Re: [sage-combinat-devel] Re: tickets 10632 and 10485

2011-02-07 Thread Nicolas M. Thiery
On Sat, Feb 05, 2011 at 12:45:11PM -0800, Anne Schilling wrote:
 Besides, I don't remember looking at a crystal of with index
 set; but that might be just me.
 
 The edges are colored by i for i in I.

Oops, I fumbled my typing. It should have read: ``I don't remember
looking at the graph of a crystal with *large* index set''.

Cheers,
Nicolas
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http://Nicolas.Thiery.name/

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Re: [sage-combinat-devel] Re: tickets 10632 and 10485

2011-02-07 Thread Daniel Bump

After Nicolas' revised #10723 and Anne's two patches there is
one error after sage -t on doc/en/thematic_tutorials/lie/affine_crystals.rst.

File 
/home/bump/src/sage-4.6.2.alpha3/devel/sage-queue/doc/en/thematic_tutorials/lie/affine_crystals.rst,
 line 165:
sage: K.classical_decomposition()
Expected:
The crystal of tableaux of type ['B', 3] and shape(s) [[0.5, 0.5, 0.5]]

Got:
The tensor product of the crystals (The crystal of spins for type ['B', 3], 
The crystal of tableaux of type ['B', 3] and shape(s) [[]])

Aside: why is the expected result shape [[0.5, 0.5, 0.5]]? After all

sage: CrystalOfTableaux(B3,shape=[1/2,1/2,1/2])
The crystal of tableaux of type ['B', 3] and shape(s) [[1/2, 1/2, 1/2]]

Dan

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Re: [sage-combinat-devel] Re: tickets 10632 and 10485

2011-02-07 Thread Daniel Bump

There are some other failures after Anne's patch in 
sage_object.pyx.

I had a related query in this message from last September,
in connection with #7922. I think the answer is that the
release manager should rebuild the pickle jar, but I am
not certain of this.

Perhaps Nicolas can comment?

http://groups.google.com/group/sage-combinat-devel/msg/890e4e19fe5fc69e

After #10632

sage -t  -force_lib devel/sage/sage/structure/sage_object.pyx

Failed:
_class__sage_combinat_crystals_affine_AffineCrystalFromClassicalAndPromotion_with_category_element_class__.sobj
_class__sage_combinat_crystals_tensor_product_CrystalOfTableaux_with_category_element_class__.sobj
_class__sage_combinat_crystals_tensor_product_TensorProductOfCrystalsWithGenerators_with_category__.sobj
_class__sage_combinat_crystals_tensor_product_TensorProductOfCrystalsWithGenerators_with_category_element_class__.sobj
Successfully unpickled 582 objects.
Failed to unpickle 4 objects.

Dan

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Re: [sage-combinat-devel] Re: tickets 10632 and 10485

2011-02-07 Thread Anne Schilling

Do you have the latest version of #10632 since I changed this on Friday
and made the KR crystal use the new CrystalOfTableaux code instead of a
tensor product.


Oops, I had overlooked that there is a new version of #10632. With the current
versions of #10732, 10632 and 10485, the only failed tests are the ones
in sage_object.pyx that I mentioned in my other message.


Ok, it might be good if an expert could confirm that these errors have to
do with the pickle jar.


I tried to input things like shape = [(2*s+1)/2,...] in the KR code, but then
sage complained. I do not know why. So now I use shape = [s+0.5,...] and I 
suppose
this is why the output is with 0.5 instead of 1/2.


If you import QQ from sage.rings.all, then I think you can:

shapes = [ [i+QQ(1)/QQ(2) for i in sh]+[QQ(1)/QQ(2)]*(r-len(sh)) for sh in 
shapes ]


Thank you. This is now incorporated in the new updated patches.

Anne

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Re: [sage-combinat-devel] Re: tickets 10632 and 10485

2011-02-07 Thread Daniel Bump

Nicolas wrote:

 Yup, I guess we can safely update the pickle jar in that case
 also. But that's not the release manager's job :-) 

I was hoping it was.

   See the
 documentation of sage.structure.sage_object.unpickle_all for how to
 analyze this a bit further (using the debug option), and how to
 rebuild a pickle jar.  Note that only the broken pickles should be
 updated from the rebuilt pickle jar to the current one.

I have looked at that doc and I am still quite baffled
as to what to do. (And why.)

This bears on both #7922 and #10632.

Anyway, here's Arlo Guthrie singing I don't wanna pickle:

http://www.youtube.com/watch?v=g266Uwp6ZnI

Dan

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[sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?

2011-02-07 Thread RegB
I respectfully disagree with some of the comments about copy editors.
One doesn't need to be a mathematician or an entry level programmer
to recognize that the installation guide is;
a) one of the first documents that many SAGE users use.
b) in need of some edits, particularly with respect to the sequence of
operations.
A good, even fair, copy editor would recognize this and could produce
a much more usable guide with little more than copy/paste.
Even I am able to point to passages that need to be moved before other
passages, e.g. setting environment variables PROBABLY needs to be
moved
earlier.
.
{Just a non-programmer, non-mathematician's opinion}
PS Not a copy editor either (-:


On Jan 30, 10:13 am, Niles nil...@gmail.com wrote:
 Hello all,

 I'm glad we've had a chance to think about this, and I hope we keep
 thinking about it, but I hope we can also *take action!*  The current
 status is this:

  * The sage add on Meta Stackexchange exists -- go vote for it if you
 want to :)
    http://meta.stackoverflow.com/questions/74983/open-source-advertising...

 * The add points to a wiki page which aims to address programmers
 interested in contributing:
    http://wiki.sagemath.org/StackOverflowLanding

 * Now that we've thought about whether, and what kind, of programmers
 may or may not be useful, and what they may or may not be good at,
 what should appear on that page?  Currently it gives an organized list
 of links for learning about sage, and another about the development
 process.  What's missing, I think, is a list of suggestions, or
 specific ideas, which are interesting and appropriate.  Clearly we
 won't agree perfectly on this, but maybe there are some generally good
 ideas which can emerge anyway?

 thanks everyone!
 Niles

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[sage-devel] sage -b doesn't rerun Cython on quaternion_algebra_element.pyx

2011-02-07 Thread Jeroen Demeyer
This is a problem I discovered when upgrading from sage-4.5.3 to a
candidate 4.6.2.alpha4.  Probably, the problem has existed for a while,
it just surfaced or got noticed now.

The problem is that the file
sage/algebras/quatalg/quaternion_algebra_element.cpp
is *not* recreated from the corresponding .pyx file when upgrading.
This then causes a compile error.

The file
sage/algebras/quatalg/quaternion_algebra_element.pyx
includes (using Cython's include statement)
sage/ext/gmp.pxi
and the latter file was changed some Sage versions ago.


The following happens:
$ ./sage -b

--
sage: Building and installing modified Sage library files.


Installing c_lib
scons: `install' is up to date.
=== setup.py 
Updating Cython code
Time to execute 0 commands: 1.31130218506e-05 seconds
Finished compiling Cython code (time = 0.0120220184326 seconds)
running install
running build
running build_py
running build_ext
building 'sage.algebras.quatalg.quaternion_algebra_element' extension
building 'sage.calculus.riemann' extension
[...]
building 'sage.symbolic.pynac' extension
building 'sage.symbolic.ring' extension
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPIC
-I/mnt/usb1/scratch/jdemeyer/sage-4.5.3-4.6.2.alpha4/local/include/FLINT/ 
-I/mnt/usb1/scratch/jdemeyer/sage-4.5.3-4.6.2.alpha4/local/include
-I/mnt/usb1/scratch/jdemeyer/sage-4.5.3-4.6.2.alpha4/local/include/csage
-I/mnt/usb1/scratch/jdemeyer/sage-4.5.3-4.6.2.alpha4/devel/sage/sage/ext
-I/mnt/usb1/scratch/jdemeyer/sage-4.5.3-4.6.2.alpha4/local/include/python2.6
-c sage/algebras/quatalg/quaternion_algebra_element.cpp -o
build/temp.linux-x86_64-2.6/sage/algebras/quatalg/quaternion_algebra_element.o
-w
[trouble...]

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[sage-devel] Re: sage -b doesn't rerun Cython on quaternion_algebra_element.pyx

2011-02-07 Thread Volker Braun
Do you have a trac ticket number? The problem is 

is_cython_file = lambda f:fnmatch.fnmatch(f,'*.{pyx,pxd,pxi}')

in parse_deps() in setup.py:633. Python does currently not support 
curly-bracket matching:

sage: from glob import glob, fnmatch
sage: is_cython_file = lambda f:fnmatch.fnmatch(f,'*.{pyx,pxd,pxi}')
sage: is_cython_file('test.pyx')
False

Volker

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[sage-devel] Multidimensional root finding with GSL

2011-02-07 Thread Joris Vankerschaver
Dear all,

Has there been any effort so far in wrapping the root-finding routines
in GSL?  Or are there better alternatives for numerical root finding
of vector-valued functions in Sage?  All I could find is this mission
statement, but it doesn't look as if this was ever completed (I'd
love to be wrong):

http://wiki.sagemath.org/days4/projects/numerical

I wouldn't mind wrapping these beasts myself (using, say, the code in
sage/gsl/ode as a starting point), but I have no experience with
Cython so it will take some time...

All the best,
Joris

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Re: [sage-devel] Re: Sage does (did?) build with an arm processor, but the tests don't pass

2011-02-07 Thread Peter Jeremy
On 2011-Feb-06 11:13:57 +0100, Burcin Erocal bur...@erocal.org wrote:
I am not sure what the speed of the cephes implementation is compared
to that of the C library though. The float evaluations are used for
plotting, so any slow down in the numerical approximation of these
functions will degrade plotting performance significantly.

Note that cephes is used to implement functions that aren't available
in the base system libraries and an implementation that exists is
going to produce better results than one that doesn't.

As for speed, if that's a concern, I suggest you try some benchmarks.
But note that correctly handling all the exceptional conditions
available in IEEE754 and providing accuracy to 1 ULP or so can mean
the code is slower than a sloppy implementation - and I'm aware
that some libm implementations have some quite sloppy code.  Whilst
plotting probably doesn't require much precision in most cases, other
uses of libm functions do expect precise results.

On another note, if Cephes is only included for the evaluation of these
few functions, I am not convinced it should be shipped in the standard
distribution. There are quite a few libraries already in Sage, which
have this capability. For example, can't we just use GSL to evaluate
gamma on Cygwin?

One issue is that Sage expects that the gamma() family exists in libm,
similarly with the other libm functions.  If they are implemented
elsewhere, this is likely to require changes to header includes and
linking for some libraries.  There's the associated problem of
identifying the functions that are either missing or inadequately
implemented in the host libm and locating alternative implementations
within Sage.

It's also worth noting that this is the 3rd platform where cephes is
needed - it was initially introduced as part of Cygwin support.  I've
found it necessary for the FreeBSD port and now it seems necessary for
the ARM port.  If you want to start de-bloating Sage, there are lots
of other low-hanging fruit.

Note that since FreeBSD is gradulally implementing the missing parts
of libm, the functions that are needed from cephes (or equivalent)
changes between FreeBSD versions.  #9543 therefore includes scripts to
only select those parts of cephes that are missing from the base OS.
It also provides some include and linker trickery to make the split of
functions between two libm.so files transparent to consumer apps.

-- 
Peter Jeremy


pgpHFCeDV9fcG.pgp
Description: PGP signature


Re: [sage-devel] Re: sage -b doesn't rerun Cython on quaternion_algebra_element.pyx

2011-02-07 Thread Jeroen Demeyer
On 2011-02-07 17:52, Volker Braun wrote:
 Do you have a trac ticket number?

Now yes: #10751

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[sage-devel] test Flask-based notebook

2011-02-07 Thread Jason Grout
We need people to test the new flask-based notebook that was done at the 
January Sage Days in Seattle (I believe mainly by Mike Hansen, Rado 
Kirov, and Dan Drake).  The latest repository of code and instructions 
for installing it are here:


https://code.google.com/r/rkirov-flask/

Please try downloading and testing it.  Try lots of things in it. 
Hammer it as hard as you can.  And report back about any failures or 
problems you see.


This rewrite of the twisted.py parts of the notebook is the first step 
in a notebook rewrite.  It makes the code *way* simpler to understand 
and maintain.


It would also be very interesting to see if this code is more scalable 
than the current notebook.  For example, I wonder if running this 
flask-based notebook on top of, say, nginx using uwsgi, would scale 
better?  It would also be interesting to see if changing our polling 
strategy to long-polling would help (I don't think we long-poll 
currently, do we? See http://en.wikipedia.org/wiki/Push_technology for a 
definition of long-polling).


Of course, back up your worksheets before doing this, or start the 
notebook with a different notebook directory.


Thanks,

Jason

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Re: [sage-devel] test Flask-based notebook

2011-02-07 Thread didier deshommes
On Mon, Feb 7, 2011 at 3:27 PM, Jason Grout jason-s...@creativetrax.com wrote:
 It would also be very interesting to see if this code is more scalable than
 the current notebook.  For example, I wonder if running this flask-based
 notebook on top of, say, nginx using uwsgi, would scale better?  It would
 also be interesting to see if changing our polling strategy to long-polling
 would help (I don't think we long-poll currently, do we? See
 http://en.wikipedia.org/wiki/Push_technology for a definition of
 long-polling).

Keep in mind that if you are using long-polling techniques you cannot
use servers that adhere to the  WSGI standard, since it's not part of
it. uwsgi has some experimental support for asynchronous operations
but you must know what you're doing:
http://projects.unbit.it/uwsgi/wiki/AsyncSupport .

didier


 Of course, back up your worksheets before doing this, or start the notebook
 with a different notebook directory.

 Thanks,

 Jason

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Re: [sage-devel] Re: FAQ suggestion: I'm a programmer, how can I contribute to Sage?

2011-02-07 Thread David Kirkby
On 2 February 2011 20:44, Robert Bradshaw rober...@math.washington.edu wrote:
 On Wed, Feb 2, 2011 at 7:33 AM, David Kirkby david.kir...@onetel.net wrote:

 Do you believe it would be easier to attract funding if those
 considering funding a project could see a set of goals and plans? Or
 do you think people/companies considering funding software projects
 would not care if a project had a plan?

 Most grant proposals and other requests for funding have very specific
 plans, people, timelines, etc. attached to them.

I realise that.  However, it's also highly likely the individuals
reviewing the grant applications would look on the Sage web site.

 In light of your (and
 other people's) concerns, I think it would be very good if there were
 a more central location to see this, what people were working on, and
 status reports.

I would add to that

1) What the goals are, even if there is nobody working on them. Two
obvious advantages to having this would be:
 * It could attract a student to work on a project, if he/she knows it
is a goal, but nobody is working on it.
 * It could attract a commercial company to sponsor a particular piece
of work if they realised one of Sage's goals would be beneficial to
them.

2) Archive the status reports - move them from a Wiki to a read-only
section of the web site. Just like the FreeBSD does.


http://www.freebsd.org/news/status/report-2009-04-2009-09.html
http://www.freebsd.org/news/status/report-2008-10-2008-12.html
http://www.freebsd.org/news/status/report-2008-07-2008-09.html

This would help get more realistic estimates of time for different
tasks. Predicting times for software development is notoriously very
difficult, even when people are paid to do the work. But making
predictions based on the times to do similar work is one of the
standard methods. It's not perfect, but is one of the better ways.

With expereice of porting Sage to Solaris, I'd have a much better idea
of the times to port to AIX or HP-UX.

 I may have come across as portraying sage development
 as too individualistic--much work is done by individuals, but the
 level of a single grant with one or more PIs, their collaborators,
 students, etc. with clear-cut goals and timelines has provided a good
 level of organization that gets things done, but the funded grants
 tend to be of narrower focus than all of Sage.

Grants applications should have well defined goals - if not they would
never be funded.

 A steering committee might be a good idea, we have JSage which
 somewhat fulfills this role.

As a closed group, I think many of us would appreciate more openness,
for more people to have an input. But ultimately William started the
project, so he should have by far the most say of the goals. But I do
think we need a set of goals, and some plan how to achieve them.

 - Robert

Dave

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Re: [sage-devel] Re: Sage does (did?) build with an arm processor, but the tests don't pass

2011-02-07 Thread David Kirkby
On 6 February 2011 09:59, Dima Pasechnik dimp...@gmail.com wrote:
 Hi Burcin,
 indeed, here is another case of buggy libc/libm.
 The same workaround as for Cygwin should do the trick (provided that
 cephes works on ARM)
 Would installing cephes spkg break things on non-Cygwin, or this is
 safe?
 Dmitrii

IIRC Cephes is only installed on Cygwin and FreeBSD. If there was a
need for it on a particular CPU, I don't see why it could not be
installed on that CPU, whilst not doing so on x86, SPARC etc.

Dave

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[sage-devel] #10741 - needs review

2011-02-07 Thread Justin C. Walker
Hi, all,

I'm looking for a kind soul to check the fix for #10741, which deals with 
left/right matrix actions on binary quadratic forms (in BinaryQF).  The code, 
as it is now, does not produce an associative action, i.e.,
  Q.matrix_action_right(M).matrix_action_right(N) !=
Q.matrix_action_right(M*N)
and similarly for the left action.

The fix is simple (just swap the choice of matrix elements used in each case: 
columns for right action, rows for left).

I'm willing to condone a modest level of bribery :-}

Justin

--
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Director
Institute for the Enhancement of the Director's income
---
--
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it doesn't work out that way.
  - Casey Stengel
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Re: [sage-devel] test Flask-based notebook

2011-02-07 Thread David Kirkby
On 7 February 2011 21:27, Jason Grout jason-s...@creativetrax.com wrote:
 We need people to test the new flask-based notebook that was done at the
 January Sage Days in Seattle (I believe mainly by Mike Hansen, Rado Kirov,
 and Dan Drake).  The latest repository of code and instructions for
 installing it are here:

 https://code.google.com/r/rkirov-flask/

 Please try downloading and testing it.  Try lots of things in it. Hammer it
 as hard as you can.  And report back about any failures or problems you see.

 This rewrite of the twisted.py parts of the notebook is the first step in a
 notebook rewrite.  It makes the code *way* simpler to understand and
 maintain.

 It would also be very interesting to see if this code is more scalable than
 the current notebook.  For example, I wonder if running this flask-based
 notebook on top of, say, nginx using uwsgi, would scale better?

 Jason

We could do a lot worst than ask on an Apache list, asking for advice
about how to make a scalable server. Or reading the Apache
documentation might give us some ideas.

Dave

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[sage-devel] Re: test Flask-based notebook

2011-02-07 Thread Jason Grout

On 2/7/11 4:36 PM, David Kirkby wrote:


We could do a lot worst than ask on an Apache list, asking for advice
about how to make a scalable server. Or reading the Apache
documentation might give us some ideas.


Yep.  Another idea (that has also been suggested a lot before) is to 
write an app that hammers the server or use one of the many existing web 
application stress-testing systems to actually test the notebook and log 
things to see where the bottlenecks are.


Jason


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[sage-devel] Re: mackichan software is interested in integrating sage

2011-02-07 Thread Barry
I came across this thread while browsing the web, and I think I should
correct a mistaken opinion.

I feel my job as CEO is to keep track of what is happening in the
mathematical market place, to keep aware of possible competitors and
of possible opportunities. It is true that I am interested in how hard
it would be to integrate Sage into Scientific WorkPlace.

However, the assumption that this means we are disenchanted with
SciFace or MathSoft is incorrect. Our relationship with SciFace has
been outstanding now for about twelve years. They have always been
responsive and helpful to us. I also consider the SciFace employees to
be good friends. Our relationship with MathSoft is shorter, but it has
also been very good. They have been very friendly and cooperative, and
we have no complaints at all with them.

I understand that a short conversation on the floor of the AMS
exhibits is not likely to be highly nuanced, so this mistaken
impression is understandable. However it is not in fact true.

--Barry MacKichan

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[sage-devel] Re: test Flask-based notebook

2011-02-07 Thread Jason Grout

On 2/7/11 4:02 PM, didier deshommes wrote:

On Mon, Feb 7, 2011 at 3:27 PM, Jason Groutjason-s...@creativetrax.com  wrote:

It would also be very interesting to see if this code is more scalable than
the current notebook.  For example, I wonder if running this flask-based
notebook on top of, say, nginx using uwsgi, would scale better?  It would
also be interesting to see if changing our polling strategy to long-polling
would help (I don't think we long-poll currently, do we? See
http://en.wikipedia.org/wiki/Push_technology for a definition of
long-polling).


Keep in mind that if you are using long-polling techniques you cannot
use servers that adhere to the  WSGI standard, since it's not part of
it. uwsgi has some experimental support for asynchronous operations
but you must know what you're doing:
http://projects.unbit.it/uwsgi/wiki/AsyncSupport .



Thanks.  That link (along with lots of other background reading) was 
extremely useful.


Jason


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[sage-devel] Re: Sage does (did?) build with an arm processor, but the tests don't pass

2011-02-07 Thread Dima Pasechnik
If I recall right, Cephes provides complex.h, which is simply missing
on Cygwin.

Yes, indeed, special functions are also implemented in GSL.
Implementing them well on a FPU
seems to be an art on its own.
Would be nice to have them all under a uniform interface:
gamma.libm, gamma.gsl, etc.
(maybe even gamma.cephes)

It's easy to provide an ARM-specific workaround for gamma, based on
GSL, say --- just to satisfy
the corresponding doctests.

Dima

On Feb 8, 6:31 am, David Kirkby david.kir...@onetel.net wrote:
 On 6 February 2011 09:59, Dima Pasechnik dimp...@gmail.com wrote:

  Hi Burcin,
  indeed, here is another case of buggy libc/libm.
  The same workaround as for Cygwin should do the trick (provided that
  cephes works on ARM)
  Would installing cephes spkg break things on non-Cygwin, or this is
  safe?
  Dmitrii

 IIRC Cephes is only installed on Cygwin and FreeBSD. If there was a
 need for it on a particular CPU, I don't see why it could not be
 installed on that CPU, whilst not doing so on x86, SPARC etc.

 Dave

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Re: [sage-devel] Re: Sage does (did?) build with an arm processor, but the tests don't pass

2011-02-07 Thread David Kirkby
On 8 February 2011 05:17, Dima Pasechnik dimp...@gmail.com wrote:
 If I recall right, Cephes provides complex.h, which is simply missing
 on Cygwin.

snip

 Dima

I noticed on the R mailing list that there is an experimental patch
for Cygwin for complex support: Hopefully there will be support in
Cygwin very soon.

Dave

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