[sage-devel] Re: polymake and other optional spkg

[maxthemouse]

>
> > Another thing that does not work is "sage -
> > lisp" which gave the clisp prompt. I found this rather convenient
> > since I could just use the clisp within sage. Is there any plan/
> > interest to switch the this lisp interface to ecl? Does ecl use
> > readline?
>
> For now you can at least start sage then type
>
> sage: !ecl
>
> to start ecl.  It appears to not make any use of ecl.  I don't know if
> this is just
> a compilation problem or an ecl limitation.
>

Thanks, I forgot about that way to do it. The lack of readline makes
it rather unfriendly though. I am just a beginner with lisp myself.

> The Sage <--> lisp interface already works fine:
>
> sage: lisp.eval('(+ 2 3)')
> '5'
>

Using 4.0 and 4.0.1 I get a long traceback that ends with:
RuntimeError: Unable to start Lisp because the command 'clisp-
noreadline --silent -on-error abort' failed.

Sage was compiled from source on Scientific Linux 5.1. I don't have a
global clisp available though.
I figured that it was something that had just not been looked at yet
in the transition to ecl.

Adam

> I'm not sure why %gap works but not %lisp:
>
> sage: %lisp
> ERROR: Magic function `lisp` not found.
> sage: %gap
>   --> Switching to Gap <--
> gap:
>
> That should be consider a bug.
>
> OK, two tickets:
>
>   (1) make "sage -lisp" run ecl:  
> http://trac.sagemath.org/sage_trac/ticket/6287
>
>   (2) make %lisp work and run ecl + readline 
> mode:http://trac.sagemath.org/sage_trac/ticket/6288
>
>  -- William
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[sage-devel] Sage 4.0.2.rc0 released

[Nick Alexander]

Hi all,

Here's Sage 4.0.2.rc0. Come and get it while it's hot:

  http://sage.math.washington.edu/home/ncalexan/releases

We merged all of the tickets with positive review on trac (save one
that depended on a still-unreviewed ticket), and updated to the
current upstream for seven spkgs. You're probably wondering why this
is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
pretty soon, and we've already merged all the code we could from trac,
so we're cutting it off here. In addition, William is giving a talk at
MEGA on Thursday, and it would be nice to have a fresh new release for
that. So please build and test soon, and we'll get this tested and
released.

== Notable new features ==

* Updated to current upstream of Singular, MPIR, FLINT, numpy, scipy,
m4ri, and pynac
* sage -br calls gcc in parallel when MAKE is set
* New script for automatically downloading and testing patches from a
trac ticket -- this was used to create this release, but will be
packaged with rc1

== Known issues ==

* There's a doctest failure with Singular on 32-bit machines, where
Singular seems to be choosing different representatives for the
integers mod 2^32 on 32 and 64 bit architectures. Martin Albrecht will
hopefully chime in on the "right" fix for this.
* The new scipy will have doctest failures with gfortran, but works
fine with g95. In particular, we patch scipy.optimize.optimize for
g95, but not gfortran -- and the unpatched version has unusual
behavior for find_maximum_on_interval (which calls
scipy.optimize.optimize.fminbound).

== List of closed tickets ==

This will come with the release email for the next rc; if you want to
see it right away, it's here:

  
http://trac.sagemath.org/sage_trac/query?status=closed&group=resolution&milestone=sage-4.0.2

Thanks,
-Craig and Nick


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[sage-devel] Re: Tutorial topics for SciPy'09 Conference

[Fernando Perez]

Hi all,

In order to proceed with contacting speakers, we'd now like to get
some feedback from you.  This Doodle poll should take no more than a
couple of minutes to fill out (no password or registration required):

http://doodle.com/hb5bea6fivm3b5bk

So please let us know which topics you are most interested in, and
we'll do our best to accommodate everyone.  Keep in mind that speaker
availability and balancing out the topics means that the actual
tutorials offered probably won't be exactly the list of top 8 voted
topics, but the feedback will certainly help us steer the decision
process.

Thanks for your time,

Dave Peterson and Fernando Perez

On Mon, Jun 1, 2009 at 10:22 PM, Fernando Perez wrote:
> Hi all,
>
> The time for the Scipy'09 conference is rapidly approaching, and we
> would like to both announce the plan for tutorials and solicit
> feedback from everyone on topics of interest.
>
> Broadly speaking, the plan is something along the lines of  what we
> had last year: one continuous 2-day tutorial  aimed at introductory
> users, starting from the very basics, and in parallel a set of
> 'advanced' tutorials, consisting of a series of 2-hour sessions on
> specific  topics.
>
> We will request that the presenters for the advanced tutorials keep
> the 'tutorial' word very much in mind, so that the sessions really
> contain hands-on learning work and not simply a 2-hour long slide
> presentation.  We will  thus require that all the tutorials will be
> based on tools that the attendees can install at least 2 weeks in
> advance on all  platforms (no "I released it last night" software).
>
> With that in mind, we'd like feedback from all of you on possible
> topics for the advanced tutorials.  We have space for 8 slots total,
> and here are in no particular order some possible topics.  At this
> point there are no guarantees yet that we can get presentations for
> these, but we'd like to establish a first list of preferred topics to
> try and secure the presentations as soon as possible.
>
> This is simply a list of candiate topics that various people have
> informally suggested so far:
>
> - Mayavi/TVTK
> - Advanced topics in matplotlib
> - Statistics with Scipy
> - The TimeSeries scikit
> - Designing scientific interfaces with Traits
> - Advanced numpy
> - Sparse Linear Algebra with Scipy
> - Structured and record arrays in numpy
> - Cython
> - Sage - general tutorial
> - Sage - specific topics, suggestions welcome
> - Using GPUs with PyCUDA
> - Testing strategies for scientific codes
> - Parallel processing and mpi4py
> - Graph theory with Networkx
> - Design patterns for efficient iterator-based scientific codes.
> - Symbolic computing with sympy
>
> We'd like to hear from any ideas on other possible topics of interest,
> and we'll then run a doodle poll  to gather quantitative feedback with
> the final list of candidates.
>
> Many thanks,
>
> f
>

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[sage-devel] Not able to compile sage-4.0.1

[nitu]

Hi All,
I am trying to build sage-4.0.1 and getting the following error:
Build environment :
#uname -a
SunOS smath01 5.10 Generic_137137-09 sun4v sparc SUNW,Sun-Fire-T200
Compiler used:
Sunstudio 12

cfg/shared.c: In function `store_single_arg':
cfg/shared.c:727: error: wrong type argument to unary plus
cfg/shared.c:727: error: wrong type argument to unary minus
make[5]: *** [shared.o] Error 1
make[5]: Leaving directory `/export/home/sfw/sage-4.0.1/spkg/build/
gnutls-2.2.1.p1/src/src'

Please help me to resolve this issue

Regards,
Nitu

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[sage-devel] Re: Not able to compile sage-4.0.1

[William Stein]

On Mon, Jun 15, 2009 at 10:01 AM, nitu wrote:
>
> Hi All,
> I am trying to build sage-4.0.1 and getting the following error:
> Build environment :
> #uname -a
> SunOS smath01 5.10 Generic_137137-09 sun4v sparc SUNW,Sun-Fire-T200
> Compiler used:
> Sunstudio 12

Building Sage using the Sun Studio compiler is not supported.
Actually, even building Sage on Solaris is not supported, even using
GCC.  There is a project to finish up porting Sage to Solaris, which is
currently ongoing.   It is possible to build Sage on Sparc Solaris (not T2)
using a custom built binutils and GCC-4.3.2.  Building with GCC-4.4.0 does
not work yet, though D. Kirkby has made major progress toward this in
the last few days.

 -- William

>
> cfg/shared.c: In function `store_single_arg':
> cfg/shared.c:727: error: wrong type argument to unary plus
> cfg/shared.c:727: error: wrong type argument to unary minus
> make[5]: *** [shared.o] Error 1
> make[5]: Leaving directory `/export/home/sfw/sage-4.0.1/spkg/build/
> gnutls-2.2.1.p1/src/src'
>
> Please help me to resolve this issue
>
> Regards,
> Nitu
>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Categories restart

[Nicolas M. Thiery]

Hi!

On Wed, Jun 10, 2009 at 02:12:26AM -0700, Robert Bradshaw wrote:
> 
> As many of us have stated on IRC and elsewhere, lots of us reviewing  
> the categories stuff got burned out after Sage days and then busy  
> with lots of other stuff. There's lots of good code here that should  
> go in, and it's a blocker for much of the sage-combinat stuff as well.
> 
> I've just reviewed http://trac.sagemath.org/sage_trac/ticket/6110  
> (pickle decorator) and put a patch up at http://trac.sagemath.org/ 
> sage_trac/ticket/6121 (pickle metaclass) that needs review.  A lot of  
> us have reservations about shipping a modified cPickle, so I propose  
> we proceed by using the metaclass in Category (and elsewhere as  
> needed) so we can get onto the really interesting stuff.

By the way: do you have an alternative plan for #5985 (cPickle
modification for dynamic classes)? If not, would you or Craig mind
finish reviewing it? Then it and #5991 could go in, possibly even
maybe for 4.0.2?

By the way, what's the status for #5598 (coerce declare)?

Thanks in advance,
Nicolas
--
Nicolas M. Thiéry "Isil" 
http://Nicolas.Thiery.name/

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Minh Nguyen]

On Mon, Jun 15, 2009 at 7:13 AM, Nick Alexander wrote:
>



> == List of closed tickets ==
>
> This will come with the release email for the next rc; if you want to
> see it right away, it's here:
>
>  
> http://trac.sagemath.org/sage_trac/query?status=closed&group=resolution&milestone=sage-4.0.2

As tickets are getting merged, I'm keeping up with the release note
for sage-4.0.2. For the record, here's a list of closed tickets,
excluding those that have "wontfix" or "invalid" resolutions:

* Closed Tickets:

#6285: fixed due to #6244

Merged in Sage 4.0.2.alpha0

#2256: Craig Citro: matrix inverse over CC raises ZeroDivisionError
[Reviewed by Jason Grout, Nick Alexander]
#2513: Craig Citro: Weird printing issues with gcc, caused by LANG
environment variable [Reviewed by William Stein]
#3391: Jason Grout: update scipy to 0.7 [Reviewed by Josh Kantor]
#3829: Burcin Erocal: wester.py disagrees with Wester!!! [Reviewed by
Alex Ghitza]
#5321: Martin Albrecht: follow up to #5287: improve mq.SR usability
even more [Reviewed by Burcin Erocal]
#5371: Michael Abshoff, Rob Beezer: change autosave defaults [Reviewed
by Rob Beezer, Kiran Kedlaya]
#5431: Mike Hansen: Command line parser fails on hex values with 'e'
[Reviewed by Robert Bradshaw]
#5444: Mike Hansen: ellipses + float = boom [Reviewed by Robert Bradshaw]
#5454: Robert Bradshaw: Add coercion documentation to the reference
manual [Reviewed by David Loeffler]
#5510: Martin Albrecht: update M4RI interface [Reviewed by Jason Grout]
#5539: John Palmieri: "sage -docbuild" could use a better error
message [Reviewed by Minh Van Nguyen]
#5701: David Joyner: Remove Guava from standard Sage [Reviewed by Robert Miller]
#5771: John Palmieri: %latex should issue a warning if latex isn't
installed on the system [Reviewed by Rob Beezer]
#5842: Francis Clarke: Various number field improvements [Reviewed by
John Cremona, David Loeffler]
#5845: John Cremona: Fix precision bug in hilbert_class_polynomial()
[Reviewed by Alex Ghitza, Jim Stankewicz]
#5975: Robert Beezer, Fidel Barrera Cruz: Implement latex output for
(combinatorial) graphs [Reviewed by John Palmieri]
#5976: Dan Shumow: Add an Elliptic Curve Isogeny object [Reviewed by
John Cremona, David Kohel]
#6014: David Joyner: hexads in S(5,6,12) and mathematical blackjack
[Reviewed by Dan Gordon]
#6017: Provide methods for graphs to set options for latex printing
[closed due to #5975]
#6034: Martin Albrecht: update Singular to newest upstream release
[Reviewed by Kiran Kedlaya]
#6044: Maite Aranes: Enhanced reduction modulo ideals of number fields
[Reviewed by John Cremona, David Loeffler]
#6046: John Cremona: Implement local and global heights for number
field elements [Reviewed by Francis Clarke, Nick Alexander]
#6089: John Palmieri: view command: don't always use jsMath [Reviewed
by Rob Beezer]
#6108: Mike Hansen: sage -tp skips all.py!! [Reviewed by Nick Alexander]
#6110: Carl Witty, Nicolas Thiery: implement a "decorator" to allow
pickling nested classes [Reviewed by Robert Bradshaw, Nicolas Thiery]
#6121: Robert Bradshaw, Nicolas Thiery: use metaclasses to support
nested class pickling [Reviewed by Nicolas Thiery]
#6123: Robert Miller: expose partition refinement functions to Python
[Reviewed by Nick Alexander]
#6140: Jason Grout: Upgrade numpy to 1.3.0 [Reviewed by Josh Kantor]
#6178: David Loeffler: Hermite normal form over PIDs [Reviewed by John Cremona]
#6185: Martin Albrecht: Add SBox -> CNF Conversion [Reviewed by Yann
Laigle-Chapuy]
#6188: David Loeffler: Add more files in sage/rings/number_field to
reference [Reviewed by John Cremona]
#6193: John Cremona: implement elliptic logarithm [Reviewed by Robert Bradshaw]
#6201: Alex Ghitza: CC() raises exception instead of returning 0
[Reviewed by John Palmieri]
#6205: Nick Alexander: add __invert__ to number field morphism
[Reviewed by Craig Citro]
#6211: Burcin Erocal: typesetting exp sometimes broken [Reviewed by
Nick Alexander]
#6213: Craig Citro: easy addition of an alias to eta product (trivial
ticket to deal with) [Reviewed by David Loeffler]
#6218: Nick Alexander: small changes to jacobian_morphism to make
hyperelliptic curve arithmetic faster [Reviewed by Kiran Kedlaya]
#6221: Minh Van Nguyen: typos in Lagrange interpolation polynomial
[Reviewed by Nick Alexander]
#6222: Minh Van Nguyen: typos in super-increasing code [Reviewed by
Nick Alexander]
#6225: Harald Schilly: add link to irc in notebook help page [Reviewed
by Nick Alexander]
#6226: Michael Abshoff, Florent Hivert, Minh Van Nguyen: developer's
#guide: sections on formatting docstrings and trac guidelines
[Reviewed by John Palmieri, Minh Van Nguyen]
#6229: Yann Laigle-Chapuy: efficiency in Lagrange polynomial
interpolation (easy fix...) [Reviewed by Minh Van Nguyen]
#6234: Craig Citro: make parallel GCC'ing of Sage library not
experimental [Reviewed by Nick Alexander]
#6244: Burcin Erocal: conjugate() in sage-4.0 is broken [Reviewed by
Nick Alexander]
#6250: Nicolas Thiery: Standardize MatrixGroup_ga

[sage-devel] Re: Sage 4.0.2.rc0 released

[Dan Drake]

On Mon, 15 Jun 2009 at 12:13AM -0700, Nick Alexander wrote:
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
> 
>   http://sage.math.washington.edu/home/ncalexan/releases
> 
> We merged all of the tickets with positive review on trac (save one
> that depended on a still-unreviewed ticket), and updated to the
> current upstream for seven spkgs. You're probably wondering why this
> is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
> pretty soon, and we've already merged all the code we could from trac,
> so we're cutting it off here. In addition, William is giving a talk at
> MEGA on Thursday, and it would be nice to have a fresh new release for
> that. So please build and test soon, and we'll get this tested and
> released.

On 64-bit Ubuntu 9.04, compiling with SAGE_CHECK=yes, quaddouble fails
its check. Log at

http://sage.math.washington.edu/home/drake/4.0.2.rc0-install.log


Dan

-- 
---  Dan Drake 
-  KAIST Department of Mathematical Sciences
---  http://mathsci.kaist.ac.kr/~drake


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[sage-devel] Re: Sage 4.0.2.rc0 released

[Burcin Erocal]

On Mon, 15 Jun 2009 08:49:29 +
Minh Nguyen  wrote:


> #6268: Burcin Erocal: Typesetting of sec(x), csc(x), cot(x) are broken
> [Reviewed by Nick Alexander]

Credit for this should go to John Palmieri. In my late night effort to
quickly fix this, I didn't notice that his patch essentially does the
same thing.

Sorry for the inconvenience.

Burcin 


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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 11:09 AM, Dan Drake wrote:
> On Mon, 15 Jun 2009 at 12:13AM -0700, Nick Alexander wrote:
>> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>>
>>   http://sage.math.washington.edu/home/ncalexan/releases
>>
>> We merged all of the tickets with positive review on trac (save one
>> that depended on a still-unreviewed ticket), and updated to the
>> current upstream for seven spkgs. You're probably wondering why this
>> is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
>> pretty soon, and we've already merged all the code we could from trac,
>> so we're cutting it off here. In addition, William is giving a talk at
>> MEGA on Thursday, and it would be nice to have a fresh new release for
>> that. So please build and test soon, and we'll get this tested and
>> released.
>
> On 64-bit Ubuntu 9.04, compiling with SAGE_CHECK=yes, quaddouble fails
> its check. Log at
>
>    http://sage.math.washington.edu/home/drake/4.0.2.rc0-install.log
>
>

In alpha2, m4ri fails to build on OS X 10.5 PPC (the computer in Craig
Citro's office).  I'm trying rc0 now:

checking mm_malloc.h presence... no
checking for mm_malloc.h... no
checking for a sed that does not truncate output... /usr/bin/sed
checking the number of available CPUs... 1
checking the number of available CPUs... 1
checking for x86 cpuid 0x0 output... unknown
checking for the processor vendor... Unknown
./configure: line 21951: 0524288: value too great for base (error
token is "0524288")
Error configuring libm4ri

real0m20.973s
user0m4.610s
sys 0m10.475s
sage: An error occurred while installing libm4ri-20090512
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /Users/wstein/build/sage-4.0.2.alpha3/install.log.  Describe your
computer, operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/Users/wstein/build/sage-4.0.2.alpha3/spkg/build/libm4ri-20090512 and
type 'make'.
Instead type "/Users/wstein/build/sage-4.0.2.alpha3/sage -sh"
in order to set all environment variables correctly, then cd to
/Users/wstein/build/sage-4.0.2.alpha3/spkg/build/libm4ri-20090512
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/libm4ri-20090512] Error 1

real0m22.532s
user0m5.135s
sys 0m10.813s
python: can't open file
'/Users/wstein/build/sage-4.0.2.alpha3/devel/sage/doc/common/builder.py':
[Errno 2] No such file or directory
./sage -b
There is no directory '/Users/wstein/build/sage-4.0.2.alpha3/devel/sage'

real0m0.089s
user0m0.024s
sys 0m0.051s
make: *** [testlong] Error 1
pdlc424:~ wstein$ cd
pdlc424:~ wstein$ ./bb

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Craig Citro]

> In alpha2, m4ri fails to build on OS X 10.5 PPC (the computer in Craig
> Citro's office).  I'm trying rc0 now:
>
> checking mm_malloc.h presence... no
> checking for mm_malloc.h... no
> checking for a sed that does not truncate output... /usr/bin/sed
> checking the number of available CPUs... 1
> checking the number of available CPUs... 1
> checking for x86 cpuid 0x0 output... unknown
> checking for the processor vendor... Unknown
> ./configure: line 21951: 0524288: value too great for base (error
> token is "0524288")
> Error configuring libm4ri
>

We hit this exact same error on another machine (which I'd forgotten
until William mentioned this error). I'm hoping that Martin Albrecht
will say "oh, it's just " -- Martin, is this something obvious? If
not, just let me know and I'll start digging. But after your instant
fix for the libsingular 64 bit OSX bug, I figure I should let you try
and fix it first ... ;)

-cc

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Minh Nguyen]

Hi Burcin,

On Mon, Jun 15, 2009 at 9:11 AM, Burcin Erocal wrote:
>
> On Mon, 15 Jun 2009 08:49:29 +
> Minh Nguyen  wrote:
>
> 
>> #6268: Burcin Erocal: Typesetting of sec(x), csc(x), cot(x) are broken
>> [Reviewed by Nick Alexander]
>
> Credit for this should go to John Palmieri. In my late night effort to
> quickly fix this, I didn't notice that his patch essentially does the
> same thing.
>
> Sorry for the inconvenience.

The working release note has been changed accordingly. You can find my
working draft at

http://sage.math.washington.edu/home/mvngu/doc/changelog/sage-4.0.2.txt

-- 
Regards
Minh Van Nguyen

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[sage-devel] Re: polymake and other optional spkg

[William Stein]

On Mon, Jun 15, 2009 at 9:06 AM, maxthemouse wrote:
>
>
>>
>> > Another thing that does not work is "sage -
>> > lisp" which gave the clisp prompt. I found this rather convenient
>> > since I could just use the clisp within sage. Is there any plan/
>> > interest to switch the this lisp interface to ecl? Does ecl use
>> > readline?
>>
>> For now you can at least start sage then type
>>
>> sage: !ecl
>>
>> to start ecl.  It appears to not make any use of ecl.  I don't know if
>> this is just
>> a compilation problem or an ecl limitation.
>>
>
> Thanks, I forgot about that way to do it. The lack of readline makes
> it rather unfriendly though. I am just a beginner with lisp myself.
>
>> The Sage <--> lisp interface already works fine:
>>
>> sage: lisp.eval('(+ 2 3)')
>> '5'
>>
>
> Using 4.0 and 4.0.1 I get a long traceback that ends with:
> RuntimeError: Unable to start Lisp because the command 'clisp-
> noreadline --silent -on-error abort' failed.
>
> Sage was compiled from source on Scientific Linux 5.1. I don't have a
> global clisp available though.
> I figured that it was something that had just not been looked at yet
> in the transition to ecl.

No -- it's my fault.  I was testing on an install that I upgraded, and
which still had clisp sitting around.

This is now

http://trac.sagemath.org/sage_trac/ticket/6294

I think we (=sage devel team) did a very bad job switching
from clisp to ecl.  Sorry about the inconvenience.


 -- William

>
> Adam
>
>> I'm not sure why %gap works but not %lisp:
>>
>> sage: %lisp
>> ERROR: Magic function `lisp` not found.
>> sage: %gap
>>   --> Switching to Gap <--
>> gap:
>>
>> That should be consider a bug.
>>
>> OK, two tickets:
>>
>>   (1) make "sage -lisp" run ecl:  
>> http://trac.sagemath.org/sage_trac/ticket/6287
>>
>>   (2) make %lisp work and run ecl + readline 
>> mode:http://trac.sagemath.org/sage_trac/ticket/6288
>>
>>  -- William
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Not able to compile sage-4.0.1

[nitu]

Hi William,
Thanks for replying, I am using gcc 3.4.6 not sunstudio 12 for
building sage, sorry for the confusion. My project involves building
sage on both soalris 10 as well as opensolaris on various x64
platforms. What I should do now, where from can I get gcc-4.3.2 and
custom binutils, please advise

Regards,
Nitu

On Jun 15, 1:29 pm, William Stein  wrote:
> On Mon, Jun 15, 2009 at 10:01 AM, nitu wrote:
>
> > Hi All,
> > I am trying to build sage-4.0.1 and getting the following error:
> > Build environment :
> > #uname -a
> > SunOS smath01 5.10 Generic_137137-09 sun4v sparc SUNW,Sun-Fire-T200
> > Compiler used:
> > Sunstudio 12
>
> Building Sage using the Sun Studio compiler is not supported.
> Actually, even building Sage on Solaris is not supported, even using
> GCC.  There is a project to finish up porting Sage to Solaris, which is
> currently ongoing.   It is possible to build Sage on Sparc Solaris (not T2)
> using a custom built binutils and GCC-4.3.2.  Building with GCC-4.4.0 does
> not work yet, though D. Kirkby has made major progress toward this in
> the last few days.
>
>  -- William
>
>
>
> > cfg/shared.c: In function `store_single_arg':
> > cfg/shared.c:727: error: wrong type argument to unary plus
> > cfg/shared.c:727: error: wrong type argument to unary minus
> > make[5]: *** [shared.o] Error 1
> > make[5]: Leaving directory `/export/home/sfw/sage-4.0.1/spkg/build/
> > gnutls-2.2.1.p1/src/src'
>
> > Please help me to resolve this issue
>
> > Regards,
> > Nitu
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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[sage-devel] Re: Not able to compile sage-4.0.1

[William Stein]

On Mon, Jun 15, 2009 at 10:01 AM, nitu wrote:
>
> Hi All,
> I am trying to build sage-4.0.1 and getting the following error:
> Build environment :
> #uname -a
> SunOS smath01 5.10 Generic_137137-09 sun4v sparc SUNW,Sun-Fire-T200
> Compiler used:
> Sunstudio 12
>
> cfg/shared.c: In function `store_single_arg':
> cfg/shared.c:727: error: wrong type argument to unary plus
> cfg/shared.c:727: error: wrong type argument to unary minus
> make[5]: *** [shared.o] Error 1
> make[5]: Leaving directory `/export/home/sfw/sage-4.0.1/spkg/build/
> gnutls-2.2.1.p1/src/src'
>
> Please help me to resolve this issue
>

There is work in the Sage project to create a GCC spkg that
automatically builds from source both binutils and GCC-4.4.0.  This
hasn't been completed yet.  When it gets done, then we have to finish
porting Sage to build with GCC-4.4.0 on Solaris.  Once both of those
things happens, then I think you can start working on build testing on
solaris.  Until then, you should probably wait, or build test on Linux
+ Sun hardware.

 -- William

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[sage-devel] Re: LaTeX versions of (combinatorial) graphs

[William Stein]

On Mon, Jun 15, 2009 at 7:15 AM, Rob Beezer wrote:
>
> The tkz-graph package for LaTeX has many options for rendering a
> (combinatorial) graph.  Version 4.0.2alpha of Sage will have support
> for selecting these options and creating LaTeX code for graphs - which
> can be used in your own documents, seen at the command line with view
> (), and displayed in the notebook by the usual methods.

Just out of curiosity what computes the layout of the graph?  Does
Sage give the vertex positions, then tikz takes care of the *text
labels* and edge positions?  Or can tikz actually plot a layout?

>
> Right now, the only option you can select is to use one of the six or
> so built-in "styles" of the tkz-graph package.  A sample of the "Art"
> style is at
>
> http://trac.sagemath.org/sage_trac/attachment/ticket/5975/petersen-latex.png
>
> However, with this functionality now working, it will be possible to
> extend the range of possibilities.  What would you like to see added
> next?  Take a look through the 68-page manual at
>
> http://altermundus.com/downloads/packages/TKZdoc-graph.pdf
>
> and reply with your thoughts on what would be most useful to do first.
>
> Rob
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: polymake and other optional spkg

[William Stein]

On Mon, Jun 15, 2009 at 6:03 AM, Marshall Hampton wrote:
>
> I care about the polymake spkg, and I know a few users who do too.  It
> would be nice to fix it; the last time I tried to install it I got
> some errors I didn't understand at all so I'm not sure what exactly
> the problem is.  Its probably out of date anyway, so it might be best
> to start from scratch if it is to be fixed.

I hope somebody will try. The first time I ever heard of Polymake was
at Berkeley, where a lot of grad students wanted to use Polymake, but
couldn't build it (literally -- it was impossible because of lack of
RAM on their laptops).  So I spent a day and got it to build into sage
with some hacks.  It was somewhat painful.   Polymake really is the
"Sage of polytopes", and is equally heavy.   I hope somebody else will
do work and figure out how to build polymake into any sage well...

> Although the current included polytope code is somewhat disjointed,
> buggy, and incomplete, it is progressing and getting closer to
> polymake's functionality.  I think this actually makes the polymake
> spkg more important since it helps clarify what functionality needs to
> be added.
>
> -M. Hampton
>
> On Jun 14, 8:57 am, William Stein  wrote:
>> Hi,
>>
>> In case anybody cares about the optional Sage polymake spkg, I've
>> moved it from optional to experimental, since it doesn't work at all.
>>  See below.    Also, note that the fricas spkg no longer works (unless
>> the user has clisp systemwide) because we switched to ECL for our
>> lisp.  I've tested and all other optional spkg's work on sage.math.
>>
>> polymake-2.2.p5/SPKG.txt
>> Finished extraction
>> 
>> Host system
>> uname -a:
>> Linux sage.math.washington.edu 2.6.24-23-server #1 SMP Wed Apr 1
>> 22:14:30 UTC 2009 x86_64 GNU/Linux
>> 
>> 
>> GCC Version
>> gcc -v
>> Using built-in specs.
>> Target: x86_64-linux-gnu
>> Configured with: ../src/configure -v
>> --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr
>> --enable-shared --with-system-zlib --libexecdir=/usr/lib
>> --without-included-gettext --enable-threads=posix --enable-nls
>> --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2
>> --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
>> --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu
>> --host=x86_64-linux-gnu --target=x86_64-linux-gnu
>> Thread model: posix
>> gcc version 4.2.4 (Ubuntu 4.2.4-1ubuntu3)
>> 
>> /bin/ls: cannot access gmp-*.spkg: No such file or directory
>> Using  to build polymake
>> tar: /scratch/wstein/build/sage-4.0.2.alpha3/spkg/standard/.spkg:
>> Cannot open: No such file or directory
>> tar: Error is not recoverable: exiting now
>> tar: Child returned status 2
>> tar: Error exit delayed from previous errors
>> The gmp.spkg seems to be broken - installs from binaries require that
>> you download the latest gmp.spkg
>>
>> real    0m0.011s
>> user    0m0.000s
>> sys     0m0.010s
>> sage: An error occurred while installing polymake-2.2.p5
>> Please email sage-develhttp://groups.google.com/group/sage-devel
>> explaining the problem and send the relevant part of
>> of /scratch/wstein/build/sage-4.0.2.alpha3/install.log.  Describe your
>> computer, operating system, etc.
>> If you want to try to fix the problem, yourself *don't* just cd to
>> /scratch/wstein/build/sage-4.0.2.alpha3/spkg/build/polymake-2.2.p5 and
>> type 'make'.
>> Instead type "/scratch/wstein/build/sage-4.0.2.alpha3/sage -sh"
>> in order to set all environment variables correctly, then cd to
>> /scratch/wstein/build/sage-4.0.2.alpha3/spkg/build/polymake-2.2.p5
>> (When you are done debugging, you can type "exit" to leave the
>> subshell.)
>>
>> --
>> William Stein
>> Associate Professor of Mathematics
>> University of Washingtonhttp://wstein.org
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: typesetting partial derivatives

[William Stein]

On Sun, Jun 14, 2009 at 11:03 PM, Golam Mortuza
Hossain wrote:
>
> Hi
>
> On Sun, Jun 14, 2009 at 4:38 PM, Burcin Erocal wrote:
>> There were long discussion about the typesetting of partial derivatives
>> in the new system, but I don't think we got to a conclusion yet.
>
> I am afraid, we might never reach a conclusion in this regard :-)

Yes we will.  It doesn't have to be unanimous, but we will reach a conclusion.

 -- William

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Martin Albrecht]

> checking mm_malloc.h presence... no
> checking for mm_malloc.h... no
> checking for a sed that does not truncate output... /usr/bin/sed
> checking the number of available CPUs... 1
> checking the number of available CPUs... 1
> checking for x86 cpuid 0x0 output... unknown
> checking for the processor vendor... Unknown
> ./configure: line 21951: 0524288: value too great for base (error
> token is "0524288")
> Error configuring libm4ri

Here's the line that triggers it:

  ax_l2_size=$((0`$sysctl_exe -n hw.l2cachesize 2>/dev/null` / 1024))

in src/m4/ax_cache_size.m4.

sysctrl reports 524288 which looks about right. It seems the shell tries to 
interpret the value as octal because we add a leading zero. Can you try:

  http://sage.math.washington.edu/home/malb/spkgs/libm4ri-20090615.spkg

?

Martin



-- 
name: Martin Albrecht
_pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
_otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
_www: http://www.informatik.uni-bremen.de/~malb
_jab: martinralbre...@jabber.ccc.de



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[sage-devel] Re: div and curl

[Marshall Hampton]

OK, I'll try to improve it then.

-Marshall

On Jun 14, 11:10 pm, Nick Alexander  wrote:
> On 14-Jun-09, at 8:56 PM, Marshall Hampton wrote:
>
>
>
> > I care, I have written div and curl routines for my multivariable calc
> > classes before, but they were more hackish than yours.  I will try to
> > review that ticket soon, if no one beats me to it.
>
> Unfo, it's definitely needs work -- it's just a sage script that shows
> how one could do it.
>
> Nick
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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 1:26 PM, Martin
Albrecht wrote:
>
>> checking mm_malloc.h presence... no
>> checking for mm_malloc.h... no
>> checking for a sed that does not truncate output... /usr/bin/sed
>> checking the number of available CPUs... 1
>> checking the number of available CPUs... 1
>> checking for x86 cpuid 0x0 output... unknown
>> checking for the processor vendor... Unknown
>> ./configure: line 21951: 0524288: value too great for base (error
>> token is "0524288")
>> Error configuring libm4ri
>
> Here's the line that triggers it:
>
>  ax_l2_size=$((0`$sysctl_exe -n hw.l2cachesize 2>/dev/null` / 1024))
>
> in src/m4/ax_cache_size.m4.
>
> sysctrl reports 524288 which looks about right. It seems the shell tries to
> interpret the value as octal because we add a leading zero. Can you try:
>
>  http://sage.math.washington.edu/home/malb/spkgs/libm4ri-20090615.spkg
>
> ?

Craig's asleep/busy, but I'm not so... I've tested it and your new
spkg gets passed this problem, and appears to build fine.  Also, I ran
the test suite and all tests pass.

William

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[sage-devel] Re: Tutorial topics for SciPy'09 Conference

[Jason Grout]

Fernando Perez wrote:
> Hi all,
> 
> In order to proceed with contacting speakers, we'd now like to get
> some feedback from you.  This Doodle poll should take no more than a


Does "you" mean "people attending scipy09", or does it mean "sage 
developers, whether or not you are attending scipy09"?

Thanks,

Jason


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[sage-devel] Re: Sage 4.0.2.rc0 released

[davidloeffler]

Is there a copy anywhere we can use with sage -upgrade?

David

On Jun 15, 9:13 am, Nick Alexander  wrote:
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
>  http://sage.math.washington.edu/home/ncalexan/releases
>
> We merged all of the tickets with positive review on trac (save one
> that depended on a still-unreviewed ticket), and updated to the
> current upstream for seven spkgs. You're probably wondering why this
> is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
> pretty soon, and we've already merged all the code we could from trac,
> so we're cutting it off here. In addition, William is giving a talk at
> MEGA on Thursday, and it would be nice to have a fresh new release for
> that. So please build and test soon, and we'll get this tested and
> released.
>
> == Notable new features ==
>
> * Updated to current upstream of Singular, MPIR, FLINT, numpy, scipy,
> m4ri, and pynac
> * sage -br calls gcc in parallel when MAKE is set
> * New script for automatically downloading and testing patches from a
> trac ticket -- this was used to create this release, but will be
> packaged with rc1
>
> == Known issues ==
>
> * There's a doctest failure with Singular on 32-bit machines, where
> Singular seems to be choosing different representatives for the
> integers mod 2^32 on 32 and 64 bit architectures. Martin Albrecht will
> hopefully chime in on the "right" fix for this.
> * The new scipy will have doctest failures with gfortran, but works
> fine with g95. In particular, we patch scipy.optimize.optimize for
> g95, but not gfortran -- and the unpatched version has unusual
> behavior for find_maximum_on_interval (which calls
> scipy.optimize.optimize.fminbound).
>
> == List of closed tickets ==
>
> This will come with the release email for the next rc; if you want to
> see it right away, it's here:
>
>  http://trac.sagemath.org/sage_trac/query?status=closed&group=resoluti...
>
> Thanks,
> -Craig and Nick
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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 3:28 PM, davidloeffler wrote:
>
> Is there a copy anywhere we can use with sage -upgrade?
>

You could use the clean build I just made:

 sage -upgrade
http://sage.math.washington.edu/home/wstein/build/sage-4.0.2.rc0/

William

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[sage-devel] Re: [codenode-devel] Re: Re: notebook on the app engine

[Jason Grout]

William Stein wrote:
> On Sun, Jun 14, 2009 at 10:16 PM, David Joyner wrote:
>> Excellent!
>>
>> Once/if you get Sage running on it, will students of mine (<100 total)
>> be able to use it
>> and share their assignments with me?
> 
> You can't run Sage on the Google Ap Engine.

Couldn't you have a Google App Engine application call the simple http 
api to make some public notebook somewhere perform calculations?  I'm 
thinking of something like the remote sagetex that Dan announced the 
other day.  I'm not sure if this would make anything better (I'm not 
even sure why Google App Engine is so important), but using the simple 
http api might help somewhere.

Thanks,

Jason


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[sage-devel] Re: t2.math.washington.edu

[William Stein]

On Mon, Jun 15, 2009 at 3:38 PM, Dr. David
Kirkby wrote:
> William Stein wrote:
>>
>> On Sun, Jun 14, 2009 at 3:16 PM, Dr. David
>
>>> Could one or both of you verify you pick up gcc 4.4.0 when you log in,
>>> and
>>> that the compiler will compile a simple c program. It should be ok, but
>>> no
>>> so easy for me to check how it works for others, as the paths are in my
>>> own
>>> directory.
>>
>> yep it works:
>
> Good
>
>> wst...@t2:~/tmp$ gcc sage.c
>> wst...@t2:~/tmp$ ./a.out
>> sage:
>> sage:
>> wst...@t2:~/tmp$ gcc -v
>> Using built-in specs.
>> Target: sparc-sun-solaris2.10
>> Configured with: ../gcc-4.4.0/configure --with-gnu-as
>> --with-as=/home/kirkby/bin/as --with-gnu-ld
>> --with-ld=/home/kirkby/bin/ld --with-gmp=/home/kirkby/dependencies/
>> --with-mpfr=/home/kirkby/dependencies/
>> --enable-languages=c,c++,fortran --prefix=/home/kirkby/dependencies/
>> Thread model: posix
>> gcc version 4.4.0 (GCC)
>>
>>
>>> At a later date, I'll build a complete new gcc which should be easily
>>> downloadable and work for anyone without messing around with enviroment
>>> variables and editing hard-coded paths.
>>
>> And even better also make a GCC spkg that includes binutils, which
>> anybody can (probably) build.
>
> I've been thinking about the use of the GNU binutils, and in particular the
> GNU linker. I think it might actually be better to use the Sun assembler and
> linker.

I am happy with whichever option works, and encourage you to try
whatever you want to see.   Thanks for investigating this.

>
> I would not be surprised if two of the three issues I've come across (sqlite
> and linbox) might actually disappear if the Sun linker was used, rather than
> that GNU one. The sqlite issue was clearly related to the linking, and so I
> think is the linbox, since it fails to find libraries which clearly exist.
> The sqlite issue a bug in libtool, but I don't think that bug would have
> mattered with the Sun linker.
>
> There are a few reasons I am thinking this:
>
> 1) The gcc compiler Sun ship in /usr/sfw/bin uses the Sun tools. I would
> have thought if the GNU ones worked better with the compiler, Sun would have
> used them. (They do in fact ship the GNU compler and linker, but don't use
> them)
>
> 2) The guy from Sun on the sqlite mailing list suggested the Sun linker
> would be preferable.
>
> 3) The developer of libtool advised against the use of the GNU linker.
>
> 4) Past experience of mine.
>
> 5) A 64-bit port is likely to be easier with the Sun tools.
>
> 6) There is a front end for the Sun compiler and linker that takes gcc
> options, which might be a useful way of getting the performance of the Sun
> compiler, but without changing all the options.
>
> I just created a small shell script, which should (in the process of
> compiling it) build gcc with the only requirement being that the three
> source files gcc-$version.tar.gz, mpfr-$version.tar.gz and
> gmp-$version.tar.gz all exist. I think there are sufficient other files in
> /usr/sfw/bin to enable this to be built.
>
> That shell script could be converted to a .spkg file - I'd just rather get
> it right first in a script I fully understand and can edit quickly.

If you can make a straightforward automated shell script way to build GCC,
then I can very easily make an spkg from that.

Any chance you make it depend on MPIR instead of GMP?
http://mpir.org/
mpir is a drop-in replacement for gmp, which I like better for various reasons.

---
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

SAGE-4.0.2:

On OS X 10.5 Intel (bsd.math.washington.edu) the following 3 tests fail:

sage -t -long "devel/sage/doc/en/bordeaux_2008/birds_other.rst"
A mysterious error (perhaps a memory error?) occurred, which may have
crashed doctest.
 [23.2 s]

sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
**
File 
"/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.pyx",
line 501:
sage: P(2^32-1)
Expected:
-1
Got:
4294967295
**
1 items had failures:

sage -t -long "devel/sage/sage/rings/number_field/number_field_element.pyx"
**
File 
"/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/rings/number_field/number_field_element.pyx",
line 2092:
sage: [L(6).valuation(P) for P in L.primes_above(6)]
Expected:
[2, 2, 4]
Got:
[4, 2, 2]
**
1 items had failures:
   1 of  10 in __main__.example_56
***Test Failed*** 1 failures.
For whitespace errors, see the file
/Users/was/build/sage-4.0.2.rc0/tmp/.doctest_number_field_element.py
 [9.9 s]
sage -t -long 
"devel/sage/sage/rings/number_field/number_field_element_quadratic.pyx"


---

The number_field_element_quadratic.pyx failure looks easy to fix.  You
probably already know about the singular.pyx failure.

The birds_other.rst failure is sporadic and is *not* new to
sage-4.0.2.  Often it doesn't fail.  I've seen it in sage-4.0 too.
Other times it fails as follows, which suggests the multithreaded
bernoulli code of David Harvey might be involved (since it's the top
of the traceback).  I've cc'd David in case anything jumps out at him.

wst...@bsd:~/build/sage-4.0.2.rc0$ ./sage -t
devel/sage/doc/en/bordeaux_2008/birds_other.rst
sage -t  "devel/sage/doc/en/bordeaux_2008/birds_other.rst"



Unhandled SIGBUS: A bus error occured in SAGE.
This probably occured because a *compiled* component
of SAGE has a bug in it (typically accessing invalid memory)
or is not properly wrapped with _sig_on, _sig_off.
You might want to run SAGE under gdb with 'sage -gdb' to debug this.
SAGE will now terminate (sorry).


**
File 
"/Users/was/build/sage-4.0.2.rc0/devel/sage/doc/en/bordeaux_2008/birds_other.rst",
line 212:
sage: w = bernoulli(10, num_threads=16) # 1.87 seconds
Exception raised:
Traceback (most recent call last):
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
  File "", line 1, in 
w = bernoulli(Integer(10), num_threads=Integer(16)) #
1.87 seconds###line 212:
sage: w = bernoulli(10, num_threads=16) # 1.87 seconds
  File 
"/Users/was/build/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/rings/arith.py",
line 259, in bernoulli
return sage.rings.bernmm.bernmm_bern_rat(n, num_threads)
RuntimeError
**
File 
"/Users/was/build/sage-4.0.2.rc0/devel/sage/doc/en/bordeaux_2008/birds_other.rst",
line 213:
sage: w = bernoulli(10, algorithm='pari')   # 28 seconds
Exception raised:
Traceback (most recent call last):
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
  File "", line 1, in 
w = bernoulli(Integer(10), algorithm='pari')   # 28
seconds###line 213:
sage: w = bernoulli(10, algorithm='pari')   # 28 seconds
  File 
"/Users/was/build/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/rings/arith.py",
line 243, in bernoulli
x = pari(n).bernfrac() # Use the PARI C library
RuntimeError
Traceback (most recent call last):
  File "/Users/was/build/sage-4.0.2.rc0/tmp/birds_other.py", line 226,
in 
runner=runner)
  File "/Users/was/build/sage-4.0.2.rc0/local/bin/sagedoctest.py",
line 54, in testmod_returning_runner
run

[sage-devel] Re: [codenode-devel] Re: Re: notebook on the app engine

[William Stein]

On Mon, Jun 15, 2009 at 3:40 PM, Jason Grout wrote:
>
> William Stein wrote:
>> On Sun, Jun 14, 2009 at 10:16 PM, David Joyner wrote:
>>> Excellent!
>>>
>>> Once/if you get Sage running on it, will students of mine (<100 total)
>>> be able to use it
>>> and share their assignments with me?
>>
>> You can't run Sage on the Google Ap Engine.
>
> Couldn't you have a Google App Engine application call the simple http
> api to make some public notebook somewhere perform calculations?  I'm
> thinking of something like the remote sagetex that Dan announced the
> other day.  I'm not sure if this would make anything better (I'm not
> even sure why Google App Engine is so important), but using the simple
> http api might help somewhere.

I can't imagine that would do anything but make things worse.  It
would simply introduce an extra layer of complexity and probably just
increase the chances that things would break and feel slower, while
probably reducing security.   I see no win to this approach for
anybody at all.  Please correct me if I'm wrong (since then I would
learn something).

--- William

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[sage-devel] cocoalib5

[William Stein]

Hi Sage-Devel,

I was sitting next to John Abbott (of the Cocoa project) at a
conference today (MEGA), and we started chatting.  It was pretty
embarasing that there *still* isn't a cocoalib spkg.   I don't know
how we've been so lazy not to make one.Anyways, I just made one
and posted a link to it here:

http://trac.sagemath.org/sage_trac/ticket/6298

It should be easy to install into any version of Sage in < 2 minutes:

   sage -i libcocoa-0.9930.spkg

then do

   sage -sh
   cd SAGE_ROOT/local/lib/cocoa-0.9930/src/examples/

and you can make any of the examples, e.g.,

   make ex-NF
   ./ex-NF

Read the source code for examples to see how they work, etc.

No, I didn't write a Cython / libcocoa interface or something that
uses the cocoalib5 server to do anything in Sage.

 -- William

-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Martin Albrecht]

> sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
> **
> File
> "/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.pyx
>", line 501:
> sage: P(2^32-1)
> Expected:
> -1
> Got:
> 4294967295

Is that with my the fix at

  
http://trac.sagemath.org/sage_trac/attachment/ticket/6051/singular_exp_overflow.patch

or without? It seems (since you are using a 32-bit system) all that needs to 
be done is to fix the doctest. 

On 32-bit we used to switch to a slower implementation (before the fix linked 
above) at 2^30 while on 64-bit only at 2^62. It turns out we always have to 
switch at 2^30 since Singular seems to be using an int somewhere. It should 
return 4294967295 on both 32-bit and 64-bit as far as I can see.

Martin


-- 
name: Martin Albrecht
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_otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
_www: http://www.informatik.uni-bremen.de/~malb
_jab: martinralbre...@jabber.ccc.de



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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 4:19 PM, Martin
Albrecht wrote:
>
>> sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
>> **
>> File
>> "/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.pyx
>>", line 501:
>>     sage: P(2^32-1)
>> Expected:
>>     -1
>> Got:
>>     4294967295
>
> Is that with my the fix at
>
>  http://trac.sagemath.org/sage_trac/attachment/ticket/6051/singular_exp_overflow.patch
>
> or without? It seems (since you are using a 32-bit system) all that needs to
> be done is to fix the doctest.

No, I had not applied your patch.  However, I just did, and the above
issue remains.

> On 32-bit we used to switch to a slower implementation (before the fix linked
> above) at 2^30 while on 64-bit only at 2^62. It turns out we always have to
> switch at 2^30 since Singular seems to be using an int somewhere. It should
> return 4294967295 on both 32-bit and 64-bit as far as I can see.

Speaking of Singular, I'm at MEGA right now and Wolfram Decker (I
guess) gave everybody a big flier that says (among other things):

   "The Singular team would like to open the development process of
Singular to its users and encourage *you* to participate.  So if you
would like to
*Learn* Singular,
*Contribute* to the library,
*Implement* new stuff,
 ..."

then come to our meeting Wednesday, June 17, 3 p.m.:

 * license of Singular clarified
 * libsingular
 * trac, support lists,
 * more frequent releases
 * nightly builds
 * better debug and profiling support
 * on the way to singular 4.0:  C++ wrapper classes for all major
singular types, developer level source code docs, Singular as a
library.
 * 1 hour: your wishlist and discussion

Sounds good to me!  You writing libsingular seems to have really got
some people really excited.

 -- William



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Possible coercion bug

[Jason Bandlow]

Robert Bradshaw wrote:
> On Jun 9, 2009, at 9:47 AM, Jason Bandlow wrote:
> 
>>> On Jun 9, 2009, at 8:29 AM, Jason Bandlow wrote:
>>>
 Hi,

 I ran across the following behavior in sage-3.4.1 and sage-4.0 (I
 don't
 have 4.0.1 yet), and I find it fairly disturbing.

 sage: d = {'a': 1} # Create some object
 sage: d
 {'a': 1}
 sage: type(d) = type({})   # Attempt to check the type but
#  foolishly use = instead of ==

 TypeError: cannot coerce type '' into a
 SymbolicExpression.# An error is expected

 sage: d# But now my data is gone!
 d
 sage: type(d)  # Replaced by a symbolic variable
 
>> Robert Bradshaw wrote:
>>> This isn't a coercion issue, it's because of how functions are
>>> defined in Sage using the "f(x) = expr" notation using the preparser.
>>> I think that's too useful to get rid of. We could special case a
>>> warning for "type(x) = ..." but I'm not sure if that's the best idea.
>> Interesting!  This means the problem is worse than I thought.  
>> Anytime we
>> have data 'd' and 'e' and a function 'f', doing
>>
>> sage: f(d) = e# Instead of f(d) == e
>>
>> will raise a TypeError and replace 'd' with a symbolic variable.
>> Fortunately, though,
>>
>> sage: if f(d) = e:  # The usual reason to check equality
>>
>> raises a SyntaxError first, so maybe this problem isn't so serious.
> 
> Yes, I think it's fairly rare to want to do this. Probably should be  
> added to an FAQ somewhere at least, as it's a surprising and subtle  
> side effect.

First of all, thanks very much for the explanations, Robert.  Is there a
particular FAQ where I could add a brief description of this?


-Jason

> 
>> Still, it seems like it should be possible for the preparser to check
>> whether f(d) evaluates to something (in which case, the assignment is
>> going to fail anyway) before it makes the argument(s) symbolic  
>> variables.
> 
> You don't want to dissallow
> 
> sage: f(x) = x^2
> [do some stuff with f]
> sage: f(x) = x^3
> [do some stuff with the new f]
> 
> - Robert
> 
> 
> 
> > 
> 


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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[David Joyner]

Sorry, I don't understand your example.
If
A1 = matrix([[a1,b1],[c1,d1]])
A2 = matrix([[a2,b2],[c2,d2]])
then
A1.*A2 = 



On Mon, Jun 15, 2009 at 10:52 AM, paramaniac wrote:
>
> Dear Sage Developers,
>
> It would be very nice if Sage supported the element-wise
> multiplication of matrices like the .* operator in Octave/Matlab.
>
> EXAMPLE:
>
> sigma, tau, beta = var('sigma tau beta')
> A = matrix([[-1/tau, sigma/tau],[sigma/tau, -1/tau]])
> B = matrix([[beta/tau, 0],[0, beta/tau]])
> C = matrix([[1,0],[0,1]])
> D = matrix([[0,0],[0,0]])
> I = identity_matrix(2)
> s, t = var('s t')
> P = C*(s*I-A)^(-1)*B+D
> P = P.simplify_rational()
>
> RGA = P .* P.inverse().transpose()
>
> Regards,
> Lukas
>
> >
>

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Jason Grout]

paramaniac wrote:
> Dear Sage Developers,
> 
> It would be very nice if Sage supported the element-wise
> multiplication of matrices like the .* operator in Octave/Matlab.
> 


I was about to point out the recent thread about this, but then realized 
it was you that started that thread and acknowledged the response.  Are 
you saying that you would like to see the code mentioned in that thread 
(http://groups.google.com/group/sage-support/browse_thread/thread/011a3be7944100dd/fc37571d035a25c6?show_docid=fc37571d035a25c6)
 
incorporated into Sage as a function, maybe as P.hadamard_product() or 
something?

Jason


> EXAMPLE:
> 
> sigma, tau, beta = var('sigma tau beta')
> A = matrix([[-1/tau, sigma/tau],[sigma/tau, -1/tau]])
> B = matrix([[beta/tau, 0],[0, beta/tau]])
> C = matrix([[1,0],[0,1]])
> D = matrix([[0,0],[0,0]])
> I = identity_matrix(2)
> s, t = var('s t')
> P = C*(s*I-A)^(-1)*B+D
> P = P.simplify_rational()
> 
> RGA = P .* P.inverse().transpose()
> 
> Regards,
> Lukas
> 
> > 
> 


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[sage-devel] Re: Sage 4.0.2.rc0 released

[Martin Albrecht]

On Monday 15 June 2009, William Stein wrote:
> On Mon, Jun 15, 2009 at 4:19 PM, Martin
>
> Albrecht wrote:
> >> sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
> >> **
> >> File
> >> "/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.
> >>pyx ", line 501:
> >> sage: P(2^32-1)
> >> Expected:
> >> -1
> >> Got:
> >> 4294967295
> >
> > Is that with my the fix at
> >
> >  http://trac.sagemath.org/sage_trac/attachment/ticket/6051/singular_exp_o
> >verflow.patch
> >
> > or without? It seems (since you are using a 32-bit system) all that needs
> > to be done is to fix the doctest.
>
> No, I had not applied your patch.  However, I just did, and the above
> issue remains.

Yes, the issue remains. One should change the doctest, i.e. the behaviour we 
expect now is the wrong behaviour.

Martin

-- 
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[sage-devel] Feature Request: element-wise multiplication of matrices

[paramaniac]

Dear Sage Developers,

It would be very nice if Sage supported the element-wise
multiplication of matrices like the .* operator in Octave/Matlab.

EXAMPLE:

sigma, tau, beta = var('sigma tau beta')
A = matrix([[-1/tau, sigma/tau],[sigma/tau, -1/tau]])
B = matrix([[beta/tau, 0],[0, beta/tau]])
C = matrix([[1,0],[0,1]])
D = matrix([[0,0],[0,0]])
I = identity_matrix(2)
s, t = var('s t')
P = C*(s*I-A)^(-1)*B+D
P = P.simplify_rational()

RGA = P .* P.inverse().transpose()

Regards,
Lukas

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[sage-devel] Re: Not able to compile sage-4.0.1

[Dr. David Kirkby]

Dr. David Kirkby wrote:
> nitu wrote:
>> Hi All,
>> I am trying to build sage-4.0.1 and getting the following error:
>> Build environment :
>> #uname -a
>> SunOS smath01 5.10 Generic_137137-09 sun4v sparc SUNW,Sun-Fire-T200
>> Compiler used:
>> Sunstudio 12
>>
>> cfg/shared.c: In function `store_single_arg':
>> cfg/shared.c:727: error: wrong type argument to unary plus
>> cfg/shared.c:727: error: wrong type argument to unary minus
>> make[5]: *** [shared.o] Error 1
>> make[5]: Leaving directory `/export/home/sfw/sage-4.0.1/spkg/build/
>> gnutls-2.2.1.p1/src/src'
>>
>> Please help me to resolve this issue
>>
>> Regards,
>> Nitu
> 
> 
> 

As William said, there is work in progress to get Sage working with GCC 
on SPARC (I'm working on that). I have built and run it on my Blade 
2000, though it fails some tests. Also the GUI failed to work for me, as 
there was no server listening on port 8000. Others have had the GUI 
working.

A long term aim of using the Sun compilers, perhaps with Sun's GCC front 
end to the Sun compiler would be a a good idea.

The Sun compilers are a lot more fussy than the GNU ones, which is a 
good thing, BUT since a lot of people use gcc, a lot of code will not 
get passed Sun Studio 12.

If you can make any fixes to the code which would allow bits to compile 
with the Sun compiler, without breaking it on the GNU one, that would be 
useful.

But the truth is, you are not going to be able to quickly build Sage 
with the Sun compiler. Even with gcc it is not easy, but it can be 
done.I think it would be at least weeks of work to get it to build with 
Sun Studio - probably months.

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[paramaniac]

> Sorry, I don't understand your example.
> If
> A1 = matrix([[a1,b1],[c1,d1]])
> A2 = matrix([[a2,b2],[c2,d2]])
> then

A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])

Regards,
Lukas


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[sage-devel] "Dynamic Galois Theory"

[William Stein]

Hi Sage-Devel,

There is a talk right now at MEGA about "Dynamic Galois Theory" (lazy
arithmetic in QQbar!).  It's an IMHO horribly misnamed topic described
here:  http://hlombardi.free.fr/publis/GaloisDynamic09.pdf
It's really basically how to use Groebner basis to do lazy
computations in splitting fields of polynomials, i.e., the main case
in which one would ever use QQbar, and looks pretty interesting.

 -- William


-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 5:09 PM, Martin
Albrecht wrote:
>
> On Monday 15 June 2009, William Stein wrote:
>> On Mon, Jun 15, 2009 at 4:19 PM, Martin
>>
>> Albrecht wrote:
>> >> sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
>> >> **
>> >> File
>> >> "/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.
>> >>pyx ", line 501:
>> >>     sage: P(2^32-1)
>> >> Expected:
>> >>     -1
>> >> Got:
>> >>     4294967295
>> >
>> > Is that with my the fix at
>> >
>> >  http://trac.sagemath.org/sage_trac/attachment/ticket/6051/singular_exp_o
>> >verflow.patch
>> >
>> > or without? It seems (since you are using a 32-bit system) all that needs
>> > to be done is to fix the doctest.
>>
>> No, I had not applied your patch.  However, I just did, and the above
>> issue remains.
>
> Yes, the issue remains. One should change the doctest, i.e. the behaviour we
> expect now is the wrong behaviour.

This is now

http://trac.sagemath.org/sage_trac/ticket/6300

a blocker for sage-4.0.2.

William

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[William Stein]

On Mon, Jun 15, 2009 at 5:26 PM, paramaniac wrote:
>
>> Sorry, I don't understand your example.
>> If
>> A1 = matrix([[a1,b1],[c1,d1]])
>> A2 = matrix([[a2,b2],[c2,d2]])
>> then
>
> A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])
>

(1) we aren't going to add the .* notation A1 .* A2 to sage, since
there has to be a *very* very strong
demand to ever add anything new the preparser.  We haven't added
anything in as long as I can
remember.  The last thing I wanted to add (implicit multiplication)
even got voted down.

(2) I would love to add a fast optimized function that does multiply
component wise.

William

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[sage-devel] Re: Feature Request: element-wise multiplication of

[Nick Alexander]

> (1) we aren't going to add the .* notation A1 .* A2 to sage, since
> there has to be a *very* very strong

+1 to not adding this.

> (2) I would love to add a fast optimized function that does multiply
> component wise.

This is now http://trac.sagemath.org/sage_trac/ticket/6301

Nick

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Jason Grout]

William Stein wrote:
> On Mon, Jun 15, 2009 at 5:26 PM, paramaniac wrote:
>>> Sorry, I don't understand your example.
>>> If
>>> A1 = matrix([[a1,b1],[c1,d1]])
>>> A2 = matrix([[a2,b2],[c2,d2]])
>>> then
>> A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])
>>
> 
> (1) we aren't going to add the .* notation A1 .* A2 to sage, since
> there has to be a *very* very strong
> demand to ever add anything new the preparser.  We haven't added

I think William meant "never add"...



> (2) I would love to add a fast optimized function that does multiply
> component wise.


+1

Jason


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[sage-devel] Re: cocoalib5

[John Cremona]

It built fine for me (on top of 4.0.1) -- is that enough for a positive review?

John

2009/6/15 William Stein :
>
> Hi Sage-Devel,
>
> I was sitting next to John Abbott (of the Cocoa project) at a
> conference today (MEGA), and we started chatting.  It was pretty
> embarasing that there *still* isn't a cocoalib spkg.   I don't know
> how we've been so lazy not to make one.    Anyways, I just made one
> and posted a link to it here:
>
>    http://trac.sagemath.org/sage_trac/ticket/6298
>
> It should be easy to install into any version of Sage in < 2 minutes:
>
>   sage -i libcocoa-0.9930.spkg
>
> then do
>
>   sage -sh
>   cd SAGE_ROOT/local/lib/cocoa-0.9930/src/examples/
>
> and you can make any of the examples, e.g.,
>
>   make ex-NF
>   ./ex-NF
>
> Read the source code for examples to see how they work, etc.
>
> No, I didn't write a Cython / libcocoa interface or something that
> uses the cocoalib5 server to do anything in Sage.
>
>  -- William
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washington
> http://wstein.org
>
> >
>

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[John Cremona]

2009/6/15 Jason Grout :
>
> William Stein wrote:
>> On Mon, Jun 15, 2009 at 5:26 PM, paramaniac wrote:
 Sorry, I don't understand your example.
 If
 A1 = matrix([[a1,b1],[c1,d1]])
 A2 = matrix([[a2,b2],[c2,d2]])
 then
>>> A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])
>>>
>>
>> (1) we aren't going to add the .* notation A1 .* A2 to sage, since
>> there has to be a *very* very strong
>> demand to ever add anything new the preparser.  We haven't added
>
> I think William meant "never add"...
>

No, he meant what he said!

John

>
>
>> (2) I would love to add a fast optimized function that does multiply
>> component wise.
>
>
> +1
>
> Jason
>
>
> >
>

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[sage-devel] Re: [sage-edu] ANN: openopt 0.24 - free numerical optimization framework

[William Stein]

On Mon, Jun 15, 2009 at 5:47 PM, dmitrey wrote:
>
> Hi all,
> OpenOpt 0.24, a free Python-written numerical optimization framework
> with some own solvers and connections to tens of 3rd party ones, has
> been released.
>
> BSD license allows to use it in both free opensource and commercial
> closed-code software.
>
> Currently we have ~80 unique visitors daily, 15% of the ones visit
> installation webpage, and some more install it via PYPI, Debian and
> Alt Linux repository, mac.softpedia.com, darwinports.com,
> pythonxy.com, mloss.org.
>
> Our homepage:
> http://openopt.org
>
> Introduction to the framework:
> http://openopt.org/Foreword
>
> All release details are here:
> http://openopt.org/Changelog
> or
> http://forum.openopt.org/viewtopic.php?id=110
>

I've posted an updated spkg here:

   http://sage.math.washington.edu/home/wstein/patches/openopt-0.24.spkg

so you can try it by typing

  sage -i http://sage.math.washington.edu/home/wstein/patches/openopt-0.24.spkg

Also, could somebody please referee this:

http://trac.sagemath.org/sage_trac/ticket/6302

it's about adding openopt as an optional sage spkg.

William

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[William Stein]

On Mon, Jun 15, 2009 at 6:17 PM, John Cremona wrote:
>
> 2009/6/15 Jason Grout :
>>
>> William Stein wrote:
>>> On Mon, Jun 15, 2009 at 5:26 PM, paramaniac wrote:
> Sorry, I don't understand your example.
> If
> A1 = matrix([[a1,b1],[c1,d1]])
> A2 = matrix([[a2,b2],[c2,d2]])
> then
 A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])

>>>
>>> (1) we aren't going to add the .* notation A1 .* A2 to sage, since
>>> there has to be a *very* very strong
>>> demand to ever add anything new the preparser.  We haven't added
>>
>> I think William meant "never add"...
>>
>
> No, he meant what he said!
>
> John

"When I use a word," Humpty Dumpty said, in a rather scornful tone,
"it means just what I choose it to mean—neither more nor less."

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[sage-devel] Re: cocoalib5

[William Stein]

On Mon, Jun 15, 2009 at 6:14 PM, John Cremona wrote:
>
> It built fine for me (on top of 4.0.1) -- is that enough for a positive 
> review?

It would be nice if you looked in the spkg and verified that:


* SPKG.txt looks good

* there is an hg repo

* the spkg-install file doesn't install a keylogger :-)

 - William

>
> John
>
> 2009/6/15 William Stein :
>>
>> Hi Sage-Devel,
>>
>> I was sitting next to John Abbott (of the Cocoa project) at a
>> conference today (MEGA), and we started chatting.  It was pretty
>> embarasing that there *still* isn't a cocoalib spkg.   I don't know
>> how we've been so lazy not to make one.    Anyways, I just made one
>> and posted a link to it here:
>>
>>    http://trac.sagemath.org/sage_trac/ticket/6298
>>
>> It should be easy to install into any version of Sage in < 2 minutes:
>>
>>   sage -i libcocoa-0.9930.spkg
>>
>> then do
>>
>>   sage -sh
>>   cd SAGE_ROOT/local/lib/cocoa-0.9930/src/examples/
>>
>> and you can make any of the examples, e.g.,
>>
>>   make ex-NF
>>   ./ex-NF
>>
>> Read the source code for examples to see how they work, etc.
>>
>> No, I didn't write a Cython / libcocoa interface or something that
>> uses the cocoalib5 server to do anything in Sage.
>>
>>  -- William
>>
>> --
>> William Stein
>> Associate Professor of Mathematics
>> University of Washington
>> http://wstein.org
>>
>> >
>>
>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Google wants to make Python 5x faster

[javier]

This looks like good news for sage:

http://code.google.com/p/unladen-swallow/wiki/ProjectPlan
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[sage-devel] Re: cocoalib5

[John Cremona]

2009/6/15 William Stein :
>
> On Mon, Jun 15, 2009 at 6:14 PM, John Cremona wrote:
>>
>> It built fine for me (on top of 4.0.1) -- is that enough for a positive 
>> review?
>
> It would be nice if you looked in the spkg and verified that:
>
>
> * SPKG.txt looks good
>
> * there is an hg repo
>
> * the spkg-install file doesn't install a keylogger :-)

Done!

>
>  - William
>
>>
>> John
>>
>> 2009/6/15 William Stein :
>>>
>>> Hi Sage-Devel,
>>>
>>> I was sitting next to John Abbott (of the Cocoa project) at a
>>> conference today (MEGA), and we started chatting.  It was pretty
>>> embarasing that there *still* isn't a cocoalib spkg.   I don't know
>>> how we've been so lazy not to make one.    Anyways, I just made one
>>> and posted a link to it here:
>>>
>>>    http://trac.sagemath.org/sage_trac/ticket/6298
>>>
>>> It should be easy to install into any version of Sage in < 2 minutes:
>>>
>>>   sage -i libcocoa-0.9930.spkg
>>>
>>> then do
>>>
>>>   sage -sh
>>>   cd SAGE_ROOT/local/lib/cocoa-0.9930/src/examples/
>>>
>>> and you can make any of the examples, e.g.,
>>>
>>>   make ex-NF
>>>   ./ex-NF
>>>
>>> Read the source code for examples to see how they work, etc.
>>>
>>> No, I didn't write a Cython / libcocoa interface or something that
>>> uses the cocoalib5 server to do anything in Sage.
>>>
>>>  -- William
>>>
>>> --
>>> William Stein
>>> Associate Professor of Mathematics
>>> University of Washington
>>> http://wstein.org
>>>
>>> >
>>>
>>
>> >
>>
>
>
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washington
> http://wstein.org
>
> >
>

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[sage-devel] Re: Sage 4.0.2.rc0 released

[John Cremona]

Built fine and passed all tests on 64-bit Ubuntu.

Built fine, 2 test failyres on 32-bit Suse:  the singular.pyx issue
already reported, and

**
File 
"/local/jec/sage-4.0.2.rc0/devel/sage/sage/rings/number_field/number_field_element.pyx",
line 2092:
sage: [L(6).valuation(P) for P in L.primes_above(6)]
Expected:
[2, 2, 4]
Got:
[4, 2, 2]
**

That is on old issue: L.primes_above(6) tries to sort the primes but
there are tie-break situations where the order is not determined;  and
pari's output is often different on 32-or 64-bit machines.  Unless
someone can come up with a reliable way of sorting primes in a number
field (currently "sorted by residue degree first, then by
underlying prime (or equivalently, by norm).")  this doctest
should be changed so as not to depend on the order.

John

2009/6/15 William Stein :
>
> On Mon, Jun 15, 2009 at 5:09 PM, Martin
> Albrecht wrote:
>>
>> On Monday 15 June 2009, William Stein wrote:
>>> On Mon, Jun 15, 2009 at 4:19 PM, Martin
>>>
>>> Albrecht wrote:
>>> >> sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
>>> >> **
>>> >> File
>>> >> "/Users/was/build/sage-4.0.2.rc0/devel/sage/sage/libs/singular/singular.
>>> >>pyx ", line 501:
>>> >>     sage: P(2^32-1)
>>> >> Expected:
>>> >>     -1
>>> >> Got:
>>> >>     4294967295
>>> >
>>> > Is that with my the fix at
>>> >
>>> >  http://trac.sagemath.org/sage_trac/attachment/ticket/6051/singular_exp_o
>>> >verflow.patch
>>> >
>>> > or without? It seems (since you are using a 32-bit system) all that needs
>>> > to be done is to fix the doctest.
>>>
>>> No, I had not applied your patch.  However, I just did, and the above
>>> issue remains.
>>
>> Yes, the issue remains. One should change the doctest, i.e. the behaviour we
>> expect now is the wrong behaviour.
>
> This is now
>
> http://trac.sagemath.org/sage_trac/ticket/6300
>
> a blocker for sage-4.0.2.
>
> William
>
> >
>

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[sage-devel] Re: Google wants to make Python 5x faster

[William Stein]

On Mon, Jun 15, 2009 at 6:48 PM, javier wrote:
>
> This looks like good news for sage:
>
> http://code.google.com/p/unladen-swallow/wiki/ProjectPlan

Deja vu:

http://groups.google.com/group/sage-devel/browse_thread/thread/cc860333635b8aa5/9f0724949f7bbb92

 -- William

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[sage-devel] Re: Sage 4.0.2.rc0 released

[William Stein]

On Mon, Jun 15, 2009 at 7:01 PM, John Cremona wrote:
>
> Built fine and passed all tests on 64-bit Ubuntu.
>
> Built fine, 2 test failyres on 32-bit Suse:  the singular.pyx issue
> already reported, and
>
> **
> File 
> "/local/jec/sage-4.0.2.rc0/devel/sage/sage/rings/number_field/number_field_element.pyx",
> line 2092:
>    sage: [L(6).valuation(P) for P in L.primes_above(6)]
> Expected:
>    [2, 2, 4]
> Got:
>    [4, 2, 2]
> **
>
> That is on old issue: L.primes_above(6) tries to sort the primes but
> there are tie-break situations where the order is not determined;  and
> pari's output is often different on 32-or 64-bit machines.  Unless
> someone can come up with a reliable way of sorting primes in a number
> field (currently "sorted by residue degree first, then by
>        underlying prime (or equivalently, by norm).")  this doctest
> should be changed so as not to depend on the order.
>
> John

Thanks.  This is now:

   http://trac.sagemath.org/sage_trac/ticket/6303

By the way, Nick Alexander just got very busy and release management
for sage-4.0.2 has switched from Craig + Nick
to Craig + William(=me) for the finish.

William

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[sage-devel] Re: Google wants to make Python 5x faster

[Bill Hart]

Should we take this as a sign that raising awareness of a project on
the sage devel list is a good way to raise its profile generally and
make it happen.

I think so!!  ;-)

(or we could just say if you are google and you have lots of money you
can make all manner of interesting things happen.)

Bill.

On 15 June, 18:02, William Stein  wrote:
> On Mon, Jun 15, 2009 at 6:48 PM, javier wrote:
>
> > This looks like good news for sage:
>
> >http://code.google.com/p/unladen-swallow/wiki/ProjectPlan
>
> Deja vu:
>
> http://groups.google.com/group/sage-devel/browse_thread/thread/cc8603...
>
>  -- William
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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Bill Hart]

Can I ask what applications this "Hadamard product" has?

Bill.

On 15 June, 17:32, William Stein  wrote:
> On Mon, Jun 15, 2009 at 6:17 PM, John Cremona wrote:
>
> > 2009/6/15 Jason Grout :
>
> >> William Stein wrote:
> >>> On Mon, Jun 15, 2009 at 5:26 PM, paramaniac 
> >>> wrote:
> > Sorry, I don't understand your example.
> > If
> > A1 = matrix([[a1,b1],[c1,d1]])
> > A2 = matrix([[a2,b2],[c2,d2]])
> > then
>  A1.*A2 = matrix([[a1*a2, b1*b2],[c1*c2, d1*d2]])
>
> >>> (1) we aren't going to add the .* notation A1 .* A2 to sage, since
> >>> there has to be a *very* very strong
> >>> demand to ever add anything new the preparser.  We haven't added
>
> >> I think William meant "never add"...
>
> > No, he meant what he said!
>
> > John
>
> "When I use a word," Humpty Dumpty said, in a rather scornful tone,
> "it means just what I choose it to mean—neither more nor less."
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[sage-devel] Defining symbolic function with custom latex_name

[Golam Mortuza Hossain]

Hi,

On Tue, Jun 9, 2009 at 9:12 PM, Nick Alexander wrote:
>
>> (2) keyword "latex_name":  If I understand correctly, the new
>> "SFunction" class can be given keyboard argument
>> "latex_name=LaTeX".  It would be really cool if we could define a
>> symbolic function as
>> 
>> riemann(x) = function('riemann', x, latex_name="\\mathcal{R}")
>
> That's the function I want.

A patch is posted and reviews are welcome.

http://trac.sagemath.org/sage_trac/ticket/6290

This will allow keyword  arguments to pass down to underlying
SFunction class in new symbolics.

Cheers,
Golam

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Jaap Spies]

John Cremona wrote:
> Built fine and passed all tests on 64-bit Ubuntu.
> 
> Built fine, 2 test failyres on 32-bit Suse:  the singular.pyx issue
> already reported, and
> 
> **
> File 
> "/local/jec/sage-4.0.2.rc0/devel/sage/sage/rings/number_field/number_field_element.pyx",
> line 2092:
> sage: [L(6).valuation(P) for P in L.primes_above(6)]
> Expected:
> [2, 2, 4]
> Got:
> [4, 2, 2]
> **
> 
> That is on old issue: L.primes_above(6) tries to sort the primes but
> there are tie-break situations where the order is not determined;  and
> pari's output is often different on 32-or 64-bit machines.  Unless
> someone can come up with a reliable way of sorting primes in a number
> field (currently "sorted by residue degree first, then by
> underlying prime (or equivalently, by norm).")  this doctest
> should be changed so as not to depend on the order.
> 

Same here on Fedora 9, 32 bit.

Jaap


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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Tim Lahey]

On Jun 15, 2009, at 1:14 PM, Bill Hart wrote:

>
> Can I ask what applications this "Hadamard product" has?
>
> Bill.

I've never heard it called that, but element-wise multiplication
is useful for tensors.

Cheers,

Tim.

---
Tim Lahey
PhD Candidate, Systems Design Engineering
University of Waterloo
http://www.linkedin.com/in/timlahey

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Jason Grout]

Bill Hart wrote:
> Can I ask what applications this "Hadamard product" has?

(Tim: The term is from linear algebra)

http://en.wikipedia.org/wiki/Matrix_multiplication#Hadamard_product says 
it is used in JPG compression, for example.

http://planetmath.org/encyclopedia/HadamardProduct.html

Also, a google search for hadamard product applications turns up 
http://buzzard.ups.edu/courses/2007spring/projects/million-paper.pdf 
(maybe Rob Beezer knows this person?)

Perhaps naming the function "hadamard_product" isn't the best idea if 
this term is not generally known.  I can imagine it would cause some 
problems for people trying to find it if they didn't know the name...

Thanks,

Jason


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[sage-devel] Re: Defining symbolic function with custom latex_name

[William Stein]

On Mon, Jun 15, 2009 at 7:22 PM, Golam Mortuza
Hossain wrote:
>
> Hi,
>
> On Tue, Jun 9, 2009 at 9:12 PM, Nick Alexander wrote:
>>
>>> (2) keyword "latex_name":  If I understand correctly, the new
>>> "SFunction" class can be given keyboard argument
>>> "latex_name=LaTeX".  It would be really cool if we could define a
>>> symbolic function as
>>> 
>>> riemann(x) = function('riemann', x, latex_name="\\mathcal{R}")
>>
>> That's the function I want.
>
> A patch is posted and reviews are welcome.
>
> http://trac.sagemath.org/sage_trac/ticket/6290
>
> This will allow keyword  arguments to pass down to underlying
> SFunction class in new symbolics.

Awesome!  I made a comment requesting a little more documentation.

William

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[William Stein]

On Mon, Jun 15, 2009 at 7:34 PM, Jason Grout wrote:
>
> Bill Hart wrote:
>> Can I ask what applications this "Hadamard product" has?

I've never used it, but I guess it must be really really important in
numerical computation, since most shockingly it is the *default* for
A*B in numpy!!

sage: import numpy
sage: a = numpy.array([[1,2],[3,4]])
sage: a*a
array([[1, 4],
   [9, 16]], dtype=object)

The above seems so utterly insanely wrong to a mathematician like me,
it boggles my mind every time I see it :-).

I once years ago benchmarked numpy for matrix multiplication and
didn't realize that it does it componentwise, and was just shocked
that somehow they seemed to have found an O(n^2) algorithm :-).

William




>
> (Tim: The term is from linear algebra)
>
> http://en.wikipedia.org/wiki/Matrix_multiplication#Hadamard_product says
> it is used in JPG compression, for example.
>
> http://planetmath.org/encyclopedia/HadamardProduct.html
>
> Also, a google search for hadamard product applications turns up
> http://buzzard.ups.edu/courses/2007spring/projects/million-paper.pdf
> (maybe Rob Beezer knows this person?)
>
> Perhaps naming the function "hadamard_product" isn't the best idea if
> this term is not generally known.  I can imagine it would cause some
> problems for people trying to find it if they didn't know the name...
>
> Thanks,
>
> Jason
>
>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Nick Alexander]

>> That is on old issue: L.primes_above(6) tries to sort the primes but
>> there are tie-break situations where the order is not determined;   
>> and
>> pari's output is often different on 32-or 64-bit machines.  Unless
>> someone can come up with a reliable way of sorting primes in a number
>> field (currently "sorted by residue degree first, then by
>>underlying prime (or equivalently, by norm).")  this doctest
>> should be changed so as not to depend on the order.

I even changed the doctest, thinking you had made this unique.  Let's  
just verify the sorted list is correct, and not worry about the  
ordering.

Nick

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Jason Grout]

William Stein wrote:
> On Mon, Jun 15, 2009 at 7:34 PM, Jason Grout 
> wrote:
>> Bill Hart wrote:
>>> Can I ask what applications this "Hadamard product" has?
> 
> I've never used it, but I guess it must be really really important in
> numerical computation, since most shockingly it is the *default* for
> A*B in numpy!!
> 
> sage: import numpy
> sage: a = numpy.array([[1,2],[3,4]])
> sage: a*a
> array([[1, 4],
>[9, 16]], dtype=object)


It's just default because you aren't using the numpy "matrix" class, 
just the "array" class.  Of course, the product of two arrays is the 
element-wise product.  See http://www.scipy.org/NumPy_for_Matlab_Users

"In NumPy the basic type is a multidimensional array. Operations on 
these arrays in all dimensionalities including 2D are elementwise 
operations. However, there is a special matrix type for doing linear 
algebra, which is just a subclass of the array class. Operations on 
matrix-class arrays are linear algebra operations."

That said, the matrix class is not very well supported (there are 
movements on the numpy mailing list to correct this), so we use the 
array class and the "dot" method in Sage.

Jason


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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Dag Sverre Seljebotn]

William Stein wrote:
> On Mon, Jun 15, 2009 at 7:34 PM, Jason Grout 
> wrote:
>> Bill Hart wrote:
>>> Can I ask what applications this "Hadamard product" has?
> 
> I've never used it, but I guess it must be really really important in
> numerical computation, since most shockingly it is the *default* for
> A*B in numpy!!
> 
> sage: import numpy
> sage: a = numpy.array([[1,2],[3,4]])
> sage: a*a
> array([[1, 4],
>[9, 16]], dtype=object)
> 
> The above seems so utterly insanely wrong to a mathematician like me,
> it boggles my mind every time I see it :-).

I tend to really think of array manipulation and linear algebra as 
totally different things -- NumPy does the former, Sage the latter.

To take the JPEG example for Hadamard product from Wikipedia (where you 
e.g. need to multiply each pixel in a transformed image block by a 
coefficient), I'd be quite happy have a 2D image block and multiply that 
(componentwise) with another 2D array.

BUT, expressed as linear algebra, I would definitely let the image be a 
vector, and the coefficients a diagonal matrix which operates on it.

I tend to just avoid using the word "matrix" for a 2D NumPy array. 
Matrices and vectors are concepts in linear algebra -- if I have a 3D 
array in NumPy it can definitely be a vector in writing, and a 1D array 
can be a diagonal matrix in writing, and so on.

If that was too vague: Another example is that to actually multiply a 
diagonal matrix with another matrix in NumPy's array expression I'd tend 
to do

vector_of_diagonal * the_matrix

which works because of broadcasting:

In [11]: np.array([[1,2,3]]).T * np.identity(3)
Out[11]:
array([[ 1.,  0.,  0.],
[ 0.,  2.,  0.],
[ 0.,  0.,  3.]])

The "Sage way" of doing that would likely be to have a seperate 
DiagonalMatrix type or so; so in a sense NumPy is rawer and more 
lower-level. Both have their place.


-- 
Dag Sverre

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Dag Sverre Seljebotn]

Jason Grout wrote:
> William Stein wrote:
>> On Mon, Jun 15, 2009 at 7:34 PM, Jason Grout 
>> wrote:
>>> Bill Hart wrote:
 Can I ask what applications this "Hadamard product" has?
>> I've never used it, but I guess it must be really really important in
>> numerical computation, since most shockingly it is the *default* for
>> A*B in numpy!!
>>
>> sage: import numpy
>> sage: a = numpy.array([[1,2],[3,4]])
>> sage: a*a
>> array([[1, 4],
>>[9, 16]], dtype=object)
> 
> 
> It's just default because you aren't using the numpy "matrix" class, 
> just the "array" class.  Of course, the product of two arrays is the 
> element-wise product.  See http://www.scipy.org/NumPy_for_Matlab_Users

For reasons which should be clear in my other post, I really dislike the 
entire concept of the matrix class in NumPy, well supported or not. 
Either do array manipulation or linear algebra, but something in between 
just muddies all the concepts. (I.e. they don't have Vector or 
DiagonalMatrix and so on -- it's just a quick hack to bolt linear 
algebra * and ** operators on to array manipulation.)

-- 
Dag Sverre

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[sage-devel] Re: Sage 4.0.2.rc0 released

[John Cremona]

2009/6/15 Nick Alexander :
>
>>> That is on old issue: L.primes_above(6) tries to sort the primes but
>>> there are tie-break situations where the order is not determined;
>>> and
>>> pari's output is often different on 32-or 64-bit machines.  Unless
>>> someone can come up with a reliable way of sorting primes in a number
>>> field (currently "sorted by residue degree first, then by
>>>        underlying prime (or equivalently, by norm).")  this doctest
>>> should be changed so as not to depend on the order.
>
> I even changed the doctest, thinking you had made this unique.  Let's
> just verify the sorted list is correct, and not worry about the
> ordering.

The weird thing is that when I now look at the code for
primes_above(), it does not do the sorting I described in the
docstring -- though I clearly remember writing the code!  I *am*
therefore going to change primes_above() to do what it says, but also
change the doctest which failed so that it is independent of the
ordering.

John

>
> Nick
>
> >
>

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Kevin Horton]

On 15 Jun 2009, at 03:13, Nick Alexander wrote:

>
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
> http://sage.math.washington.edu/home/ncalexan/releases

libm4ri failed to build on a G4 PowerBook with OS X 10.5:

checking the number of available CPUs... 1
checking the number of available CPUs... 1
checking for x86 cpuid 0x0 output... unknown
checking for the processor vendor... Unknown
./configure: line 21951: 0524288: value too great for base (error  
token is "0524288")
Error configuring libm4ri

real0m22.950s
user0m5.321s
sys 0m10.465s
sage: An error occurred while installing libm4ri-20090512
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /Applications/sage-4.0.2.rc0/install.log.  Describe your computer,  
operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/Applications/sage-4.0.2.rc0/spkg/build/libm4ri-20090512 and type  
'make'.
Instead type "/Applications/sage-4.0.2.rc0/sage -sh"
in order to set all environment variables correctly, then cd to
/Applications/sage-4.0.2.rc0/spkg/build/libm4ri-20090512
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/libm4ri-20090512] Error 1

real316m58.820s
user212m58.490s
sys 45m58.686s
python: can't open file '/Applications/sage-4.0.2.rc0/devel/sage/doc/ 
common/builder.py': [Errno 2] No such file or directory



--
Kevin Horton
Ottawa, Canada




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[sage-devel] Re: Sage 4.0.2.rc0 released

[John Cremona]

2009/6/15 John Cremona :
> 2009/6/15 Nick Alexander :
>>
 That is on old issue: L.primes_above(6) tries to sort the primes but
 there are tie-break situations where the order is not determined;
 and
 pari's output is often different on 32-or 64-bit machines.  Unless
 someone can come up with a reliable way of sorting primes in a number
 field (currently "sorted by residue degree first, then by
        underlying prime (or equivalently, by norm).")  this doctest
 should be changed so as not to depend on the order.
>>
>> I even changed the doctest, thinking you had made this unique.  Let's
>> just verify the sorted list is correct, and not worry about the
>> ordering.
>
> The weird thing is that when I now look at the code for
> primes_above(), it does not do the sorting I described in the
> docstring -- though I clearly remember writing the code!  I *am*
> therefore going to change primes_above() to do what it says, but also
> change the doctest which failed so that it is independent of the
> ordering.

Patch up at #6303:  http://trac.sagemath.org/sage_trac/ticket/6303

John

>
> John
>
>>
>> Nick
>>
>> >>
>>
>

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[Rob Beezer]

On Jun 15, 10:34 am, Jason Grout  wrote:
> Also, a google search for hadamard product applications turns up
> http://buzzard.ups.edu/courses/2007spring/projects/million-paper.pdf
> (maybe Rob Beezer knows this person?)

Elizabeth Million was a student in a course of mine a few years ago
and this was her final project paper.  I asked her to polish it up and
she contributed it as Section HP of my textbook (which I see now has a
consistent problem with the subscripts on the Hadamard identity):

http://linear.ups.edu/jsmath/latest/fcla-jsmath-latestli101.html

Exercise T30 talks about connections with the singular value
decomposition, and her original paper contains some more involved
theorems and results that she didn't work up for the section of the
book.  So the operation is not without interest, I believe.

Working with Elizabeth, it was obvious to me that this was
consistently called the Hadamard Product by those who studied it.
However, I would agree that "elementwise_product()" would be much more
obvious to one browsing the available functions.  So having
"hadamard_product()" as a synonym, or at least prominently included in
the documentation would be desirable.

Given the apparent ease of implementing this, I'd consider it a useful
addition.

Rob
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[sage-devel] Re: Sage 4.0.2.rc0 released

[David Harvey]

On Jun 15, 9:57 am, William Stein  wrote:

> File 
> "/Users/was/build/sage-4.0.2.rc0/devel/sage/doc/en/bordeaux_2008/birds_other.rst",
> line 212:
>     sage: w = bernoulli(10, num_threads=16)     # 1.87 seconds
> Exception raised:
>     Traceback (most recent call last):

[...]

This is now http://sagetrac.org/sage_trac/ticket/6304.

david

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[sage-devel] complex_plot and fractals

[Jason Grout]

I just tried to implement a quick, fast mandelbrot set plot.  I posted 
my results (with the puzzling error) here: http://sagenb.org/home/pub/578/

The error that I get is that when passing a Cython-created CC number to 
complex_plot, I get an error "float required"---something about the 
fast_float stuff.  However, when I wrap that in a Python function which 
merely returns the exact same thing, there is no error.

Can someone look at the worksheet and see offhand what the problem is? 
Is it an error in my code, in fast_float, complex_plot, or something else?

Thanks,

Jason


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[sage-devel] Re: LaTeX versions of (combinatorial) graphs

[Rob Beezer]

On Jun 15, 3:03 am, William Stein  wrote:
> Just out of curiosity what computes the layout of the graph?  Does
> Sage give the vertex positions, then tikz takes care of the *text
> labels* and edge positions?  Or can tikz actually plot a layout?

The tkz-graph package is really more about presentation ("looks") than
about computation.  It will do simple things like circular and grid
layouts, paths on lines at 45-degree angles, etc.  It will easily
"bend" edges, which is useful for digraphs when there is an edge going
both ways between two vertices.  But on the whole, I think matters
regarding layouts are best handled within Sage itself, and then just
scaled linearly to fit bounding boxes, etc.

The strengths of tkz-graph are the placements and styles of labels on
vertices and edges, and the styles of the vertices and edges
themselves.  For example, edges can be of one color with thin black
borders, and at crossings there is an obvious "under and over"
appearance which helps the eye track an edge in a messy looking
graph.  Edge labels can appear in the middle of an edge (suitably
rotated to align with the edge), included inside a rectangle with a
colored border, with Latex math objects for contents, typeset
properly.

And finally, as Latex code they can be employed by all the support
Sage has for Latex, and they can be employed in other documents
without the whole business of including image files produced by some
other mechanism.


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[sage-devel] Is 4.0.2 closed yet?

[John Cremona]

Does the release of an rc0 mean that 4.0.2 is closed to new patches?

I have one at #4290 (new feature, but not too important), a bug fix at
#5307 (Tate's algorithm over number fields) and a post-review mini
patch at #6273 waiting for a mini review

John

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[sage-devel] Re: Is 4.0.2 closed yet?

[John Cremona]

Thanks Nick -- 2 out of three reviewed in under 10 minutes must set a
record!  It's the quality of the patches which counts, of course.

John

2009/6/15 John Cremona :
> Does the release of an rc0 mean that 4.0.2 is closed to new patches?
>
> I have one at #4290 (new feature, but not too important), a bug fix at
> #5307 (Tate's algorithm over number fields) and a post-review mini
> patch at #6273 waiting for a mini review
>
> John
>

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Kevin Horton]

On 15 Jun 2009, at 03:13, Nick Alexander wrote:

>
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
> http://sage.math.washington.edu/home/ncalexan/releases


On OS X 10.5 Intel, four tests failed.  The first two failures were  
exactly as already reported by William Stein:

sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
sage -t -long "devel/sage/sage/rings/number_field/ 
number_field_element.pyx"

I had two tests that reported failures with "mysterious errors".  I  
ran both tests again, and this time they passed.  I have no idea what  
could have caused these errors.

sage -t -long "devel/sage/sage/tests/book_stein_ent.py"
A mysterious error (perhaps a memory error?) occurred, which may have  
crashed doctest.
 [1.9 s]
sage -t -long "devel/sage/sage/tests/book_stein_modform.py"
A mysterious error (perhaps a memory error?) occurred, which may have  
crashed doctest.
 [1.8 s]

--
Kevin Horton
Ottawa, Canada




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[sage-devel] Strange behaviour with loading files and numpy

[Pogon]

Hi,
I'm not sure if it's a bug or it's me doing something wrong.

I have two files:

test1.sage containing nothing but
   print numpy.random.normal(0,(2*0.0061*0.33)^(1/2),1)

and

test2.sage containing
   load "test1.sage"


I import numpy
sage: import numpy

Now
sage: load "test1.sage"
returns values always smaller than 1
thats the right distribution, the same i get when using the notebook-
interface

but
sage: load "test2.sage"
very often returns values bigger than 1,
thats a whole different distribution

My system is ubuntu-9.04-amd64 on Pentium Dual Core
sage-4.0.1 from 2009-06-06

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[sage-devel] Re: Strange behaviour with loading files and numpy

[Marshall Hampton]

I'm not sure what is happening but I would guess that at some point
the ^(1/2) gets turned into ^(0), and then your standard deviation
goes from .06... to 1.  I.e., it seems like maybe the preparser
doesn't catch these nested loadings.

-M. Hampton

On Jun 15, 1:54 pm, Pogon  wrote:
> Hi,
> I'm not sure if it's a bug or it's me doing something wrong.
>
> I have two files:
>
> test1.sage containing nothing but
>print numpy.random.normal(0,(2*0.0061*0.33)^(1/2),1)
>
> and
>
> test2.sage containing
>load "test1.sage"
>
> I import numpy
> sage: import numpy
>
> Now
> sage: load "test1.sage"
> returns values always smaller than 1
> thats the right distribution, the same i get when using the notebook-
> interface
>
> but
> sage: load "test2.sage"
> very often returns values bigger than 1,
> thats a whole different distribution
>
> My system is ubuntu-9.04-amd64 on Pentium Dual Core
> sage-4.0.1 from 2009-06-06
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[sage-devel] Re: Sage 4.0.2.rc0 released

[Marshall Hampton]

I only got the known singular.pyx and and number_field_element.pyx
failures on an intel mac running 10.4.11.

-M. Hampton

On Jun 15, 1:13 am, Nick Alexander  wrote:
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
>  http://sage.math.washington.edu/home/ncalexan/releases
>
> We merged all of the tickets with positive review on trac (save one
> that depended on a still-unreviewed ticket), and updated to the
> current upstream for seven spkgs. You're probably wondering why this
> is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
> pretty soon, and we've already merged all the code we could from trac,
> so we're cutting it off here. In addition, William is giving a talk at
> MEGA on Thursday, and it would be nice to have a fresh new release for
> that. So please build and test soon, and we'll get this tested and
> released.
>
> == Notable new features ==
>
> * Updated to current upstream of Singular, MPIR, FLINT, numpy, scipy,
> m4ri, and pynac
> * sage -br calls gcc in parallel when MAKE is set
> * New script for automatically downloading and testing patches from a
> trac ticket -- this was used to create this release, but will be
> packaged with rc1
>
> == Known issues ==
>
> * There's a doctest failure with Singular on 32-bit machines, where
> Singular seems to be choosing different representatives for the
> integers mod 2^32 on 32 and 64 bit architectures. Martin Albrecht will
> hopefully chime in on the "right" fix for this.
> * The new scipy will have doctest failures with gfortran, but works
> fine with g95. In particular, we patch scipy.optimize.optimize for
> g95, but not gfortran -- and the unpatched version has unusual
> behavior for find_maximum_on_interval (which calls
> scipy.optimize.optimize.fminbound).
>
> == List of closed tickets ==
>
> This will come with the release email for the next rc; if you want to
> see it right away, it's here:
>
>  http://trac.sagemath.org/sage_trac/query?status=closed&group=resoluti...
>
> Thanks,
> -Craig and Nick
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[sage-devel] Re: complex_plot and fractals

[Tom Boothby]

The error isn't in your code, I've duplicated this with much simpler code.

{{{
%cython
from sage.rings.all import CC
def foo(z):
return CC(z)
}}}

{{{
complex_plot(foo,(0,1),(0,1))
///
Traceback (click to the left for traceback)
...
TypeError: a float is required
}}}

{{{
complex_plot(lambda z: foo(z),(0,1),(0,1))
///
[pretty picture]
}}}



On Mon, Jun 15, 2009 at 12:09 PM, Jason
Grout wrote:
>
> I just tried to implement a quick, fast mandelbrot set plot.  I posted
> my results (with the puzzling error) here: http://sagenb.org/home/pub/578/
>
> The error that I get is that when passing a Cython-created CC number to
> complex_plot, I get an error "float required"---something about the
> fast_float stuff.  However, when I wrap that in a Python function which
> merely returns the exact same thing, there is no error.
>
> Can someone look at the worksheet and see offhand what the problem is?
> Is it an error in my code, in fast_float, complex_plot, or something else?
>
> Thanks,
>
> Jason
>
>
> >
>

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[sage-devel] Re: Google wants to make Python 5x faster

[bsdz]

On 15 June, 17:48, javier  wrote:
> This looks like good news for sage:
>
> http://code.google.com/p/unladen-swallow/wiki/ProjectPlan

The idea of rewriting of Python's VM to use LLVM is a similar goal to
that of Parrot's VM (http://www.parrot.org/). What makes it more
interesting is that they plan to port the existing Python 2.6 code
base instead writing a new Python interpreter like we are in the Pynie
project (http://code.google.com/p/pynie/).

Looks very interesting. I hope it pans out :)
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[sage-devel] Re: Strange behaviour with loading files and numpy

[Pogon]

yes, you're right, just tested it, works when replacing 1/2 by .5

so, will this get fixed?

maybe someone with more dev-knowledge could trac a bug ...

On Jun 15, 11:18 pm, Marshall Hampton  wrote:
> I'm not sure what is happening but I would guess that at some point
> the ^(1/2) gets turned into ^(0), and then your standard deviation
> goes from .06... to 1.  I.e., it seems like maybe the preparser
> doesn't catch these nested loadings.
>
> -M. Hampton
>
> On Jun 15, 1:54 pm, Pogon  wrote:
>
> > Hi,
> > I'm not sure if it's a bug or it's me doing something wrong.
>
> > I have two files:
>
> > test1.sage containing nothing but
> >    print numpy.random.normal(0,(2*0.0061*0.33)^(1/2),1)
>
> > and
>
> > test2.sage containing
> >    load "test1.sage"
>
> > I import numpy
> > sage: import numpy
>
> > Now
> > sage: load "test1.sage"
> > returns values always smaller than 1
> > thats the right distribution, the same i get when using the notebook-
> > interface
>
> > but
> > sage: load "test2.sage"
> > very often returns values bigger than 1,
> > thats a whole different distribution
>
> > My system is ubuntu-9.04-amd64 on Pentium Dual Core
> > sage-4.0.1 from 2009-06-06
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[sage-devel] Re: Tutorial topics for SciPy'09 Conference

[Fernando Perez]

On Mon, Jun 15, 2009 at 6:24 AM, Jason Grout wrote:
>
> Fernando Perez wrote:
>> Hi all,
>>
>> In order to proceed with contacting speakers, we'd now like to get
>> some feedback from you.  This Doodle poll should take no more than a
>
>
> Does "you" mean "people attending scipy09", or does it mean "sage
> developers, whether or not you are attending scipy09"?

Any feedback is welcome, though it seems to make more sense if you're
coming to the conference, since the poll is about picking topics for
the tutorials sessions. But ideas, feedback, suggestions are in
general welcome either via the poll or via list or private email.

Since Sage is listed as a candidate topic, votes on a Sage tutorial
with comments on specific ideas that someone would be willing to
present would be very welcome.  In the end, the actual choices of
topics will be determined by what we can get speakers to present, so
that kind of information is obviously very relevant.

Cheers,

f

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[sage-devel] Re: Is 4.0.2 closed yet?

[William Stein]

On Mon, Jun 15, 2009 at 9:33 PM, John Cremona wrote:
>
> Does the release of an rc0 mean that 4.0.2 is closed to new patches?

Yes, I think it does.  But don't worry 4.0.3 is only moments away :-).

William

>
> I have one at #4290 (new feature, but not too important), a bug fix at
> #5307 (Tate's algorithm over number fields) and a post-review mini
> patch at #6273 waiting for a mini review
>
> John
>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Feature Request: element-wise multiplication of matrices

[William Stein]

On Mon, Jun 15, 2009 at 8:39 PM, Jason Grout wrote:
>
> William Stein wrote:
>> On Mon, Jun 15, 2009 at 7:34 PM, Jason Grout 
>> wrote:
>>> Bill Hart wrote:
 Can I ask what applications this "Hadamard product" has?
>>
>> I've never used it, but I guess it must be really really important in
>> numerical computation, since most shockingly it is the *default* for
>> A*B in numpy!!
>>
>> sage: import numpy
>> sage: a = numpy.array([[1,2],[3,4]])
>> sage: a*a
>> array([[1, 4],
>>        [9, 16]], dtype=object)
>
>
> It's just default because you aren't using the numpy "matrix" class,
> just the "array" class.

I know.

> "In NumPy the basic type is a multidimensional array. Operations on
> these arrays in all dimensionalities including 2D are elementwise
> operations. However, there is a special matrix type for doing linear
> algebra, which is just a subclass of the array class. Operations on
> matrix-class arrays are linear algebra operations."

This is orthogonal to the above, but maybe I took too many courses on
object oriented design back when I was a CS undergrad in the early
90's, but subclasses in an object oriented-system should satisfy an
"isa" relationship.  Subclassing and changing the semantics of *
violates that.   Here, "isa" would mean that "any matrix is an array
with extra structure".   Of course there is an exception to every
rule, and consistency is the hobgoblin of little minds, etc. :-)

 -- William

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[sage-devel] Can Trac 6266 get a positive review now?

[Dr. David Kirkby]

This was my first patch

http://trac.sagemath.org/sage_trac/ticket/6266

so things did not go quite to plan. The basic code works, but 'ddrake' 
commented I'd put too many stars in the SPGK.txt, as they were supposed 
to be a for list. He changed the sPKG.txt file, made a package. My code 
worked for him, and I've just tried the package he made with the revised 
SPKG.txt, and it works for me too.

So can it be changed?


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[sage-devel] Re: Sage 4.0.2.rc0 released

[John H Palmieri]

On Jun 15, 12:13 am, Nick Alexander  wrote:
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:

The following response to this release announcement was autogenerated
by the Sage docbot:

"Someone didn't format their reST correctly, so building the reference
manual now produces warnings/errors."



Actually, there is no docbot and this wasn't autogenerated, but it
should be. Well, actually, it would be nice if there were a docbot,
but it shouldn't have to send such messages because we should be
taking care of it before it gets to this stage: people should be
checking that the reference manual builds correctly before submitting
their patches, and then also before submitting positive reviews for
someone else's patches.

For this release, I get these warnings:

WARNING: /Applications/sage_builds/sage-4.0.2.rc0-upgrade/devel/sage-
new/doc/en/reference/coercion.rst:242: (WARNING/2) Explicit markup
ends without a blank line; unexpected unindent.
WARNING: /Applications/sage/local/lib/python2.5/site-packages/sage/
coding/code_constructions.py:docstring of
sage.coding.code_constructions.ToricCode:60: (ERROR/3) Unexpected
indentation.
WARNING: /Applications/sage/local/lib/python2.5/site-packages/sage/
coding/linear_code.py:docstring of sage.coding.linear_code.wtdist_gap:
8: (WARNING/2) Bullet list ends without a blank line; unexpected
unindent.
WARNING: /Applications/sage_builds/sage-4.0.2.rc0-upgrade/devel/sage-
new/doc/en/reference/sage/misc/misc.rst:6: (WARNING/2) autodoc can't
import/find class 'sage.misc.misc.MainClass.NestedClass', it reported
error: "No module named MainClass", please check your spelling and
sys.path
WARNING: /Applications/sage_builds/sage-4.0.2.rc0-upgrade/devel/sage-
new/doc/en/reference/sage/misc/misc.rst:6: (WARNING/2) autodoc can't
import/find class
'sage.misc.misc.MainClass.NestedClass.NestedSubClass', it reported
error: "No module named MainClass.NestedClass", please check your
spelling and sys.path
WARNING: /Applications/sage/local/lib/python2.5/site-packages/sage/
rings/number_field/number_field_element.so:docstring of
sage.rings.number_field.number_field_element.NumberFieldElement.abs:1:
(WARNING/2) Inline interpreted text or phrase reference start-string
without end-string.
WARNING: /Applications/sage_builds/sage-4.0.2.rc0-upgrade/devel/sage-
new/doc/en/reference/sage/rings/polynomial/symmetric_ideal.rst:52:
duplicate citation AB2007, other instance in /Applications/sage_builds/
sage-4.0.2.rc0-upgrade/devel/sage-new/doc/en/reference/sage/rings/
polynomial/symmetric_reduction.rst
WARNING: /Applications/sage_builds/sage-4.0.2.rc0-upgrade/devel/sage-
new/doc/en/reference/sage/rings/polynomial/symmetric_reduction.rst:23:
duplicate citation AB2007, other instance in /Applications/sage_builds/
sage-4.0.2.rc0-upgrade/devel/sage-new/doc/en/reference/sage/rings/
polynomial/symmetric_ideal.rst

  John

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Kiran Kedlaya]

All tests pass under 64-bit Fedora 10.

Kiran

On Jun 15, 3:13 am, Nick Alexander  wrote:
> Hi all,
>
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
>  http://sage.math.washington.edu/home/ncalexan/releases
>
> We merged all of the tickets with positive review on trac (save one
> that depended on a still-unreviewed ticket), and updated to the
> current upstream for seven spkgs. You're probably wondering why this
> is rc0 instead of alpha0 -- we'd like to get 4.0.2 pushed out the door
> pretty soon, and we've already merged all the code we could from trac,
> so we're cutting it off here. In addition, William is giving a talk at
> MEGA on Thursday, and it would be nice to have a fresh new release for
> that. So please build and test soon, and we'll get this tested and
> released.
>
> == Notable new features ==
>
> * Updated to current upstream of Singular, MPIR, FLINT, numpy, scipy,
> m4ri, and pynac
> * sage -br calls gcc in parallel when MAKE is set
> * New script for automatically downloading and testing patches from a
> trac ticket -- this was used to create this release, but will be
> packaged with rc1
>
> == Known issues ==
>
> * There's a doctest failure with Singular on 32-bit machines, where
> Singular seems to be choosing different representatives for the
> integers mod 2^32 on 32 and 64 bit architectures. Martin Albrecht will
> hopefully chime in on the "right" fix for this.
> * The new scipy will have doctest failures with gfortran, but works
> fine with g95. In particular, we patch scipy.optimize.optimize for
> g95, but not gfortran -- and the unpatched version has unusual
> behavior for find_maximum_on_interval (which calls
> scipy.optimize.optimize.fminbound).
>
> == List of closed tickets ==
>
> This will come with the release email for the next rc; if you want to
> see it right away, it's here:
>
>  http://trac.sagemath.org/sage_trac/query?status=closed&group=resoluti...
>
> Thanks,
> -Craig and Nick
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[sage-devel] Re: Strange behaviour with loading files and numpy

[William Stein]

On Tue, Jun 16, 2009 at 12:24 AM, Pogon wrote:
>
> yes, you're right, just tested it, works when replacing 1/2 by .5
>
> so, will this get fixed?

This is now

   http://trac.sagemath.org/sage_trac/ticket/6305

William

>
> maybe someone with more dev-knowledge could trac a bug ...
>
> On Jun 15, 11:18 pm, Marshall Hampton  wrote:
>> I'm not sure what is happening but I would guess that at some point
>> the ^(1/2) gets turned into ^(0), and then your standard deviation
>> goes from .06... to 1.  I.e., it seems like maybe the preparser
>> doesn't catch these nested loadings.
>>
>> -M. Hampton
>>
>> On Jun 15, 1:54 pm, Pogon  wrote:
>>
>> > Hi,
>> > I'm not sure if it's a bug or it's me doing something wrong.
>>
>> > I have two files:
>>
>> > test1.sage containing nothing but
>> >    print numpy.random.normal(0,(2*0.0061*0.33)^(1/2),1)
>>
>> > and
>>
>> > test2.sage containing
>> >    load "test1.sage"
>>
>> > I import numpy
>> > sage: import numpy
>>
>> > Now
>> > sage: load "test1.sage"
>> > returns values always smaller than 1
>> > thats the right distribution, the same i get when using the notebook-
>> > interface
>>
>> > but
>> > sage: load "test2.sage"
>> > very often returns values bigger than 1,
>> > thats a whole different distribution
>>
>> > My system is ubuntu-9.04-amd64 on Pentium Dual Core
>> > sage-4.0.1 from 2009-06-06
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Can Trac 6266 get a positive review now?

[William Stein]

On Tue, Jun 16, 2009 at 1:17 AM, Dr. David
Kirkby wrote:
>
> This was my first patch
>
> http://trac.sagemath.org/sage_trac/ticket/6266
>
> so things did not go quite to plan. The basic code works, but 'ddrake'
> commented I'd put too many stars in the SPGK.txt, as they were supposed
> to be a for list. He changed the sPKG.txt file, made a package. My code
> worked for him, and I've just tried the package he made with the revised
> SPKG.txt, and it works for me too.
>
> So can it be changed?

yep, done, and merged.

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[sage-devel] Re: Can Trac 6266 get a positive review now?

[Dan Drake]

On Tue, 16 Jun 2009 at 12:17AM +0100, Dr. David Kirkby wrote:
> This was my first patch
> 
> http://trac.sagemath.org/sage_trac/ticket/6266
> 
> so things did not go quite to plan. The basic code works, but 'ddrake'
> commented I'd put too many stars in the SPGK.txt, as they were
> supposed to be a for list. He changed the sPKG.txt file, made a
> package. My code worked for him, and I've just tried the package he
> made with the revised SPKG.txt, and it works for me too.
> 
> So can it be changed?

Yep. I'll update the ticket in a moment.

Dan

-- 
---  Dan Drake 
-  KAIST Department of Mathematical Sciences
---  http://mathsci.kaist.ac.kr/~drake


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Description: Digital signature

[sage-devel] sage-4.0.2.rc1

[William Stein]

Hi,

I've created sage-4.0.2.rc1 which is here:

  
http://sage.math.washington.edu/home/wstein/release/4.0.2/rc1/sage-4.0.2.rc1/dist/sage-4.0.2.rc1.tar

You can upgrade by doing

 sage -upgrade 
http://sage.math.washington.edu/home/wstein/release/4.0.2/rc1/sage-4.0.2.rc1/

The todo list to finish this release:

   1. Build test everywhere, and ensure that Sage builds automatically
and passes all tests on all supported platforms.

   2. See if "#6240 -- singular interface failure on itanium" is still
around on itanium after the singular upgrade

   3. Fix "#6303 [with patch, needs work] sage-4.0.2.rc0 test
failure" (Cremona's patch broke other things).

See http://trac.sagemath.org/sage_trac/milestone/sage-4.0.2 which
lists only 3 open tickets for 4.0.2.  All other tickets are targeted
for 4.0.3 (or later).

1 above is difficult and very very important -- it hasn't happened
since Sage-3.4.2.  Please report any build or testing failures, no
matter how small.

Note that there *should* still be the failure related to #6303 on some
platforms.

 - William

-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Nick Alexander]

On 15-Jun-09, at 4:22 PM, John H Palmieri wrote:

>
> On Jun 15, 12:13 am, Nick Alexander  wrote:
>> Hi all,
>>
>> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
> The following response to this release announcement was autogenerated
> by the Sage docbot:
>
> "Someone didn't format their reST correctly, so building the reference
> manual now produces warnings/errors."

Has the reference manual ever built correctly?  (I always get tons of  
noise and tons of warnings.)  I didn't enforce a clean manual when I  
was release manager because we didn't appear to start with a clean  
manual.

I would like to see this eventually be a requirement, but not yet:  
building the docs is just too slow to make it part of my workflow.   
Why is it that hg can scan a directory for changes instantly, but this  
doc system takes minutes?

Nick

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[sage-devel] Re: Sage 4.0.2.rc0 released

[Kevin Horton]

Nick Alexander wrote:
> Hi all,
> 
> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
> 

On Ubuntu 9.04 on an EeePC 901 with Atom N270:

The following tests failed:

sage -t -long "devel/sage/sage/modules/free_module.py"
sage -t -long 
"devel/sage/sage/rings/number_field/number_field_element.pyx"
sage -t -long "devel/sage/sage/libs/singular/singular.pyx"
Total time for all tests: 19358.9 seconds

Two of the test failures were identical to those reported on other systems.  I 
don't think the following one has been reported yet:

sage -t -long "devel/sage/sage/modules/free_module.py"  
**
File "/home/kwh/apps/sage-4.0.2.rc0/devel/sage/sage/modules/free_module.py", 
line 2505:
sage: W = M.submodule([x*B[0], 2*B[1]- x*B[2]]); W
Exception raised:
Traceback (most recent call last):
  File "/home/kwh/apps/sage-4.0.2.rc0/local/bin/ncadoctest.py", line 1231, 
in run_one_test
self.run_one_example(test, example, filename, compileflags)
  File "/home/kwh/apps/sage-4.0.2.rc0/local/bin/sagedoctest.py", line 38, 
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, 
compileflags)
  File "/home/kwh/apps/sage-4.0.2.rc0/local/bin/ncadoctest.py", line 1172, 
in run_one_example
compileflags, 1) in test.globs
  File "", line 1, in 
W = M.submodule([x*B[Integer(0)], Integer(2)*B[Integer(1)]- 
x*B[Integer(2)]]); W###line 2505:
sage: W = M.submodule([x*B[0], 2*B[1]- x*B[2]]); W
  File 
"/home/kwh/apps/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/modules/free_module.py",
 line 2517, in submodule
V = self.span(gens, check=check, 
already_echelonized=already_echelonized)
  File 
"/home/kwh/apps/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/modules/free_module.py",
 line 2433, in span
self.ambient_module(), gens, check=check, 
already_echelonized=already_echelonized)
  File 
"/home/kwh/apps/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/modules/free_module.py",
 line 5378, in __init__
echelonize=True, already_echelonized=already_echelonized)
  File 
"/home/kwh/apps/sage-4.0.2.rc0/local/lib/python2.5/site-packages/sage/modules/free_module.py",
 line 4483, in __init__
basis = self._echelonized_basis(ambient, basis)
--
File "/home/kwh/apps/sage-4.0.2.rc0/devel/sage/sage/modules/free_module.py", 
line 2510:
sage: W.ambient_module()
Expected:
Ambient free module of rank 3 over the principal ideal domain Univariate 
Polynomial Ring in x over Rational Field
Got:
Ambient free module of rank 3 over the principal ideal domain Integer Ring
**

--
Kevin Horton

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[sage-devel] Re: Can Trac 6266 get a positive review now?

[Dr. David Kirkby]

Dan Drake wrote:
> On Tue, 16 Jun 2009 at 12:17AM +0100, Dr. David Kirkby wrote:
>> This was my first patch
>>
>> http://trac.sagemath.org/sage_trac/ticket/6266
>>
>> so things did not go quite to plan. The basic code works, but 'ddrake'
>> commented I'd put too many stars in the SPGK.txt, as they were
>> supposed to be a for list. He changed the sPKG.txt file, made a
>> package. My code worked for him, and I've just tried the package he
>> made with the revised SPKG.txt, and it works for me too.
>>
>> So can it be changed?
> 
> Yep. I'll update the ticket in a moment.
> 
> Dan
> 
William beat you by a few minutes!

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[sage-devel] Re: Sage 4.0.2.rc0 released

[John H Palmieri]

On Jun 15, 5:15 pm, Nick Alexander  wrote:
> On 15-Jun-09, at 4:22 PM, John H Palmieri wrote:
>
>
>
> > On Jun 15, 12:13 am, Nick Alexander  wrote:
> >> Hi all,
>
> >> Here's Sage 4.0.2.rc0. Come and get it while it's hot:
>
> > The following response to this release announcement was autogenerated
> > by the Sage docbot:
>
> > "Someone didn't format their reST correctly, so building the reference
> > manual now produces warnings/errors."
>
> Has the reference manual ever built correctly?  (I always get tons of  
> noise and tons of warnings.)  I didn't enforce a clean manual when I  
> was release manager because we didn't appear to start with a clean  
> manual.

For a few releases now, the only warnings have been about the favicon
and the "duplicate citation AB2007".  At , I've posted a patch which deals with all of
these except the favicon issue (already a patch for this at #5799) and
the problem with misc/misc.py, which I can't figure out.

> I would like to see this eventually be a requirement, but not yet:  
> building the docs is just too slow to make it part of my workflow.  
> Why is it that hg can scan a directory for changes instantly, but this  
> doc system takes minutes?

See #6187, although I don't know if anyone has any ideas for how to
fix this.

  John

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[sage-devel] Re: sage-4.0.2.rc1

[Rob Beezer]

64-bit Ubuntu 8.10 on Intel Core Duo

All tests passed as upgrade from 4.0.2.rc0

Builds from source for both 4.0.2.rc0 and 4.0.2.rc1 yield as a final
message the curious:

The following tests failed:
sage -t  devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py
# 0 doctests failed

The log doesn't offer any more clues about this.  These both resulted
from a "make ptest"

Rob

On Jun 15, 5:13 pm, William Stein  wrote:
> Hi,
>
> I've created sage-4.0.2.rc1 which is here:
>
>  http://sage.math.washington.edu/home/wstein/release/4.0.2/rc1/sage-4
>
> You can upgrade by doing
>
>  sage 
> -upgradehttp://sage.math.washington.edu/home/wstein/release/4.0.2/rc1/sage-4
>
> The todo list to finish this release:
>
>    1. Build test everywhere, and ensure that Sage builds automatically
> and passes all tests on all supported platforms.
>
>    2. See if "#6240 -- singular interface failure on itanium" is still
> around on itanium after the singular upgrade
>
>    3. Fix "#6303    [with patch, needs work] sage-4.0.2.rc0 test
> failure" (Cremona's patch broke other things).
>
> Seehttp://trac.sagemath.org/sage_trac/milestone/sage-4.0.2which
> lists only 3 open tickets for 4.0.2.  All other tickets are targeted
> for 4.0.3 (or later).
>
> 1 above is difficult and very very important -- it hasn't happened
> since Sage-3.4.2.  Please report any build or testing failures, no
> matter how small.
>
> Note that there *should* still be the failure related to #6303 on some
> platforms.
>
>  - William
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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[sage-devel] Re: Strange behaviour with loading files and numpy

[Rado]

A simple fix by moving out the code that does the literals (the part
that changes 1/2 to Integer(1)/Integer(2)) into a separate function
and made sure its called at each load.

I used my shiny new trac account to add the patch to the Trac.

Rado

On Jun 15, 6:53 pm, William Stein  wrote:
> On Tue, Jun 16, 2009 at 12:24 AM, Pogon wrote:
>
> > yes, you're right, just tested it, works when replacing 1/2 by .5
>
> > so, will this get fixed?
>
> This is now
>
>    http://trac.sagemath.org/sage_trac/ticket/6305
>
> William
>
>
>
>
>
> > maybe someone with more dev-knowledge could trac a bug ...
>
> > On Jun 15, 11:18 pm, Marshall Hampton  wrote:
> >> I'm not sure what is happening but I would guess that at some point
> >> the ^(1/2) gets turned into ^(0), and then your standard deviation
> >> goes from .06... to 1.  I.e., it seems like maybe the preparser
> >> doesn't catch these nested loadings.
>
> >> -M. Hampton
>
> >> On Jun 15, 1:54 pm, Pogon  wrote:
>
> >> > Hi,
> >> > I'm not sure if it's a bug or it's me doing something wrong.
>
> >> > I have two files:
>
> >> > test1.sage containing nothing but
> >> >    print numpy.random.normal(0,(2*0.0061*0.33)^(1/2),1)
>
> >> > and
>
> >> > test2.sage containing
> >> >    load "test1.sage"
>
> >> > I import numpy
> >> > sage: import numpy
>
> >> > Now
> >> > sage: load "test1.sage"
> >> > returns values always smaller than 1
> >> > thats the right distribution, the same i get when using the notebook-
> >> > interface
>
> >> > but
> >> > sage: load "test2.sage"
> >> > very often returns values bigger than 1,
> >> > thats a whole different distribution
>
> >> > My system is ubuntu-9.04-amd64 on Pentium Dual Core
> >> > sage-4.0.1 from 2009-06-06
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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[sage-devel] Re: Sage 4.0.2.rc0 released

[Rob Beezer]

On Jun 15, 4:22 pm, John H Palmieri  wrote:
> people should be
> checking that the reference manual builds correctly before submitting
> their patches, and then also before submitting positive reviews for
> someone else's patches.

I agree 100% with John's comments on this, and he is right that there
were just three or so warnings on recent releases.

However, I have found the documentation on documentation a bit
scattered and perhaps like others, I have relied too much on just
looking at other's work for guidance, instead of carefully
understanding the nuances before using a feature of ReST, etc.

A few days ago I got halfway through a mock module, which was meant to
be a demonstration of the docstrings, with totally fictitious code,
and instruction about the docstrings contained in the docstrings
themselves.  Maybe I'll get back to that in the next few days.

Nick is right that rebuilding the docs is a pain.  But as has been
pointed out before, you can rebuild the HTML version once in a new
branch, then only changed files get rebuilt the next time.  So as a
habit, now when I build a new branch I automatically rebuild the
reference manual right away.  Then once I have some changes, it's
pretty easy to verify the effects.

The effect of

http://trac.sagemath.org/sage_trac/ticket/5653

is to show a *formatted* docstring in the notebook after using the ?
syntax to request it.  If this is being done "on-the-fly" shouldn't it
be possible to format a file-at-a-time like you might when testing
localized changes?

Rob


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[sage-devel] announcements, history, release notes

[Dan Drake]

I was looking through the "tasks" on the trac server, and noticed #6056:
the HISTORY.txt is now very outdated. Also, nothing has been sent to
sage-announce since February.

While searching around, I found that the release tours on the wiki
sometimes link to a nonexistent release note: in
http://wiki.sagemath.org/sage-3.4.2 the link to
http://www.sagemath.org/src/announce/sage-3.4.2.txt is broken. It looks
like the 3.4 series is missing in /src/announce. If someone (Harald?)
can put those release notes in, someone could very easily fix #6056 by
just copying and pasting the release notes into HISTORY.txt.

(Also, the file
http://www.sagemath.org/src/announce/OLD_VERSIONS_HERE.txt seems to
be incorrect, and there are some other files there which have the
distinct aroma of cruft...)

Dan

-- 
---  Dan Drake 
-  KAIST Department of Mathematical Sciences
---  http://mathsci.kaist.ac.kr/~drake


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[sage-devel] Re: Sage 4.0.2.rc0 released

[Nick Alexander]

> Nick is right that rebuilding the docs is a pain.  But as has been
> pointed out before, you can rebuild the HTML version once in a new
> branch, then only changed files get rebuilt the next time.

make ptestlong does not appear to benefit from this.  I get some  
rubbish about "configuration has changed" (why?) and then it grinds  
for a very long time, checking every file.

Nick

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