08-15 15:49, Volker Braun wrote:
> Really we should get sage -i to work without ssl as long as you don't
> download from a https url.

Yes, we should:
http://trac.sagemath.org/sage_trac/ticket/13373