วันอาทิตย์ที่ 28 กุมภาพันธ์ พ.ศ. 2553

Re: [sage-devel] Any Solaris user want to review a really ugly patch ??

On 2010-Feb-28 01:48:35 +0000, "Dr. David Kirkby" <david.kirkby@onetel.net> wrote:
>and dirty ugly patch, I've changed the call to 'top' from one to 'prstat' on
>Solaris. Unlike 'top', 'prstat' is standard command.
>
>I call it 'ugly' as I don't think calling 'prstat' it an ideal way, but it is
>better than calling 'top' on Solaris.
...
>http://trac.sagemath.org/sage_trac/ticket/8391

I'll be Devil's Advocate and suggest that this is the wrong solution.
I agree that system('top') is a really bad idea but dispute that
system('prstat') is much of an advance. IMHO, rather than band-aiding
the current problem, we should fix it properly.

Note that we have had this discussion before - last August in a
thread "Where is 'top' used in Sage?"

--
Peter Jeremy

Re: [sage-devel] Is CMake OK for a standard spkg?

On 2010-Feb-28 21:32:10 -0800, Ondrej Certik <ondrej@certik.cz> wrote:
>On Sun, Feb 28, 2010 at 8:36 PM, William Stein <wstein@gmail.com> wrote:
>> On Sun, Feb 28, 2010 at 7:34 AM, Bjarke Hammersholt Roune
>> <bjarke.roune@gmail.com> wrote:
>>> Can a standard spkg in Sage use CMake?
...
>> No, at present, it is definitely not OK for a standard spkg to use CMake.
...
>> By the way, the cmake source tarball is about 3.4MB and takes 4
>> minutes to compile on sage.math.   So size and time wise it is not
>> unreasonable that it could be a standard Sage package at some point.

Another way of looking at it is that Singular is ~7.5MB (I'm not sure
how long it takes to build) so this would effectively increase the
size of Singular by nearly 50%.

>For what is worth, we use cmake in FEMhub (femhub.org) as a standard
>package and we never had any problems with that.

If CMake was widely used (and hence can be listed as a prerequisite for
building Sage - like gmake, bash etc) then it would have no overhead
for Sage. Likewise, if it was used by a number of skpgs then the
additional overhead would be amortised across lots of packages.

>I like cmake and I use it for all my projects, that involve some C++ coding.

There are lots of make-like tools available and different people use
different ones. One disadvantage of this is that where a large project
pulls in bits from lots of different sources (like Sage), this can
result in lots of different make-like tools being required. A quick
check suggests that I have accumulated 8 different ones on this system
in order to build all the software I use.

--
Peter Jeremy

Re: [sage-devel] Is CMake OK for a standard spkg?

On Sun, Feb 28, 2010 at 8:36 PM, William Stein <wstein@gmail.com> wrote:
> On Sun, Feb 28, 2010 at 7:34 AM, Bjarke Hammersholt Roune
> <bjarke.roune@gmail.com> wrote:
>> Can a standard spkg in Sage use CMake?
>>
>>  http://www.cmake.org/
>>
>> I ask because I'm seriously considering moving from a straight make
>> system for Frobby to CMake, but if that is not possible for Sage then
>> it's a non-starter. A search of sage-devel reveals that Singular is
>> moving to CMake, but it isn't clear to me from the discussion how well
>> Sage is able to deal with CMake at this time.
>>
>
> No, at present, it is definitely not OK for a standard spkg to use CMake.
> Frobby is an optional spkg, not standard, so I guess it would be OK,
> though if you use CMake, note that the vast majority of people that
> try to build Frobby will find that it immediately fails fro them,
> until they install cmake, which they may not easily be able to do.
>
> If Singular moves to CMake that could seriously be a pain for us,
> since we'll likely have to add cmake as a standard package to Sage,
> which will of course involves headaches.     CMake is not nearly as
> widely deployed as many of the components of Sage that we do build
> from source, so assuming it is installed already is not so reasonable.
>
> So quick summary: Right now Sage does not include cmake, so no
> standard package can depend on cmake.  If we are forced into including
> cmake because of a design decision by Singular that we can't get
> around, then we'll have to get cmake into sage as a standard package.
> At that point, any standard package could use cmake.
>
> By the way, the cmake source tarball is about 3.4MB and takes 4
> minutes to compile on sage.math.   So size and time wise it is not
> unreasonable that it could be a standard Sage package at some point.

For what is worth, we use cmake in FEMhub (femhub.org) as a standard
package and we never had any problems with that.

I like cmake and I use it for all my projects, that involve some C++ coding.

Ondrej

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Re: [sage-devel] gsoc ideas list

On Sun, 28 Feb 2010 at 09:02PM +0100, Burcin Erocal wrote:
> After the recent thread about Google Summer of Code [1], I set up a
> wiki page to collect project ideas:
>
> http://wiki.sagemath.org/gsoc10
>
> [1] http://groups.google.com/group/sage-devel/t/8f61382c855ddb09
>
> The application window for mentoring organizations opens in a week, so
> we need to be quick to make this page look better. ATM, it's just a
> copy of last years page with minor changes.
>
> If you think you can spare a few hours a week helping newcomers find
> their way around the Sage library and the development process, please
> volunteer to be a mentor. Most people already do this by answering
> messages on the sage-support list. This is a great opportunity to get
> a paid developer working on your favorite feature request.
>
> Feel free to add new project ideas or more text to make the already
> listed ideas well defined. There are a few guidelines I copied from
> the GSOC FAQ at the end of the page.

I just edited that page to add a project on internationalizing the
notebook, and am volunteering to be a mentor for that project. In the
past, I think Google thought of our projects as "too mathy"; this
project involves no math at all, just Python and web programming, so I
think it has a decent chance of acceptance, and would make a huge impact
on Sage. I also think it's a pretty well-defined and doable summer
project.

Dan

--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------

Re: [sage-devel] Is CMake OK for a standard spkg?

On Sun, Feb 28, 2010 at 7:34 AM, Bjarke Hammersholt Roune
<bjarke.roune@gmail.com> wrote:
> Can a standard spkg in Sage use CMake?
>
>  http://www.cmake.org/
>
> I ask because I'm seriously considering moving from a straight make
> system for Frobby to CMake, but if that is not possible for Sage then
> it's a non-starter. A search of sage-devel reveals that Singular is
> moving to CMake, but it isn't clear to me from the discussion how well
> Sage is able to deal with CMake at this time.
>

No, at present, it is definitely not OK for a standard spkg to use CMake.
Frobby is an optional spkg, not standard, so I guess it would be OK,
though if you use CMake, note that the vast majority of people that
try to build Frobby will find that it immediately fails fro them,
until they install cmake, which they may not easily be able to do.

If Singular moves to CMake that could seriously be a pain for us,
since we'll likely have to add cmake as a standard package to Sage,
which will of course involves headaches. CMake is not nearly as
widely deployed as many of the components of Sage that we do build
from source, so assuming it is installed already is not so reasonable.

So quick summary: Right now Sage does not include cmake, so no
standard package can depend on cmake. If we are forced into including
cmake because of a design decision by Singular that we can't get
around, then we'll have to get cmake into sage as a standard package.
At that point, any standard package could use cmake.

By the way, the cmake source tarball is about 3.4MB and takes 4
minutes to compile on sage.math. So size and time wise it is not
unreasonable that it could be a standard Sage package at some point.

-- william

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Re: [sage-devel] Solaris patches - please review to Sage working again.

Hi David,

I have produced a source tarball that incorporates the patches and/or
spkg's at the following tickets:

* #7867
* #8391
* #8363
* #8374
* #8375

These patches and spkg's are applied on top of Sage 4.3.3. The build
is still going on these machines:

* sage.math
* bsd.math
* winxp1 (Cygwin on boxen.math)
* t2.math
* rosemary.math

I'll report the results later on the relevant tickets.

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[sage-devel] review ticket #7608 to upgrade NetworkX to version 1.0.1

Hi folks,

Gregory McWhirter has put a lot of effort into upgrading the NetworkX
spkg to version 1.0.1. At ticket #7608 [1] is a (roughly) 500 KB patch
to the Sage library and an upgraded NetworkX spkg. Don't let the size
of the patch put you off. Most of the patch is about removing trailing
white spaces. I have commented about some issues not resolved by the
patch. I invite anyone interested in upgrading the NetworkX spkg to
review the patch and/or help with the upgrade.

[1] http://trac.sagemath.org/sage_trac/ticket/7608

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Minh Van Nguyen

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[sage-devel] Return type for coefficient

Hi,

I want to raise this issue again.

sage: P.<x,y> = PolynomialRing(QQ,2)
sage: f = 2*x*y+x+y
sage: f.coefficient({x:1,y:1})
2
sage: c = f.coefficient({x:1,y:1})
sage: c.parent()
Multivariate Polynomial Ring in x, y over Rational Field

sage: c = f.monomial_coefficient(x*y)
sage: c.parent()
Rational Field

I think there is a consensus that

1. "f.coefficient({x:1,y:1})" should return the coefficient in the
base ring
2. the method "monomial_coefficient" should accept (perhaps more
efficient to process) argument "{x:1,y:1}".

If all agrees, then I will open a ticket (if there is not already
one).


Kwankyu

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Re: [sage-devel] Can someone please close #7932

Hi David,

On Mon, Mar 1, 2010 at 12:49 PM, David Kirkby <david.kirkby@onetel.net> wrote:
> The problem reported at #7932 has been solved my Robert's undated
> Cython at #8163 fixes this issue.

Done.

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[sage-devel] Can someone please close #7932

The problem reported at #7932 has been solved my Robert's undated
Cython at #8163 fixes this issue.

Dave

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[sage-devel] Solaris patches - please review to Sage working again.

After the recent screw up, where 4.3.1 failed to build on Solaris, hopefully
4.3.4 should do.

I've got all the patches in place for 4.3.3 to build. Try it at

http://redstart.drkirkby.co.uk:8000/

The network and computer are slow, but you can see it works. Also note that both:

sage: top()

and

sage: get_memory_usage()

work, whereas they don't on 't2'

http://t2nb.math.washington.edu:8000

which is running 4.3.0.1 on 4.3.0.1

However, there are a few critical patches needed, so it would be good if someone
could review them.

1) Most important is the fix to python.

http://trac.sagemath.org/sage_trac/ticket/7867

which was necessary as a result of #6583

2) http://trac.sagemath.org/sage_trac/ticket/8391

which gets top() and get_memory_usage() working should be easy to review. This
is not critical, but the patch is very easy to review. You can see it works at

http://redstart.drkirkby.co.uk:8000/

3) http://trac.sagemath.org/sage_trac/ticket/8363
is another easy one related to cddlib

4) http://trac.sagemath.org/sage_trac/ticket/6503
is not my tickeet, but one to get pyprocessing removed from Sage. Either that
needs to be incorporated, or I need a small Solaris-specific fix. But it would
be more sensible that the complete package is removed. I just don't feel
confident to review it myself.

5) Two numerical noise patches. Again not critical, but they bring the number of
doc tests failures down to 5, which is pretty good, considering the screw ups
there have been over Solaris.

http://trac.sagemath.org/sage_trac/ticket/8374
http://trac.sagemath.org/sage_trac/ticket/8375

It would be a shame for those doctests to not pass, but they are hardly critical.

There are 5 doc test failures, and I don't have a clue how to go about debugging
them. But the main thing is to get Sage to actually build - a few test failures
is not the end of the world.

http://trac.sagemath.org/sage_trac/ticket/8397
http://trac.sagemath.org/sage_trac/ticket/8399
http://trac.sagemath.org/sage_trac/ticket/8399
http://trac.sagemath.org/sage_trac/ticket/8400
http://trac.sagemath.org/sage_trac/ticket/8401

Any help appreciated.

Dave


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[sage-devel] 0 < sqrt3 is False in QuadraticField

Hi Sage-devel,

I am currently experiencing some problems when comparing elements of a
QuadraticField. See below.

sage: Q.<sqrt3> = QuadraticField(3)
sage: 0 < sqrt3
False
sage: RR(sqrt3)
1.73205080756888

The operator < and > do not correspond :

sage: sqrt3 > Q.zero()
True
sage: Q.zero() < sqrt3 #not ok
False

Other similar behavior :

sage: -sqrt3 > Q.zero() #not ok
True
sage: -sqrt3 < Q.zero()
False
sage: sqrt3 < Q.zero()
False
sage: sqrt3 < -sqrt3 #not ok
False
sage: sqrt3 > -sqrt3
True
sage: -sqrt3 > sqrt3 #not ok
True
sage: -sqrt3 < sqrt3
False

Is this known?

Sébastien Labbé

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[sage-devel] Re: Can a test run over all polynomial rings?

Primarily what I'm wondering is if there is already a good way to do
this, since I'm not volunteering to implement it if there isn't.

Still, I don't suppose it hurts to mention what I would like. For
polynomial rings, it would be a function along the lines of

makeSomeRing(predicate)

where predicate is a function mapping rings to true/false, and
makeSomeRing returns some ring that makes pred evaluate to true and
throws an exception if it can't find any such ring. Then Sage could
detect that this method has been called and re-run the test where the
method returns a different ring each time. Or it could just be run
once by default for some preferred ring and many times given some
option to do more exhaustive testing. At the most simple, makeSomeRing
could just try pred on a fixed list of rings. Add a newly written ring
to the list as you add it to Sage, and you get the new ring tested in
every situation where the old rings are already tested. So the intent
is not to construct random rings, though the scheme could be extended
to support that as well.

This scheme applies to just about anything you might wish your test to
be parameterized by, it's just that rings is what is relevant to me
for the Frobby interface. Testing the output could be handled by
constructing the correct answer in the same ring, or by converting at
the end to some fixed ring. If this were adopted, probably there
should be a rule that the first test does not use this, so that the
tests remain useful as documentation.

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Re: [sage-devel] Re: Sage Days 20 Videos

Hi,

I will watch the videos next week and upload them to sageworldmath.blip.tv

Meanwhile you can have a look at
http://sageworldmath.mirocommunity.org/

just created

#Serge

Sébastien Labbé пишет:
>> the Videos of Sage Days 20 [1] will be available here
>
> The initial format of the videos are MP4 (huge files). I converted
> them to mpeg before uploading them. In the hope this format will make
> you happy. Suggestions are welcome.
>
> Sébastien
>

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[sage-devel] Re: Can a test run over all polynomial rings?

Hi Bjarke!

On 28 Feb., 17:18, Bjarke Hammersholt Roune <bjarke.ro...@gmail.com>
wrote:
> Is it possible to write a test that runs over all polynomial ring over
> a field in Sage? This is as opposed to a test that works in a specific
> ring that the test constructs. Obviously there are infinitely many
> possible rings that can be constructed, so the test should run over
> some representative finite subset.

A test requires some computation that has an expected output: The
computation is done, and it is checked whether the output really is as
expected.

I see several possibilities for what you describe:

1. Choose some representative polynomial rings, ideals,..., and
compute the expected result. Then, in your tests, the input is fixed,
the expected output is known, so, it is easily tested.
2. Construct a ring/ideal/... randomly. Then, of course, you don't
know the output a priori.
(a) Mark the test as "random". Then, the output of the random
computation is not checked.
(b) Do consistency tests. E.g., if you know that two different
computations on the same input will always have the same result, then
test the equality.
Example:
sage: R = PolynomialRing(QQ,'x',randint(1,5))
sage: I = R*[t for t in R.gens() if randint(0,1)]
sage: len((I^2).gens())==len(I.gens())^2
True
So, you have a somewhat random example, and test a property that
should always hold.

The disadvantage of method 1. is that you need to fix the input data.
The advantage is that you have full control on the output.

The disadvantage of 2.(a) is that this only tests whether there is an
error.

The disadvantage of 2.(b) is that it is more difficult to read for a
user -- mind that the test examples in the sage library are part of
the *documentation*.

Cheers
Simon

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[sage-devel] gsoc ideas list

Hi,

After the recent thread about Google Summer of Code [1], I set up a
wiki page to collect project ideas:

http://wiki.sagemath.org/gsoc10

[1] http://groups.google.com/group/sage-devel/t/8f61382c855ddb09


The application window for mentoring organizations opens in a week, so
we need to be quick to make this page look better. ATM, it's just a
copy of last years page with minor changes.

If you think you can spare a few hours a week helping newcomers find
their way around the Sage library and the development process, please
volunteer to be a mentor. Most people already do this by answering
messages on the sage-support list. This is a great opportunity to get a
paid developer working on your favorite feature request.


Feel free to add new project ideas or more text to make the already
listed ideas well defined. There are a few guidelines I copied from the
GSOC FAQ at the end of the page.


Cheers,
Burcin

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Re: [sage-devel] Mercurial - add configure and configure.in ???

Hi David,

On Mon, Mar 1, 2010 at 2:50 AM, Dr. David Kirkby
<david.kirkby@onetel.net> wrote:

<SNIP>

> Do the auto generated files need to be checked in?

I think so. The cddlib package checks in autogenerated files under patches/.

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[sage-devel] Graph Minor Theory in Sage !!

Hello everybody !!!!

I just submitted to trac a new patch which I hope will be the beginning of a long sequence in graph Theory. This patch lets one computes, given two graphs G and H, whether G has H as a minor. it is based on linear programming, and often slow, but there are very few if any practical algorithms available to compute it.


-- NO -- graph theory library other than Sage has it at the moment.

With a bit of luck, it may be followed by other formulations to compute Treewidth, Pathwidth, etc....

And of course... it needs review ! :-)

Nathann

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Re: [sage-devel] Re: Vote on bugs to be fixed for sage-4.4 "stabilization release".

Bjarke Hammersholt Roune wrote:
> I think the silently wrong Grobner basis has a chance to result in
> wrong papers, so that would be my top pick
>
> http://trac.sagemath.org/sage_trac/ticket/6472
>
> and I agree on the startup time
>
> http://trac.sagemath.org/sage_trac/ticket/8254
>

I just put a comment on the second trac ticket about the startup time on a quite
old Sun Blade 1000. Sage is only taking 8 seconds to start on that. Although the
processors are not that quick (dual 900 MHz), the disks are 15,000 rpm and use a
2 Gbit/s fibre channel interface. (Though it is call fibre channel, it actually
uses copper!) So the disks are local, and disks fast.

It is running a UFS file system on Solaris 10.

It suggests to me the time to read data from disk might be more of an issue than
raw CPU power.

Dave

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[sage-devel] Re: Vote on bugs to be fixed for sage-4.4 "stabilization release".

I think the silently wrong Grobner basis has a chance to result in
wrong papers, so that would be my top pick

http://trac.sagemath.org/sage_trac/ticket/6472

and I agree on the startup time

http://trac.sagemath.org/sage_trac/ticket/8254

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Re: [sage-devel] Sanity check on objects, parents and elements

> I certainly agree that 1-2 should be the general rule, I was just pointing
> out an exception. I like the idea of returning an Unknown object on RIF
> comparisons as well.

This is now #8402 (work in progress).

Florent

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[sage-devel] Can a test run over all polynomial rings?

Is it possible to write a test that runs over all polynomial ring over
a field in Sage? This is as opposed to a test that works in a specific
ring that the test constructs. Obviously there are infinitely many
possible rings that can be constructed, so the test should run over
some representative finite subset.

This is relevant to me in writing tests for the Frobby spkg, since I
want to accept as a parameter a monomial ideal in any polynomial ring.
How do I test that? I don't know what all the polynomial rings in Sage
are, and I would like the test to detect if in future someone adds a
new type of polynomial ring for which my code does not work. I looked
in the developer guide at

http://www.sagemath.org/doc/developer/conventions.html#automated-testing

and I didn't see any discussion of this. Searching sage-devel for
"parameterized test" also yields no hits. Should I test one ring and
leave it at that?

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[sage-devel] Mercurial - add configure and configure.in ???

I've had to create a patch for Solaris to python.

http://trac.sagemath.org/sage_trac/ticket/7867

The changes consist of applying a small (< 1 KB) patch downloaded from the
python web site to configure.in, then remaking the configure script.

Python's configure.in is quite large (107 KB) and the resulting 'configure'
script, along with the files in the automte.cache directory (which is not safe
to remove) are quite large

sage subshell$ hg status
M SPKG.txt
M spkg-install
? patches/autom4te.cache/output.0
? patches/autom4te.cache/traces.0
? patches/configure
? patches/configure.in
? patches/configure.in.Solaris.patch

If I check all the changed files in, there is about 1 MB. In comparison, the
patch to configure.in I downloaded from the Python web site is < 1 KB.

Do the auto generated files need to be checked in?

Dave

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[sage-devel] Is CMake OK for a standard spkg?

Can a standard spkg in Sage use CMake?

http://www.cmake.org/

I ask because I'm seriously considering moving from a straight make
system for Frobby to CMake, but if that is not possible for Sage then
it's a non-starter. A search of sage-devel reveals that Singular is
moving to CMake, but it isn't clear to me from the discussion how well
Sage is able to deal with CMake at this time.

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Re: [sage-devel] Doctest results on Solaris.

Dr. David Kirkby wrote:
> I thought I'd report the doctests results on Solaris. I know Solaris has
> never passed them all, but the number of failures is not very large now
> I've implemented something much faster to get the memory usage, which
> was screwing up some tests.
>
>
> There are 10 failures. The first two are failures are numerical noise
> issues, which are awaiting review at
>
> http://trac.sagemath.org/sage_trac/ticket/8374
> http://trac.sagemath.org/sage_trac/ticket/8375
>
> (someone please get these easy ones out of the way.)
>
> That still leaves 8 failures.

After increasing the timeout, 3 more of the tests passed, so my poor 10-year old
SPARC is not fast enough! I reckon on 't2', the SAGE_TIMEOUT should be increased
to about 1800 s to be sure there are no spurious timeout errors, as

sage -t "devel/sage/sage/schemes/elliptic_curves/heegner.py"
[440.9 s]

sage -t "devel/sage/sage/plot/plot.py"
[422.8 s]

sage -t "devel/sage/sage/rings/polynomial/symmetric_ideal.py"
[459.4 s]

So that leaves just 5 unexplained failures on Solaris

sage -t "devel/sage/sage/graphs/graph_list.py" # Segfault
sage -t "devel/sage/sage/graphs/generic_graph.py" # Segfault
sage -t "devel/sage/sage/graphs/graph.py" # Segfault
sage -t "devel/sage/sage/graphs/graph_database.py" # Segfault
sage -t "devel/sage/sage/databases/database.py" # Segfault


Dave

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Re: [sage-devel] Re: graph theory: degree() reports the degree of a self-loop as contributing 1 to total degree

Hi Nathann,

On Mon, Mar 1, 2010 at 1:44 AM, Nathann Cohen <nathann.cohen@gmail.com> wrote:

<SNIP>

> This should be easy to fix in c_graph.pyx or directly in the backends
> for dense/sparse graphs.

This is now ticket #8395

http://trac.sagemath.org/sage_trac/ticket/8395

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[sage-devel] Re: graph theory: degree() reports the degree of a self-loop as contributing 1 to total degree

> Given a graph G with one vertex v having a self-loop at v, I would
> expect the total degree of G to be 2, since the total degree is twice
> the number of edges. But this is not the case as shown below for the
> case of undirected (multi)graphs:

I never use looped graphs or multigraphs, but I agree I would expect a
2 in this situation. It fits with the fact that you can always orient
a graph in such a way that all the degrees are divided by two (+1 if
the degree is odd).

This should be easy to fix in c_graph.pyx or directly in the backends
for dense/sparse graphs. Anyway, this should not happen :

sage: G = Graph({1:[1]}); G.degree(1)
1
sage: G = Graph({1:[1]}, implementation="networkx"); G.degree(1)
2

Nathann

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[sage-devel] graph theory: degree() reports the degree of a self-loop as contributing 1 to total degree

Hi folks,

Given a graph G with one vertex v having a self-loop at v, I would
expect the total degree of G to be 2, since the total degree is twice
the number of edges. But this is not the case as shown below for the
case of undirected (multi)graphs:

[mvngu@sage mvngu]$ sage
----------------------------------------------------------------------
| Sage Version 4.3.3, Release Date: 2010-02-21 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
sage: G = Graph({1:[1]}); G
Looped graph on 1 vertex
sage: sum(G.degree())
1
sage: G.size()
0
sage: G = Graph({1:[1]}, loops=True); G
Looped graph on 1 vertex
sage: sum(G.degree())
1
sage: G.size()
0
sage: G = Graph({1:[1]}, loops=True, multiedges=True); G
Looped multi-graph on 1 vertex
sage: sum(G.degree())
1
sage: G.size()
0

The size of G is 1 because there is one edge, i.e. the single
self-loop. As shown by the above session, Sage reports the size of G
as 0. I believe this is a bug.

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Re: [sage-devel] Increase timeout for doc tests

Alex Ghitza wrote:
> On Sun, 28 Feb 2010 12:29:52 +0000, "Dr. David Kirkby" <david.kirkby@onetel.net> wrote:
>> Is there way I can increase the timeout for doctests? I've got some failures,
>> but note that some tests are taking very close to the maximum permitted (360s)
>> on my 900 MHz SPARC.
>
> Hi Dave,
>
> Have a look at the following ticket:
>
> http://trac.sagemath.org/sage_trac/ticket/8263
>
> where SAGE_TIMEOUT, SAGE_TIMEOUT_LONG, and SAGE_TIMEOUT_VALGRIND are
> described together with their default values.
>
> Just reset them to whatever you think is appropriate for your machine.
>
>
> Best,
> Alex
>
>

Thank you Alex. I'll run those tests again, with SAGE_TIMEOUT set to something a
bit longer.


Dave

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Re: [sage-devel] Increase timeout for doc tests

On Sun, 28 Feb 2010 12:29:52 +0000, "Dr. David Kirkby" <david.kirkby@onetel.net> wrote:
> Is there way I can increase the timeout for doctests? I've got some failures,
> but note that some tests are taking very close to the maximum permitted (360s)
> on my 900 MHz SPARC.

Hi Dave,

Have a look at the following ticket:

http://trac.sagemath.org/sage_trac/ticket/8263

where SAGE_TIMEOUT, SAGE_TIMEOUT_LONG, and SAGE_TIMEOUT_VALGRIND are
described together with their default values.

Just reset them to whatever you think is appropriate for your machine.


Best,
Alex


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[sage-devel] Doctest results on Solaris.

I thought I'd report the doctests results on Solaris. I know Solaris has never
passed them all, but the number of failures is not very large now I've
implemented something much faster to get the memory usage, which was screwing up
some tests.


There are 10 failures. The first two are failures are numerical noise issues,
which are awaiting review at

http://trac.sagemath.org/sage_trac/ticket/8374
http://trac.sagemath.org/sage_trac/ticket/8375

(someone please get these easy ones out of the way.)

That still leaves 8 failures.

sage -t "devel/sage/sage/schemes/elliptic_curves/heegner.py" # Segfault
sage -t "devel/sage/sage/plot/plot.py" # Segfault
sage -t "devel/sage/sage/graphs/graph_list.py" # Segfault
sage -t "devel/sage/sage/graphs/generic_graph.py" # Segfault
sage -t "devel/sage/sage/graphs/graph.py" # Segfault
sage -t "devel/sage/sage/graphs/graph_database.py" # Segfault
sage -t "devel/sage/sage/databases/database.py" # Segfault
sage -t "devel/sage/sage/rings/polynomial/symmetric_ideal.py" # Segfault
Total time for all tests: 28172.6 seconds

I'm wondering if the timeout might be too short for this rather old machine
(about 10 years old).

Full log at:

http://boxen.math.washington.edu/home/kirkby/doctest-results/1/

Comments?

Dave


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[sage-devel] Increase timeout for doc tests

Is there way I can increase the timeout for doctests? I've got some failures,
but note that some tests are taking very close to the maximum permitted (360s)
on my 900 MHz SPARC.

For example

sage -t "devel/sage/doc/en/bordeaux_2008/birds_other.rst"
[203.8 s]

sage -t "devel/sage/sage/schemes/elliptic_curves/sha_tate.py"
[259.8 s]

sage -t "devel/sage/sage/schemes/elliptic_curves/ell_generic.py"
[238.9 s]

sage -t "devel/sage/sage/groups/perm_gps/partn_ref/refinement_graphs.pyx"
[217.4 s]


So it is not beyond the bounds of possibility that if some tests are taking over
250s, then one or two might time out.


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[sage-devel] Re: Sage Days 20 Videos

> However, I find them completely *impossible* to download.  The site
> seems to be secure, e.g., and I simply can't get the worksheets.

Indeed, one must accept the certificate to access to the web site (I
learned the solution by the web site maintainer himself).

> Maybe you could also upload them to
>
> http://sage.math.washington.edu/home/slabbe/days20/

Done. I uploaded the four sage worksheets + the one pdf.

Sébastien

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Re: [sage-devel] bug on sage.combinat.tableau.insert_word() (trac #8322)

On Sun, 28 Feb 2010 22:22:48 +1100, Alex Ghitza <aghitza@gmail.com> wrote:
> It looks good to me, with one exception: "Author(s)" refers to the
> authors of the patch(es) or other code attached to the ticket, not to
> the person creating the ticket itself (that's covered by "Reported by").

Oops. I just looked at the ticket more carefully and noticed that you
are describing a fix. Nevertheless, "Author(s)" is normally filled in
when there is a patch up -- so if somebody else incorporates your fix in
a patch and adds doctests, etc., then both you and this person would be
listed as authors.


Best,
Alex


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Re: [sage-devel] bug on sage.combinat.tableau.insert_word() (trac #8322)

On Sat, 27 Feb 2010 23:55:43 -0800 (PST), Drini <pdsanchez@gmail.com> wrote:
> Since it's the first time I submit a bug report, I'm not sure if I did
> it properly.
>
> I just want to know if I didn't mess up, filling bad the values and
> boxes below the report.

Hi,

It looks good to me, with one exception: "Author(s)" refers to the
authors of the patch(es) or other code attached to the ticket, not to
the person creating the ticket itself (that's covered by "Reported by").

Other fields you can use at this time are "Keywords", or "Cc" if you
want to let somebody in particular know about this (e.g. if you have put
up a patch and have a reviewer in mind).

The "Reviewer(s)" field should be completed after the patch is reviewed,
"Merged in" is completed by the release manager, and "Work issues" is
there to give details on a ticket that's marked as "needs_work".

I hope this makes sense.


Best,
Alex


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วันเสาร์ที่ 27 กุมภาพันธ์ พ.ศ. 2553

[sage-devel] bug on sage.combinat.tableau.insert_word() (trac #8322)

Since it's the first time I submit a bug report, I'm not sure if I did
it properly.

I just want to know if I didn't mess up, filling bad the values and
boxes below the report.

I know the main report body is correct, but then the assign, keywords,
reviewer, etc. I simply don't know what to type on it.

If anyone is kind enough to explain to me, so I don't have to ask
again next time I submit a bug.

http://trac.sagemath.org/sage_trac/ticket/8322

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[sage-devel] Re: Sage Calendar for 2011

Wow, that's pretty neat. I've never seen that before. I made a quick-
and-dirty interact to show that:

var('z')
@interact
def exp_taylor(n = slider(range(1,20),default = 5)):
f = exp(z)
fn = f.taylor(z,0,n)
html('Taylor polynomial of the exponential function to order
'+str(n))
show(fn)
show(complex_plot(fn/abs(fn),(-15,15),(-15,15), axes = False,
figsize = [5,5], plot_points = 200))

-Marshall

On Feb 27, 6:57 pm, Dan Drake <dr...@kaist.edu> wrote:
> On Sat, 27 Feb 2010 at 04:16PM -0800, mhampton wrote:
> > There are all sorts of nice possibilities with complex_plot. As just
> > one example:
>
> Another idea: roots of the Taylor polynomials of the exponential
> function:http://www.mai.liu.se/~halun/complex/taylor/
>
> Dan
>
> --
> --- Dan Drake
> ----- http://mathsci.kaist.ac.kr/~drake
> -------
>
> signature.asc
> < 1KViewDownload

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Re: [sage-devel] Any Solaris user want to review a really ugly patch ??

Dr. David Kirkby wrote:
> Currently if you call
>
> top()
> or
> get_memory_usage()
>
> on a Solaris system which does not have 'top' installed, you get rubbish
> like this:
>
> http://t2nb.math.washington.edu:8000/home/pub/8/


For comparison, here is the code after the calls to 'top' replaced by calls to
'prstat'.

http://redstart.drkirkby.co.uk:8000/home/pub/0/

Note, the latter is running on my home computer, via my home network. The
machine only has a couple of 900 MHz processors and 2 GB RAM, so it is not quick.

I suspect the CPU resources for single-threaded applications is still better
than 't2' though.

Others are welcome to play on

http://redstart.drkirkby.co.uk:8000/

but bear in mind it only has 2 GB RAM!! (Luckily I have much better SPARCs than
this one).

Shame we don't have a Sage benchmark

http://trac.sagemath.org/sage_trac/ticket/6808

as I'd love to compare this 10 year old relic to 't2'!


Dave


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[sage-devel] Re: Sage Days 20 Videos

On Sat, Feb 27, 2010 at 6:10 PM, Sébastien Labbé <slabqc@gmail.com> wrote:
>> the Videos of Sage Days 20 [1] will be available here
>
> The initial format of the videos are MP4 (huge files). I converted
> them to mpeg before uploading them. In the hope this format will make
> you happy. Suggestions are welcome.
>

Thanks. Regarding the corresponding slides, they seem to be here

http://www.lirmm.fr/arith/wiki/MathInfo2010/SageDays#toc8

However, I find them completely *impossible* to download. The site
seems to be secure, e.g., and I simply can't get the worksheets.
Maybe you could also upload them to


http://sage.math.washington.edu/home/slabbe/days20/

since as is it seems impossible to get any worksheets, due to
self-signed certificates and stuff.

William

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[sage-devel] Re: Sage Days 20 Videos

> the Videos of Sage Days 20 [1] will be available here

The initial format of the videos are MP4 (huge files). I converted
them to mpeg before uploading them. In the hope this format will make
you happy. Suggestions are welcome.

Sébastien

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[sage-devel] Re: Bipartite graphs in Sage

I don't think "transfer matrix" is a standard term in this context.
To avoid confusion, I called such things "vertex-vertex incidence
matrix" in
the graph theory class I taught last term.

By the way, in enumerative combinatorics "transfer matrix" means
something totally different.

Dima

On Feb 28, 7:04 am, Jaap Spies <j.sp...@hccnet.nl> wrote:
> David Joyner wrote:
>
> >>> There was some discussion several years ago about what this should be
> >>> called. I believe this term came from Richard Brualdi's combinatorial
> >>> matrix theory book (I remember running down the hall to my advisor's
> >>> office to look it up! :), but my memory may be inaccurate.
>
> >> You remember correctly a discussion on IRC. I offered to put a scan of
> >> the relevant page on line.
>
> > I'm interested. Please do.
>
> I will not put this scan in the open. My lady friend who happens to be a lawyer,
> advised me so. I'll send it by email.
>
> Jaap

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[sage-devel] Sage Days 20 Videos

Hi,

In a few minutes (if I don't lose my connection during the night), the
Videos of Sage Days 20 [1] will be available here :

http://sage.math.washington.edu/home/slabbe/days20/

Not all the talks were recorded (...for example I did not recorded
myself!). But I got 11 of them.

Enjoy,

Sébastien

[1] https://www.lirmm.fr/arith/wiki/MathInfo2010/SageDays

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[sage-devel] Re: Bipartite graphs in Sage

On Sat, Feb 27, 2010 at 8:07 PM, Ryan Hinton <iobass@email.com> wrote:
> Actually, I've considered dropping back to the Graph class.  I'm working
> with error correcting codes whose decoding algorithms are naturally
> described as message passing on an associated graph (LDPC codes).  And the
> associated graphs are bipartite.  So naturally I used the BipartiteGraph
> class!


Aahh, very interesting. If you have coding theory patches to add,
I would be happy to try to referee them.


>
> Personally, the only bipartite "feature" I use are the partition sets. I
> often want to iterate over all of a certain node type.  I have the
> information nodes on the left and constraint nodes on the right.  In fact,
> it would probably be less work for me to use a Graph and maintain these sets
> manually.
>

Eventually, it would be nice if someone in your situration could just use the
BipartiteGraph class, since that is what is most natural.


> In general, the bipartite nature of a graph can be exploited for matching
> and coloring, planarity, etc.  So there are opportunities for optimized
> algorithms.  Take a look at trac #1941 for the big picture, and #8329,
> #8330, #8331, and #8350 (all linked from #1941) for attacks on a few
> specific issues.
>
> Enjoy!
>
> - Ryan
>
> Nathann Cohen wrote:
>>
>> Hello everybody !!!
>>
>> I followed your conversation on Sage-devel (http://bit.ly/bHTOHm), and
>> I felt a bit as an outsider as I never used this class.. Could you
>> tell me what you expect from it, or what you use it for ? I can not
>> dream of a situation in which I would prefer it to the usual Graph
>> class.....
>>
>> Thank you :-)
>>
>> Nathann
>
> ---
> Ryan Hinton
> iobass@email.com
>
>

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[sage-devel] Any Solaris user want to review a really ugly patch ??

Currently if you call

top()
or
get_memory_usage()

on a Solaris system which does not have 'top' installed, you get rubbish like this:

http://t2nb.math.washington.edu:8000/home/pub/8/

IMHO, calling 'top' to get the memory usage is not a good idea, but as a quick
and dirty ugly patch, I've changed the call to 'top' from one to 'prstat' on
Solaris. Unlike 'top', 'prstat' is standard command.

I call it 'ugly' as I don't think calling 'prstat' it an ideal way, but it is
better than calling 'top' on Solaris.

That ticket is here, if anyone wants to review it. The changes are basically
specific to Solaris, though I expanded the information somewhat, which will be
seen on any platform.

http://trac.sagemath.org/sage_trac/ticket/8391

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Re: [sage-devel] Re: Sage Calendar for 2011

On Sat, 27 Feb 2010 at 04:16PM -0800, mhampton wrote:
> There are all sorts of nice possibilities with complex_plot. As just
> one example:

Another idea: roots of the Taylor polynomials of the exponential
function: http://www.mai.liu.se/~halun/complex/taylor/

Dan

--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------

Re: [sage-devel] Re: Failure building MPIR on sage 4.3.2

> I downloaded mpir-1.3.1 outside of sage and started the compile. Yasm
> seems to have built just fine. But it failed in a different place.
> When creating libmpir.so, GCC returns the error,
>
> mpn/.libs/add_n.o: file not recognized: File format not recognized
>
> The more-or-less full log is at <http://www.hintonclan.org/iobass/mpir-
> script.txt>.

Just as a matter of curiosity in case that help what does:
file mpn/.libs/add_n.o
report?

Francois

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Re: [sage-devel] Re: Sage Calendar for 2011

mhampton wrote:
> There are all sorts of nice possibilities with complex_plot. As just
> one example:
>
> complex_plot(z*log(z)*exp((z^5+1)/(z^5-1)^(1/2)),(-1,1),(-1,1), axes =
> False, figsize = [10,10], plot_points = 1000)
>
> gives:
>
> http://www.d.umn.edu/~mhampton/zlogzz5.png
>
> Really the tip of the iceberg for that sort of stuff.
>
> -Marshall

They are the sort of things that would be nice to have as pre-installed
'published' documents - see the thread of mine

http://groups.google.com/group/sage-devel/browse_thread/thread/6580ca4cc7b3e9d7/a3d0510292702460?hl=en&ie=UTF-8&q=Should+there+be+some+*good*+examples+on+notebook%3F#a3d0510292702460

There are some nice ones too at

http://gallery.wolfram.com/

They guy that wrote this book

http://www.amazon.com/Mathematica-Guidebook-Graphics-Michael-Trott/dp/0387950109

seems an expert at making nice images. I don't know sort of brain you need to
make such things. I understand how the Mandlebrot set is produced (spent ages
coding that in assembler once), but some of the stuff people produce is
breathtaking.

PS I'm captain of a chess team called "Chaotic Equations"

Dave

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Re: [sage-devel] How do I rebuild the Sage library ?

Robert Bradshaw wrote:
> On Feb 27, 2010, at 3:58 PM, Dr. David Kirkby wrote:
>
>> I want to make a change to a couple of commands in the Sage library
>>
>> top()
>> get_memory_usage()
>>
>> both of which are defined in getusage.py. Hopefully it will solve 2 bugs.
>>
>>
>> http://trac.sagemath.org/sage_trac/ticket/6028
>> http://trac.sagemath.org/sage_trac/ticket/7153
>>
>> I've created a ticket for the changes
>>
>> http://trac.sagemath.org/sage_trac/ticket/8391
>>
>> What do I have to do to rebuild the library and check my changes are
>> working?
>
> Run sage -b
>

Thank you Robert.


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[sage-devel] Re: Sage Calendar for 2011

There are all sorts of nice possibilities with complex_plot. As just
one example:

complex_plot(z*log(z)*exp((z^5+1)/(z^5-1)^(1/2)),(-1,1),(-1,1), axes =
False, figsize = [10,10], plot_points = 1000)

gives:

http://www.d.umn.edu/~mhampton/zlogzz5.png

Really the tip of the iceberg for that sort of stuff.

-Marshall

On Feb 23, 12:26 pm, William Stein <wst...@gmail.com> wrote:
> Hi,
>
> Send me your contribution for the Sagecalendarfor 2011.
>
> If you're somebody like Tom Boothby or Marshall Hampton that makes
> amazing hi-res sage images, this means you!
>
> William
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org

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Re: [sage-devel] How do I rebuild the Sage library ?

On Feb 27, 2010, at 3:58 PM, Dr. David Kirkby wrote:

> I want to make a change to a couple of commands in the Sage library
>
> top()
> get_memory_usage()
>
> both of which are defined in getusage.py. Hopefully it will solve 2
> bugs.
>
>
> http://trac.sagemath.org/sage_trac/ticket/6028
> http://trac.sagemath.org/sage_trac/ticket/7153
>
> I've created a ticket for the changes
>
> http://trac.sagemath.org/sage_trac/ticket/8391
>
> What do I have to do to rebuild the library and check my changes are
> working?

Run sage -b

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[sage-devel] How do I rebuild the Sage library ?

I want to make a change to a couple of commands in the Sage library

top()
get_memory_usage()

both of which are defined in getusage.py. Hopefully it will solve 2 bugs.


http://trac.sagemath.org/sage_trac/ticket/6028
http://trac.sagemath.org/sage_trac/ticket/7153

I've created a ticket for the changes

http://trac.sagemath.org/sage_trac/ticket/8391

What do I have to do to rebuild the library and check my changes are working?

dave


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Re: [sage-devel] New sage wiki page for animations

Thank you for doing this!

Also, you added a link from [2] to [1] for
those commands that you moved. Well
done, IMHO.


On Sat, Feb 27, 2010 at 6:43 PM, slabbe <slabqc@gmail.com> wrote:
> Hello sage-devel,
>
> Just to make you know that I created a new page [1]  on the sage wiki
> to include animations (like .gif) made using sage. Indeed, the page
> [2] was getting huge and was containing a mix of pictures and
> animations. Then I moved four animations from [2] to [1] and added
> link to point to the new location for those four animations.
>
> You will find on [1] an animation on the Tamer and Lion enigma (see
> the page for a description of the problem!) . Feel free to add your
> animations to the page! If you do, I suggest you avoid posting long
> blocks of code and rather upload a .sage file containing the code.
>
> Sébastien Labbé
>
> [1] http://wiki.sagemath.org/animate
> [2] http://wiki.sagemath.org/pics
>
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[sage-devel] New sage wiki page for animations

Hello sage-devel,

Just to make you know that I created a new page [1] on the sage wiki
to include animations (like .gif) made using sage. Indeed, the page
[2] was getting huge and was containing a mix of pictures and
animations. Then I moved four animations from [2] to [1] and added
link to point to the new location for those four animations.

You will find on [1] an animation on the Tamer and Lion enigma (see
the page for a description of the problem!) . Feel free to add your
animations to the page! If you do, I suggest you avoid posting long
blocks of code and rather upload a .sage file containing the code.

Sébastien Labbé

[1] http://wiki.sagemath.org/animate
[2] http://wiki.sagemath.org/pics

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[sage-devel] Re: Bipartite graphs in Sage

David Joyner wrote:
>>>
>>>
>>> There was some discussion several years ago about what this should be
>>> called. I believe this term came from Richard Brualdi's combinatorial
>>> matrix theory book (I remember running down the hall to my advisor's
>>> office to look it up! :), but my memory may be inaccurate.
>>>
>>
>> You remember correctly a discussion on IRC. I offered to put a scan of
>> the relevant page on line.
>
> I'm interested. Please do.
>

I will not put this scan in the open. My lady friend who happens to be a lawyer,
advised me so. I'll send it by email.

Jaap


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[sage-devel] Re: Bipartite graphs in Sage

David Joyner wrote:
>>>
>>>
>>> There was some discussion several years ago about what this should be
>>> called. I believe this term came from Richard Brualdi's combinatorial
>>> matrix theory book (I remember running down the hall to my advisor's
>>> office to look it up! :), but my memory may be inaccurate.
>>>
>>
>> You remember correctly a discussion on IRC. I offered to put a scan of
>> the relevant page on line.
>
> I'm interested. Please do.

Hold on. I'm scanning.

Jaap

>
>>
>> Jaap
>>
>>
>>
>>> Thanks,
>>>
>>> Jason
>>>
>>>
>>
>>
>> --
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>> http://groups.google.com/group/sage-devel
>> URL: http://www.sagemath.org
>>
>


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Re: [sage-devel] Sanity check on objects, parents and elements

Hi Robert,

>> You get the point. As far as I understand a RIF only return True if the
>> interval are reduced to a single point. Is it right ? It would be better
>> to
>> return a special value like Unknown than False. But that's another
>> question...
>>
>> [...]
>
> I certainly agree that 1-2 should be the general rule, I was just pointing
> out an exception. I like the idea of returning an Unknown object on RIF
> comparisons as well.

Not my idea. This was the way it worked in MuPAD. There was a three state
boolean value, which was quite useful. Looking into python docs to see if we
can have "and" and "or" work with a 3-state booleans, I found:

" A rich comparison method may return the singleton NotImplemented if it does
not implement the operation for a given pair of arguments. By convention,
False and True are returned for a successful comparison. However, these
methods can return any value, so if the comparison operator is used in a
Boolean context (e.g., in the condition of an if statement), Python will call
bool() on the value to determine if the result is true or false. "

Wouldn't it be mor meaningful to return NotImplemented ?

Cheers,

Florent

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Re: [sage-devel] Re: Bipartite graphs in Sage

>>
>>
>> There was some discussion several years ago about what this should be
>> called. I believe this term came from Richard Brualdi's combinatorial
>> matrix theory book (I remember running down the hall to my advisor's
>> office to look it up! :), but my memory may be inaccurate.
>>
>
> You remember correctly a discussion on IRC. I offered to put a scan of
> the relevant page on line.

I'm interested. Please do.

>
> Jaap
>
>
>
>> Thanks,
>>
>> Jason
>>
>>
>
>
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[sage-devel] Re: Bipartite graphs in Sage

Jason Grout wrote:
> On 02/27/2010 01:41 PM, Rob Beezer wrote:

>>
>> This is in the BipartiteGraph class as "reduced_adjacency_matrix()."
>> I can't recall ever seeing this matrix given a name, so I don't know
>> if this is how one would expect to find it. In the research for your
>> graph theory book have you learned what others call it?
>
>
> There was some discussion several years ago about what this should be
> called. I believe this term came from Richard Brualdi's combinatorial
> matrix theory book (I remember running down the hall to my advisor's
> office to look it up! :), but my memory may be inaccurate.
>

You remember correctly a discussion on IRC. I offered to put a scan of
the relevant page on line.

Jaap

> Thanks,
>
> Jason
>
>


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[sage-devel] Re: Bipartite graphs in Sage

Jason and David,

Thanks for the education. "transfer matrix" is the most evocative to
me, but I didn't bring it up to suggest any changes - simply curious.

Rob

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Re: [sage-devel] Re: Bipartite graphs in Sage

On Sat, Feb 27, 2010 at 2:41 PM, Rob Beezer <google@beezer.cotse.net> wrote:
> On Feb 27, 6:37 am, David Joyner <wdjoy...@gmail.com> wrote:
>> There are several places where bipartite graphs
>> differ (at least in the literature) from regular graphs.
>> For example, usually the bipartite graph's adjacency matrix
>> is not square.
>
> I think an "adjacency matrix" should always be square. But for a
> bipartite graph if you order the vertices consecutively within the two
> parts of the bipartition, then you get a block matrix with zero
> matrices in the northwest and southeast corners. And the other two
> corners are transposes of each other (but not square when the
> bipartite sets are different sizes).
>
> This is in the BipartiteGraph class as "reduced_adjacency_matrix()."
> I can't recall ever seeing this matrix given a name, so I don't know
> if this is how one would expect to find it. In the research for your
> graph theory book have you learned what others call it?


I have now seen three other terms (besides the admittedly sloppy
"adjacency matrix") for this: transfer matrix, biadjacency matrix,
and reduced adjacency matrix.


>
> Rob
>
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Re: [sage-devel] Re: Bipartite graphs in Sage

On Sat, Feb 27, 2010 at 2:54 PM, Jason Grout
<jason-sage@creativetrax.com> wrote:
> On 02/27/2010 01:41 PM, Rob Beezer wrote:
>>
>> On Feb 27, 6:37 am, David Joyner<wdjoy...@gmail.com> wrote:
>>>
>>> There are several places where bipartite graphs
>>> differ (at least in the literature) from regular graphs.
>>> For example, usually the bipartite graph's adjacency matrix
>>> is not square.
>>
>> I think an "adjacency matrix" should always be square. But for a
>> bipartite graph if you order the vertices consecutively within the two
>> parts of the bipartition, then you get a block matrix with zero
>> matrices in the northwest and southeast corners. And the other two
>> corners are transposes of each other (but not square when the
>> bipartite sets are different sizes).
>>
>> This is in the BipartiteGraph class as "reduced_adjacency_matrix()."
>> I can't recall ever seeing this matrix given a name, so I don't know
>> if this is how one would expect to find it. In the research for your
>> graph theory book have you learned what others call it?


Some also call it the transfer matrix, but I don't know if that is standard.


>
>
> There was some discussion several years ago about what this should be
> called. I believe this term came from Richard Brualdi's combinatorial
> matrix theory book (I remember running down the hall to my advisor's office
> to look it up! :), but my memory may be inaccurate.


This is correct. It is defined that way on page 107 of
Brualdi-Ryser, Combinatorial Matrix Theory. The literature I am
referring to is that of coding theorists who work with graphs,
but maybe they are using non-standard terms.


>
> Thanks,
>
> Jason
>
>
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[sage-devel] Re: Bipartite graphs in Sage

On 02/27/2010 01:41 PM, Rob Beezer wrote:
> On Feb 27, 6:37 am, David Joyner<wdjoy...@gmail.com> wrote:
>> There are several places where bipartite graphs
>> differ (at least in the literature) from regular graphs.
>> For example, usually the bipartite graph's adjacency matrix
>> is not square.
>
> I think an "adjacency matrix" should always be square. But for a
> bipartite graph if you order the vertices consecutively within the two
> parts of the bipartition, then you get a block matrix with zero
> matrices in the northwest and southeast corners. And the other two
> corners are transposes of each other (but not square when the
> bipartite sets are different sizes).
>
> This is in the BipartiteGraph class as "reduced_adjacency_matrix()."
> I can't recall ever seeing this matrix given a name, so I don't know
> if this is how one would expect to find it. In the research for your
> graph theory book have you learned what others call it?


There was some discussion several years ago about what this should be
called. I believe this term came from Richard Brualdi's combinatorial
matrix theory book (I remember running down the hall to my advisor's
office to look it up! :), but my memory may be inaccurate.

Thanks,

Jason


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[sage-devel] Re: Bipartite graphs in Sage

On Feb 27, 6:37 am, David Joyner <wdjoy...@gmail.com> wrote:
> There are several places where bipartite graphs
> differ (at least in the literature) from regular graphs.
> For example, usually the bipartite graph's adjacency matrix
> is not square.

I think an "adjacency matrix" should always be square. But for a
bipartite graph if you order the vertices consecutively within the two
parts of the bipartition, then you get a block matrix with zero
matrices in the northwest and southeast corners. And the other two
corners are transposes of each other (but not square when the
bipartite sets are different sizes).

This is in the BipartiteGraph class as "reduced_adjacency_matrix()."
I can't recall ever seeing this matrix given a name, so I don't know
if this is how one would expect to find it. In the research for your
graph theory book have you learned what others call it?

Rob

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[sage-devel] Re: BipartiteGraph status

Hi Ryan,

Thanks for working on this. I didn't even know this class
existed. ;-) Some comments.

+1 to Robert Miller's suggestion that a new vertex should be assigned
to one part of the bipartition in the call, or else an error will be
raised. At a minimum, encountering such an error will let somebody
know they are dealing with something a little more specialized than a
Graph (eg if they come by a BipartiteGraph through one of the graph
generators). This strikes me as the cleanest way to go.

Is there a basic problem with add_edge() as well? I build a
BipartiteGraph, B, on 4 vertices with two disjoint edges, then add a
couple more edges to form a triangle, and then

sage: type(B)
<class 'sage.graphs.bipartite_graph.BipartiteGraph'>
sage: B.bipartite_sets()
<BOOM>
RuntimeError: Graph is not bipartite.

Robert Bradshaw has some thoughts on organization here:
http://groups.google.com/group/sage-devel/browse_thread/thread/6a2ed79ea3bd7a02

Rob


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Re: [sage-devel] Re: Bipartite graphs in Sage

Perhaps the correct thing to do is have BipartiteGraph wrap a Graph
rather than descend from it. This way at least one wouldn't ever
accidently get incorrect answers when calling graph methods that have
different definitions in the bipartite case (including methods that
may in the future get added to Graph).

- Robert


On Feb 27, 2010, at 6:37 AM, David Joyner wrote:

> First, you should pay more attention to what
> Robert Miller says instead of me, since he
> knows the code much much better. I'm cc'ing this
> back to sage-devel; hope you don't mind.
>
> There are several places where bipartite graphs
> differ (at least in the literature) from regular graphs.
> For example, usually the bipartite graph's adjacency matrix
> is not square. Also, the vertices are usually drawn
> using 2 colors, so the plot methods might be
> different. Neither of these seem to be implemented
> in Sage. (Also, the docstring has my favorite
> self-reference:
>
> sage: BipartiteGraph?
>
> yields:
>
> ...
> Docstring:
> Create a bipartite graph. See documentation: BipartiteGraph?
> ...
>
>
> Also, the EXAMPLE is not formatted correctly.)
>
>
> As for usage, the Tanner graph of a binary code is
> the bipartite graph whose adjacency matrix is the
> check matrix of the code. I'm sure there are many other
> applications but that is the one that first springs to mind.
>
>
> On Sat, Feb 27, 2010 at 8:49 AM, Nathann Cohen <nathann.cohen@gmail.com
> > wrote:
>> Hello everybody !!!
>>
>> I followed your conversation on Sage-devel (http://bit.ly/bHTOHm),
>> and
>> I felt a bit as an outsider as I never used this class.. Could you
>> tell me what you expect from it, or what you use it for ? I can not
>> dream of a situation in which I would prefer it to the usual Graph
>> class.....
>>
>> Thank you :-)
>>
>> Nathann
>>
>
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