Sage 6.2.beta6 released

[Volker Braun]

Get it from the "develop" git branch or the source tarball at http://boxen.math.washington.edu/home/release/sage-6.2.beta6/sage-6.2.beta6.tar.gz

Mini-changelog:

12bbca0 Updated Sage version to 6.2.beta6

a473d6f Trac #14800: Implement Pynac->Python callback for function::subs()

cdfaa4a Trac #15723: move CryptoMiniSat SPKG to build/pkgs

1039e08 Trac #11840: sage.symbolic.expression.Expression.collect_common_factors has no documentation

5864971 Trac #15138: BuiltinFunction._is_registered is giving false negatives

696140c Trac #14816: Implement absolute order for coxeter groups

d40939f Trac #15870: (LaTeX)-typesetting of multi-character variables wrong

a113723 Trac #15998: Restore some documentation and doctests and a function removed with #15466

76998bf Trac #15928: Typesetting errors in docstring of FiniteStateMachine._latex_transition_label_

f4ce665 Trac #13917: IndependentSets class

b5cca4c Trac #15288: Balanced Incomplete Block Designs with k=4

1d28062 Trac #16024: incorrect deleting of states in finite state machine

b2d98f2 Trac #16021: remove deprecated code in rings/

fe97289 Trac #16019: Connected components for immutable digraphs does not work

7ea77e7 Trac #15992: Python 3 preparation: Change backticks into repr()

cb8562e Trac #15991: Python 3 preparation: Rename sys.maxint to sys.maxsize

317e5ff Trac #12892: Toric fibration morphisms

416f22b Trac #10745: bug in elliptic curve gens()

b78a148 Trac #16016: FiniteStateMachine.__and__ calls intersection and FiniteStateMachine.__or__ calls union.

0fb48b1 Trac #15969: New class method: Kazhdan-Lusztig R_tilde polynomial

e231e52 Trac #14050: Cleaning up docs in Finite Coxeter Groups

10facf2 Trac #16028: bad formatting in the doc of the genus method for graphs

16f8906 Trac #15997: a typo in stirling1 numbers

d4d9b99 Trac #16032: Bug in IncidenceStructure.dual_design

b019163 Trac #10735: Simon 2-descent only returns an upper bound on the 2-Selmer rank

527c91b Trac #15988: Python 3 preparation: Add missing parentheses in list comprension

9d3d9a4 Trac #15982: Python 3 preparation: Change the syntax of the except clause

367ab0c Trac #15949: Involutions on NSym and QSym part II

f0c8b3f Trac #15705: functions PowerSeries.ogf() and egf() named wrong

f4ae33f Trac #15287: Orthogonal Arrays

f663334 Trac #9322: long time in simon_two_descent for elliptic curves

27de53f Trac #16009: Compute rank of elliptic curve defined over relative number field

16069ee Trac #11907: Modify tutorials: no more 'examples' directory

c738289 Trac #16011: Fix _torsion_bound() for elliptic curves over relative number fields

c31b2bb Trac #15351: import_statements sometimes fails

e41c9db Trac #16027: Implement q-dimension for classical and KR crystals

3b73d16 Trac #14780: allow embedding python tuples in SR

1b6930b Trac #16022: simon_two_descent sometimes gives wrong answers

72e748f Trac #16015: dateutils requires setuptools

e439592 Trac #16002: matplotlib-1.3.1 does not install

47619bc Trac #15972: IPython ProfileDirError if IPython was never run

e046d7a Trac #15942: fix md5 in sage-spkg

9db8c5c Updated Sage version to 6.2.beta5

[François Bissey]

I cannot see the pynac upgrade ticket in there, yet pynac has been updated
to 0.3.2, is it in that list under a non-obvious name?

Francois

[Maarten Derickx]

I really like the new git based workflow. It makes it much faster to update my dev version of sage, however this update failed.  Using OS X 10.9.2 I get:

lll:sage maarten$ sage -b

scons: `install' is up to date.

Updating Cython code....

Finished compiling Cython code (time = 5.498483181 seconds)

running install

running build

running build_py

running build_ext

building 'sage.symbolic.function' extension

building 'sage.symbolic.ring' extension

building 'sage.symbolic.constants_c' extension

building 'sage.symbolic.expression' extension

building 'sage.symbolic.getitem' extension

building 'sage.symbolic.pynac' extension

building 'sage.symbolic.substitution_map' extension

building 'sage.tests.cython' extension

Executing 8 commands (using 1 thread)

gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/sage/local/include -I/Applications/sage/local/include/csage -I/Applications/sage/src -I/Applications/sage/src/sage/ext -I/Applications/sage/local/include -I/Applications/sage/local/include/csage -I/Applications/sage/src -I/Applications/sage/src/sage/ext -I/Applications/sage/local/include/python2.7 -c sage/symbolic/function.cpp -o build/temp.macosx-10.9-x86_64-2.7/sage/symbolic/function.o -fno-strict-aliasing -w

In file included from sage/symbolic/function.cpp:350:0:

sage/symbolic/ginac_wrap.h:12:36: fatal error: pynac/extern_templates.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/sage/local/include -I/Applications/sage/local/include/csage -I/Applications/sage/src -I/Applications/sage/src/sage/ext -I/Applications/sage/local/include -I/Applications/sage/local/include/csage -I/Applications/sage/src -I/Applications/sage/src/sage/ext -I/Applications/sage/local/include/python2.7 -c sage/symbolic/ring.cpp -o build/temp.macosx-10.9-x86_64-2.7/sage/symbolic/ring.o -fno-strict-aliasing -w

In file included from sage/symbolic/ring.cpp:349:0:

sage/symbolic/ginac_wrap.h:12:36: fatal error: pynac/extern_templates.h: No such file or directory

compilation terminated.

[John Cremona]

On 2 April 2014 10:00, Maarten Derickx <m.derick...@gmail.com> wrote:
> I really like the new git based workflow. It makes it much faster to update
> my dev version of sage, however this update failed. Using OS X 10.9.2 I
> get:
>

DId you do "make" before "sage -b"? You should.

John

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[Francois Bissey]

You should have used “make” pynac has to be updated (the source of your problem)
and sage -b won’t do that.

Francois

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[Volker Braun]

On Wednesday, April 2, 2014 2:25:58 AM UTC+1, François wrote:

I cannot see the pynac upgrade ticket in there, yet pynac has been updated
to 0.3.2, is it in that list under a non-obvious name? 

 

 $ git log -1 build/pkgs/pynac

commit c1cf3fc54366d600d84d6a9648eced5034ea10bc

Author: Volker Braun <vbrau...@gmail.com>

Date:   Thu Mar 20 10:03:28 2014 -0400

    updated to pynac 0.3.2

$ git trac find c1cf3fc54366d600d84d6a9648eced5034ea10bc

Commit has been merged by the release manager into your current branch.

commit 3b73d1644f1b0cd0ad441c20b999d3e0b9c425d2

Merge: 1b6930b aa7287f

Author: Release Manager <rel...@sagemath.org>

Date:   Mon Mar 31 13:26:44 2014 +0100

    Trac #14780: allow embedding python tuples in SR

    

    Attached patch allows embedding Python tuples in symbolic expressions:

    {{{

    sage: t = SR._force_tuple((1, 2, x, x+1, x+2))

    sage: t

    (1, 2, x, x + 1, x + 2)

    sage: t.subs(x = 2*x^2)

    (1, 2, 2*x^2, 2*x^2 + 1, 2*x^2 + 2)

    sage: t.op[0]

    1

    sage: t.op[2]

    x

    }}}

    

    Includes pynac 0.3.2 update for explicit template instantiatitons

    

    http://boxen.math.washington.edu/home/vbraun/upstream/pynac-0.3.2.tar.bz

    2

    

    URL: http://trac.sagemath.org/14780

    Reported by: burcin

    Ticket author(s): Burcin Erocal, Volker Braun

    Reviewer(s): Volker Braun, Jean-Pierre Flori

[Maarten Derickx]

Thanks John and Francois, that indeed solved the problem.

I still have to get used a bit to the new workflow and previous time sage -b just worked, but it's good to know that I have to use make instead.

[leif]

Maarten Derickx wrote:
> Thanks John and Francois, that indeed solved the problem.
>
> I still have to get used a bit to the new workflow and previous time
> sage -b just worked, but it's good to know that I have to use make instead.

'./sage -b' never triggered the (re)build of updated (or current) spkgs;
'sage --upgrade' did, but git is no replacement of the latter, as it's
not a package manager.


-leif

> Le mercredi 2 avril 2014 11:12:04 UTC+2, François a écrit :
>
> You should have used “make” pynac has to be updated (the source of
> your problem)
> and sage -b won’t do that.
>
> Francois
>
> On 2/04/2014, at 22:00, Maarten Derickx <m.derick...@gmail.com

> <http://boxen.math.washington.edu/home/release/sage-6.2.beta6/sage-6.2.beta6.tar.gz>

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[kcrisman]

Hi there, 

Can all Mac fans try relocating a beta (or a binary, even) and seeing what happens.

http://trac.sagemath.org/ticket/16044?replyto=13#comment:9 suggests that the answer is, "Nothing good."  The question is how long ago that started happening.

Thanks, 

- kcrisman

[Volker Braun]

IMHO we always had dangling rpaths so relocation *never* worked in a satisfactory (to me) manner.

[Justin C. Walker]

I copied a good install/build of 6.2-beta0 (both 10.6.8, Dual 6-core Xeons and 10.9.2, Quad core Core i7) and ran a 'ptestlong' test. All tests passed.

HTH

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
--------

[John H Palmieri]

On Thursday, April 3, 2014 3:09:25 AM UTC-7, Justin C. Walker wrote:

On Apr 2, 2014, at 18:38 , kcrisman wrote:

> Hi there,
>
> Can all Mac fans try relocating a beta (or a binary, even) and seeing what
> happens.
>
> http://trac.sagemath.org/ticket/16044?replyto=13#comment:9 suggests that
> the answer is, "Nothing good."  The question is how long ago that started
> happening.

I copied a good install/build of 6.2-beta0 (both 10.6.8, Dual 6-core Xeons and 10.9.2, Quad core Core i7) and ran a 'ptestlong' test.  All tests passed.

A copied version is more likely to work than a renamed one, because if some paths have not been updated in the copied version, it will still be able to access the libraries (etc.) in the original version. I see test failures when I rename a build of 6.1.beta1.

--
John

[Justin C. Walker]

Hmmm...that's puzzling (but I don't know for sure what's under the hood after either a move or a rename).

I used the 'tar' command to do the copy (cf 'man tar'), FWIW. The "rename" just involves the 'mv' command unless the source and target are on different file systems. See 'man mv' for the "equivalent" commands in the latter case.

In any case, I just tried the same experiment, but this time just renaming the directory SAGE_ROOT (with the 'mv' command). The results were the same as with the copied directory (which in each case was the directory I subsequently renamed).

Again, that's sage-6.2-beta0 on both 10.6.8 and 10.9.2.

HTH

Justin

PS: FWIW, on both systems, I did the following:
- copy/rename SAGE_ROOT
- run "./sage" in the new SAGE_ROOT
- quit sage
- "MAKE=make -jn" make ptestlong

In all 4 cases, I got the "updating paths" output and a while-ish wait.

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's income
-----------
Question 43:
What if the hokey pokey
really *is* what it’s all about?
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[Sébastien Labbé]

Bonjour sage-release,

On Wednesday, April 2, 2014 2:09:20 AM UTC+2, Volker Braun wrote:

Get it from the "develop" git branch or the source tarball at http://boxen.math.washington.edu/home/release/sage-6.2.beta6/sage-6.2.beta6.tar.gz

I get an error while building matplotlib1-3.1. It seems "freetype" is missing. I copy pasted the relevant log below.

My computer is kind of old (mac osx 10.5.8) :

$ uname -a
Darwin pol 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

$ cat /Users/slabbe/Applications/sage-6.2.beta6/logs/pkgs/matplotlib-1.3.1.log
Found local metadata for matplotlib-1.3.1
Found local sources at /Users/slabbe/Applications/sage-6.2.beta6/upstream/matplotlib-1.3.1.tar.gz
Checksum: 0673384bdd92d3c6d135d7b9729a221b vs 0673384bdd92d3c6d135d7b9729a221b
matplotlib-1.3.1
====================================================
Setting up build directory for matplotlib-1.3.1
Finished set up
****************************************************
Host system:
Darwin pol 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/slabbe/Applications/sage-6.2.beta6/local/libexec/gcc/i386-apple-darwin9.8.0/4.7.3/lto-wrapper
Target: i386-apple-darwin9.8.0
Configured with: ../src/configure --prefix=/Users/slabbe/Applications/sage-6.2.beta6/local --with-local-prefix=/Users/slabbe/Applications/sage-6.2.beta6/local --with-gmp=/Users/slabbe/Applications/sage-6.2.beta6/local --with-mpfr=/Users/slabbe/Applications/sage-6.2.beta6/local --with-mpc=/Users/slabbe/Applications/sage-6.2.beta6/local --with-system-zlib --disable-multilib --disable-nls 
Thread model: posix
gcc version 4.7.3 (GCC)
****************************************************
NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the Matplotlib GUI.
Not building any matplotlib graphical backends.
patching file lib/matplotlib/tri/_tri.cpp
patching file lib/matplotlib/tri/_tri.h
patching file setup.py
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [1.3.1]
                python: yes [2.7.5 (default, Apr  5 2014, 03:09:15)  [GCC
                        4.7.3]]
              platform: yes [darwin]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.7.0]
              dateutil: yes [using dateutil version 2.2]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [using pyparsing version 2.0.1]
                 pycxx: yes [Couldn't import.  Using local copy.]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: no  [The C/C++ header for freetype2 (ft2build.h)
                        could not be found.  You may need to install the
                        development package.]
                   png: yes [pkg-config information for 'libpng' could not
                        be found. Using unknown version.]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]

OPTIONAL BACKEND EXTENSIONS
                macosx: no  [skipping due to configuration]
                qt4agg: no  [PyQt4 not found]
               gtk3agg: no  [Requires pygobject to be installed.]
             gtk3cairo: no  [Requires cairo to be installed.]
                gtkagg: no  [skipping due to configuration]
                 tkagg: no  [skipping due to configuration]
                 wxagg: no  [skipping due to configuration]
                   gtk: no  [skipping due to configuration]
                   agg: yes [installing]
                 cairo: no  [cairo not found]
             windowing: no  [skipping due to configuration]

OPTIONAL LATEX DEPENDENCIES
                dvipng: yes [version 1.12]
           ghostscript: yes [version 8.70]
                 latex: yes [version 3.1415926]
               pdftops: no

============================================================================
                        * The following required packages can not be built:
                        * freetype
Error building matplotlib package.

real    0m3.183s
user    0m0.512s
sys    0m0.573s
************************************************************************
Error installing package matplotlib-1.3.1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /Users/slabbe/Applications/sage-6.2.beta6/logs/pkgs/matplotlib-1.3.1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Users/slabbe/Applications/sage-6.2.beta6/local/var/tmp/sage/build/matplotlib-1.3.1 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 '/Users/slabbe/Applications/sage-6.2.beta6/local/var/tmp/sage/build/matplotlib-1.3.1' && '/Users/slabbe/Applications/sage-6.2.beta6/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
 

[Francois Bissey]

Same error that Karl-Dieter on OS X 10.4 see http://trac.sagemath.org/ticket/16047
for a very minimal patch for this.

François

[kcrisman]

On Saturday, April 5, 2014 5:17:14 AM UTC-4, François wrote:

Same error that Karl-Dieter on OS X 10.4 see http://trac.sagemath.org/ticket/16047
for a very minimal patch for this.

Or possibly #16084 instead/as well.