วันเสาร์ที่ 31 กรกฎาคม พ.ศ. 2553

[sage-devel] Re: sage-vmware-4.4.alpha0.zip Corrupted?

> [1]http://www.sagemath.org/mirror/win/meta/sage-vmware-4.4.alpha0.zip.me...
> [2]http://aria2.sourceforge.net/
>
> I'm not aware of a better solution to handle this problem ...
>
> H

Harald:

I think metalinks are great, indeed, the metalink file you reference
contains a torrent file reference:

http://sagemath.org/mirror/win/meta/sage-vmware-4.4.alpha0.zip.torrent

The only problem is that there is no bittorrent server up right now
seeding that torrent file, thus obviating the entry/file. I'm all for
promoting other clients, but bittorrent is widespread, stable, and
built-in to some browsers already (example: Opera).

Cheers,
Don

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Re: [sage-devel] Re: How does real_lazy work?

On Sat, Jul 31, 2010 at 2:32 PM, Simon King <simon.king@nuigalway.ie> wrote:
> I agree that this "error opening source code" sucks. The attitude to
> hide the code (and even the documentation, in some cases!) behind
> layers of abstraction seems a side-effect of the new category
> framework (perhaps not in this particular case, I don't know).

No, it is not. Introspection works fine with __getattr__. With the
following code,

def a_function():
return 'a function'
class PythonFooGetAttr:
def __getattr__(self, attr):
return a_function

I get

sage: f = PythonFooGetAttr()
sage: f.a_function??
Type: builtin_function_or_method
Base Class: <type 'builtin_function_or_method'>
String Form: <built-in function a_function>
Namespace: Interactive
Definition: f.a_function()
Source:
def a_function():
return 'a function'

The issue that you are seeing above is because RLF(3).sqrt is not
really a method. Look at the following

sage: a = RLF(3); a
3
sage: a.sqrt
1.732050807568878?
sage: type(a.sqrt)
<type 'sage.rings.real_lazy.LazyNamedUnop'>
sage: b = a.sqrt; b
sage: b()
1.732050807568878?

Introspection fails in the first case because you are trying to look
up the source code of an object. In these cases, the introspection
code will try to return the source code of the class of the object.
However, we have

sage: b.__class__.__doc__ is None
True

Cython should probably generate the file header ( "File:
sage/rings/integer.pyx (starting at line 417)\n\n", etc.) even when
the class does not have a docstring. Note that

sage: c = 3
sage: c??

works fine.

Again, please stop spreading FUD about the category code.

--Mike

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[sage-devel] Installing optional R packages.

Hi guys and gals,
I'm having some difficulty installing gstat, automap and sp into the
sage R environment.
I keep getting an error saying that the "sage R include directory is
empty"

Is there a way I can fix this?

Joal Heagney

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[sage-devel] Re: How does real_lazy work?

On 31 Jul., 23:32, Simon King <simon.k...@nuigalway.ie> wrote:
> > Does anyone with a bit more understanding of
> > python then me know what is going on in sage.rings.real_lazy and most
> > importand, is it possible to make the mechanism by which LazyWrapper
> > adds the sqrt function overwrite an already existing sqrt() function?
>
> One could simply define a *proper* sqrt method for the class in
> question, rather than relying on the __getattr__ game.

By this, I meant:
I see no way to overwrite an already existing *class method* 'sqrt'
with the LazyWrapper.__getattr__ mechanism.

Possibility 1:
One could write a short method of LazyWrapper for each name in
named_unops, kind of
def sqrt(self,*args):
return LazyNamedUnop(self._parent, self, 'sqrt')(*args)

Possibility 2:
One could go the opposite direction, namely extend/use the __getattr__
method of RingElement.

In other words, rather than defining a solid attribute 'sqrt' of
RingElement, one could implement it in such a way that sqrt is only
accessible via __getattr__.

Then, a class Foo inheriting from RingElement could overload
RingElement.sqrt in two ways:
1) provide a proper class method 'sqrt' (then, __getattr__ would not
be called), or
2) overload __getattr__, so that it gives a different anwer when
being asked for 'sqrt'.

I would advise against Possibility 2. I must admit that I find these
dynamic attributes more scary than elegant.

Cheers,
Simon

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[sage-devel] Re: How does real_lazy work?

Hi koffie,

On 31 Jul., 16:57, koffie <m.derickx.stud...@gmail.com> wrote:
> ... What goes wrong is
> that they add functions to a class in sage.rings.real_lazy in a way
> that I don't understand and in a way that seems not very compatible
> with good object oriented coding conventions.

I had a brief look at the code, and it seems that the LazyWrapper has
a custom __getattr__ method, which looks up additional arguments in a
list named_unops. If the argument name is known then an instance of
the class LazyNamedUnop is returned. When the LazyNamedUnop instance
is initialized, the given method name is looked up as a function in
"math".

So, it seems that sqrt for LazyWrapper is ultimately defined in the
module "math", which is (to my understanding) Python builtin. On the
positive side, this is easier than adding one attribute for each
function in "math". Difficult though it seems to work with such code.

> Below you what happens
> if you would want to see the source code of the sqrt function of
> elements of the Real Lazy Field

I agree that this "error opening source code" sucks. The attitude to
hide the code (and even the documentation, in some cases!) behind
layers of abstraction seems a side-effect of the new category
framework (perhaps not in this particular case, I don't know). Since I
like to learn from reading code, I find it anti-pedagogical.

> Now adding the sqrt function to RingElement (from which LazyWrapper
> eventually also derives) breakes the construction by which the sqrt
> function is added and now a.sqrt() becomes the function defined for
> RingElement. If the sqrt() function of LazyWrapper was added through
> normal class extensions there would have been no problem since the
> very general sqrt() function would get overwritten and everything
> would work as before.

Probably you are right: The sqrt method of LazyWrapper is obtained by
a __getattr__ method, but that will only be called if there is no
class attribute "sqrt". If RingElement has a class method sqrt then
LazyWrapper (ultimately inheriting from it) has as well, thus
__getattr__ is out of the game, and so the custom sqrt method of
LazyWrappper is gone.

Your example shows that it is not a theoretical consideration but
really happens. That is not nice.

> Does anyone with a bit more understanding of
> python then me know what is going on in sage.rings.real_lazy and most
> importand, is it possible to make the mechanism by which LazyWrapper
> adds the sqrt function overwrite an already existing sqrt() function?

One could simply define a *proper* sqrt method for the class in
question, rather than relying on the __getattr__ game.

Cheers,
Simon

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[sage-devel] How does real_lazy work?

Hej All,

I was doing some work on http://trac.sagemath.org/sage_trac/ticket/9094.
In trying to do it the nice way (i.e. avoiding unnessery double code
by putting the code in a common base class) I ran into trouble. The
core of all problems seems to be with real_lazy. What goes wrong is
that they add functions to a class in sage.rings.real_lazy in a way
that I don't understand and in a way that seems not very compatible
with good object oriented coding conventions. Below you what happens
if you would want to see the source code of the sqrt function of
elements of the Real Lazy Field (it returns an error). So the sqrt
function is actually there.

Now adding the sqrt function to RingElement (from which LazyWrapper
eventually also derives) breakes the construction by which the sqrt
function is added and now a.sqrt() becomes the function defined for
RingElement. If the sqrt() function of LazyWrapper was added through
normal class extensions there would have been no problem since the
very general sqrt() function would get overwritten and everything
would work as before. Does anyone with a bit more understanding of
python then me know what is going on in sage.rings.real_lazy and most
importand, is it possible to make the mechanism by which LazyWrapper
adds the sqrt function overwrite an already existing sqrt() function?

In sage 4.4.4 without any changes:

sage: a=RLF(3)
sage: a.sqrt??
Error getting source: could not find class definition
Type: LazyNamedUnop
Base Class: <type 'sage.rings.real_lazy.LazyNamedUnop'>
String Form: 1.732050807568878?
Namespace: Interactive
File: /Applications/sage/local/lib/python2.6/site-packages/sage/rings/
real_lazy.so
Definition: a.sqrt(self, *args)
Docstring [source file open failed]:
x.__init__(...) initializes x; see x.__class__.__doc__ for
signature

Call def: a.sqrt(self, *args)

Call docstring:

TESTS:
sage: a = RLF(32) sage: a.log(2) 5 sage: float(a.log(2)) 5.0

What is going on here in the background is
sage: from sage.rings.real_lazy import LazyNamedUnop sage: b
=
LazyNamedUnop(RLF, a, 'log') sage: b(2) 5 sage:
b(2)._extra_args
(2,)


In sage 4.4.4 with a sqrt method defined on RingElement

sage: a=RLF(3)
sage: a.sqrt??

Type: builtin_function_or_method
Base Class: <type 'builtin_function_or_method'>
String Form: <built-in method sqrt of
sage.rings.real_lazy.LazyWrapper object at 0x10c93e050>
Namespace: Interactive
Definition: a.sqrt(self, extend=True, all=False, name=None)
Source:
def sqrt(self, extend = True, all = False, name=None ):
"""
It computes the square root.

INPUT:

- ``extend`` - Whether to make a ring extension containing a
square root if self is not a square (default: True)

etc. etc. etc.

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[sage-devel] gcc 4.5.1 released today

I was just about to install gcc 4.5.0 on 't2' when I noticed that
4.5.1 has just been released today. I had to get it from the GNU site
directly, as the mirrors did not have it.

ftp://ftp.gnu.org/gnu/gcc/gcc-4.5.1/gcc-4.5.1.tar.bz2

for anyone that wants it. Given this is a maintenance release, with no
new features, hopefully there are less bugs than in 4.5.0.

Dave

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[sage-devel] Re: Groebner basis of Polynomials over integer

Hi!

I got some answer from the Singular team.

> So, they do not claim that slimgb works over the integers.

Indeed, slimgb apparently is designed for coefficients that form a
field. Therefore, calling slimgb on an integer example will, in
future, result in an error message.

To wrap it up:
I.groebner_basis()
does yield the correct answer (internally, the right algorithm is
chosen automatically).

If you want to choose one particular algorithm, do
I.groebner_basis(algorithm='libsingular:std')
or
I.groebner_basis(algorithm='singular:std')

It would be a mistake to do
I.groebner_basis(algorithm='libsingular:slimgb')
since slimgb isn't made for this case.

Cheers,
Simon

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[sage-devel] Re: multivariate power series with rmpoly

On Jul 30, 2:22 pm, Niles <nil...@gmail.com> wrote:
> On Jul 30, 7:36 am, mario <mario.pern...@gmail.com> wrote:
>
> > I have not tried using other rings; can you give me an example to try?
>
> Sure!  The patch works over any commutative ring that sage supports;
> here are a couple:
>
> sage: M.<a,b,c,d> = MPowerSeriesRing(GF(11),4); M
> Multivariate Power Series Ring in a, b, c, d over Finite Field of size
> 11
> sage: p = 3 + a + 7*b + 2*c^2 - 5*a^2*d - b^4 - 5*c*d^3 + 5*c^5 - c^8
> + 2*a^5*b^2*c^2 + M(0).O(10)
> sage: %time p^(-30);
>
> sage: P.<x,y,z> = PolynomialRing(ZZ,3); P
> Multivariate Polynomial Ring in x, y, z over Integer Ring
> sage: H.<f,g,h,k> = MPowerSeriesRing(P,4); H
> Multivariate Power Series Ring in f, g, h, k over Multivariate
> Polynomial Ring in x, y, z over Integer Ring
> sage: q = 1 + H(-x*y - y^2 - 4*y*z + 3*z^2 + 1)*h + H(x*y + 3*x*z +
> y)*k + H(-x^2 + y^2 + x*z - 2*z^2 + z)*f + H(-x*y + 4*x*z - z^2 +
> 2*x)*h*k + H(-y^2 + 2*z^2 + 12*y - 1)*f*g*h^2 + H(-x*y - 12*z^2 -
> y)*f^2*g^2 + H(1 + 6*z)*f*k^3 + H(0).O(5)
> sage: %time q^(-1);
>
> Also, it might make more sense to compare your code with sage's
> multivariate polynomial arithmetic directly; the multivariate power
> series patch is mostly just a wrapper for the polynomial arithmetic,
> and I haven't (yet) made any attempt to optimize it.  Here are the
> commands to construct some relevant polynomial rings:
>
> sage: Q.<x,y,z,w,v> = PolynomialRing(GF(7),5); Q
> Multivariate Polynomial Ring in x, y, z, w, v over Finite Field of
> size 7
> sage: R.<a,b,c> = PolynomialRing(RR,3); R
> Multivariate Polynomial Ring in a, b, c over Real Field with 53 bits
> of precision
>

With GF rmpoly.sage I tried your example with
GF(11)
(3+a+7*b+2*c^2-5*a^2*d-b^4-5*c*d^3+5*c^5-c^8+2*a^5*b^2*c^2+M(0).O(10)
rmpoly.sage 0.17s MPowerSeriesRing 0.19s
and 5 examples with GF(7):
rmpoly.sage MPowerSeriesRing
(1 + 2*a + 3*b + 4*d + L(0).O(16))^-5
0.16 0.09
(1 + a^3 + b^3 + c^4 + d^4 + L(0).O(15))^-20
0.01 0.03
(1 + a + b + a*b + a^2 + b^2 + Z(0).O(30))^-20
0.37 0.22
(1 + a + 2*b - a*b + 3*a^2 - b^2 + L(0).O(30))^-20
0.43 0.26
(1+a+12*b-10*a*b+13*a^2-7*b^2+L(0).O(30))^-20 0.35
0.23

so for power series on GF rmpoly is slower.

With real fields I tried the last five examples; with enough precision
it is OK (precision 100,53,53,100,170
used respectively in example 1,2,3,4,5)


rmpoly cannot do your example H.<f,g,h,k> = MPowerSeriesRing(P,4)

rmpoly cannot compete with Sage polynomials, although it is not so
bad; here is a Fateman test
sage: R.<x,y,z,t> = QQ[]
n = 15
sage: p1 = (1+x+y+z+t)^n
sage: p2 = p1 + 1
sage: time h = p1*p2
CPU times: user 9.82 s, sys: 0.01 s, total: 9.83 s
Wall time: 9.83 s

rmpoly.sage takes 47.8s, rmpoly.py19.9s

with R.<x,y,z,t> = PolynomialRing(GF(7),4) and n=20 Sage takes 0.7s,
rmpoly.sage 13.6s


To summarize rmpoly is faster than Sage only on power series on QQ;
I guess that a C library dedicated to power series would
be a few times faster than rmpoly power series on QQ .

Mario

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Re: [sage-devel] Help us test Cython?

On 07/30/2010 01:54 AM, Craig Citro wrote:
> So we're currently working on a long-overdue release of Cython with
> all kinds of snazzy new features. However, our automated testing
> system seems to keep turning up sporadic segfaults when running the
> sage doctest suite. This is obviously bad, but we're having a hard
> time reproducing this -- they seem to be *very* occasional failures
> while starting up sage, and thus far the only consistent appearance
> has been *within* our automated testing system (hudson). We've got a
> pile of dumped cores, which have mostly led us to the conclusions that
> (1) the problem occurs at a seemingly random point, so we should
> suspect some sort of memory corruption, and (2) sage does a *whole*
> lot of stuff when it starts up. ;)
> [...]
> After that, run the full test suite as many times as you're willing,
> hopefully with and without parallel doctesting (i.e. sage -tp). Then
> let us know what you turn up -- lots of random failures, or does
> everything pass? Points for machines we can ssh into and generated
> core files (ulimit -c unlimited), and even more points for anyone
> seeing consistent/repeatable failures. I'd also be very interested of
> reports that you've run the test suite N times with no failures.

Below are some results from parallel doctests on sage.math. In each of

/mnt/usb1/scratch/mpatel/tmp/sage-4.4.4-cython
/mnt/usb1/scratch/mpatel/tmp/sage-4.5.1-cython

I have run (or am still running)

./tester | tee -a ztester &

where 'tester' contains

#!/bin/bash
ulimit -c unlimited

RUNS=20
for I in `seq 1 $RUNS`;
do
LOG="ptestlong-j20-$I.log"
if [ ! -f "$LOG" ]; then
echo "Run $I of $RUNS"
nice ./sage -tp 20 -long -sagenb devel/sage > "$LOG" 2>&1

# grep -A2 -B1 dumped "$LOG"
ls -lsFtr `find -type f -name core` | grep core | tee -a "$LOG"

# Rename each core to core_cy.$I
rm -f _ren
find -name core -type f | awk '{print "mv "$0" "$0"_cy.'${I}'"}'
> _ren
. _ren
fi
done

The log files and cores (renamed to core_cy.1, etc.) are still in/under
SAGE_ROOT.

I don't know if the results tell you more than you already know. For
example,

sage-4.5.1-cython$ for x in `\ls ptestlong-j20-*`; do grep "doctests
failed" $x; done | grep -v "0 doctests failed" | sort | uniq -c
1 sage -t -long devel/sage/sage/graphs/graph.py # 2
doctests failed
19 sage -t -long devel/sage/sage/tests/startup.py # 1
doctests failed

But

sage-4.5.1-cython$ find -name core_cy\* | sort
./data/extcode/genus2reduction/core_cy.1
./data/extcode/genus2reduction/core_cy.10
./data/extcode/genus2reduction/core_cy.11
./data/extcode/genus2reduction/core_cy.12
./data/extcode/genus2reduction/core_cy.13
./data/extcode/genus2reduction/core_cy.14
./data/extcode/genus2reduction/core_cy.15
./data/extcode/genus2reduction/core_cy.16
./data/extcode/genus2reduction/core_cy.17
./data/extcode/genus2reduction/core_cy.18
./data/extcode/genus2reduction/core_cy.19
./data/extcode/genus2reduction/core_cy.2
./data/extcode/genus2reduction/core_cy.20
./data/extcode/genus2reduction/core_cy.3
./data/extcode/genus2reduction/core_cy.4
./data/extcode/genus2reduction/core_cy.5
./data/extcode/genus2reduction/core_cy.6
./data/extcode/genus2reduction/core_cy.7
./data/extcode/genus2reduction/core_cy.8
./data/extcode/genus2reduction/core_cy.9
./devel/sage-main/doc/fr/tutorial/core_cy.17
./devel/sage-main/sage/algebras/core_cy.17
./devel/sage-main/sage/categories/core_cy.4
./devel/sage-main/sage/categories/core_cy.6
./devel/sage-main/sage/combinat/root_system/core_cy.12
./devel/sage-main/sage/databases/core_cy.1
./devel/sage-main/sage/databases/core_cy.18
./devel/sage-main/sage/ext/core_cy.18
./devel/sage-main/sage/groups/matrix_gps/core_cy.5
./devel/sage-main/sage/gsl/core_cy.4
./devel/sage-main/sage/misc/core_cy.10
./devel/sage-main/sage/misc/core_cy.17
./devel/sage-main/sage/misc/core_cy.2
./devel/sage-main/sage/modular/abvar/core_cy.7
./devel/sage-main/sage/plot/plot3d/core_cy.19
./devel/sage-main/sage/rings/core_cy.20
./local/lib/python2.6/site-packages/sagenb-0.8.1-py2.6.egg/sagenb/testing/tests/core_cy.19

Should I test differently?

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Re: [sage-devel] Re: Wrong symbolic sum

On 07/31/2010 12:53 AM, Henryk Trappmann wrote:
> On Jul 29, 9:12 pm, kcrisman <kcris...@gmail.com> wrote:
>> I will point out, though, that you clearly *do* use Maxima, since you
>> tried to do this in Sage, which uses Maxima heavily.
>
> This may be, but I dont know about it.
> I know that Sage uses Maxima, but neither do I know what Maxima is,
> nor how to use it. But most importantly I dont know *when* sage uses
> Maxima.
> You can not expect from a normal sage user (even if he knows how to
> write plain sage code), that he knows what is called underneath his
> input line.

You could try using sage.misc.citation.get_systems:

sage: var('n, k');
sage: sum(1 / sum(k, k, 1, n), n, 1, infinity)
2
sage: from sage.misc.citation import get_systems
sage: get_systems('sum(1 / sum(k, k, 1, n), n, 1, infinity)')
['MPFI', 'ginac', 'GMP', 'Maxima']

A caveat:

sage: get_systems?
...
Returns a list of the systems used in running the command cmd.
Note that the results can sometimes include systems that did not
actually contribute to the computation. Due to caching and the
inability to follow all C calls, it could miss some dependencies as
well.
...

I don't know how accurate the returned list is for "typical"
computations. Is it correct for the example above? Maybe it's at least
a useful starting place for further investigation?

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วันศุกร์ที่ 30 กรกฎาคม พ.ศ. 2553

[sage-devel] Re: Wrong symbolic sum

On Jul 29, 9:12 pm, kcrisman <kcris...@gmail.com> wrote:
> I will point out, though, that you clearly *do* use Maxima, since you
> tried to do this in Sage, which uses Maxima heavily.

This may be, but I dont know about it.
I know that Sage uses Maxima, but neither do I know what Maxima is,
nor how to use it. But most importantly I dont know *when* sage uses
Maxima.
You can not expect from a normal sage user (even if he knows how to
write plain sage code), that he knows what is called underneath his
input line.

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[sage-devel] Re: new keywords for limit()

On 7/29/10 12:15 PM, D.C. Ernst wrote:

> Thanks for all the discussion! (I never thought such a small thing
> would generate so much discussion.)


Typically, the discussion is inversely proportional to the scope of the
change and the knowledge required to understand the change. See

http://bikeshed.com/

or

http://en.wikipedia.org/wiki/Parkinson%27s_Law_of_Triviality

Thanks,

Jason

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[sage-devel] Re: new keywords for limit()

On Jul 29, 4:31 pm, Jason B Hill <Jason.B.H...@Colorado.edu> wrote:
> > > > [X] minus/plus
>
> > > > [X] '-'/'+'
>
> > > > [ ] below/above
>
> > > > [X] left/right
>
> > > > [ ] from_left/from_right
>
> > > My votes are the same as Rob's.
>
> > Also my  votes are the same as Rob's :)
>
> Ditto.
>
> Jason

It seems that the votes are unanimous. I'll redo the patch sometime
after MathFest. Thanks for all the discussion.

Dana

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Re: [sage-devel] is this kind of license Sage-compatible?

On Fri, 30 Jul 2010 08:43:03 -0700, William Stein <wstein@gmail.com> wrote:
> On Friday, July 30, 2010, Dr. David Kirkby <david.kirkby@onetel.net> wrote:
> > On 07/30/10 04:06 PM, Dima Pasechnik wrote:
> > FSF - do you mean to write to<licensing@fsf.org>  asking this
> > question about the legal meaning of "should"?
> >
> FSF regularly and promptly answer GPL compatibility questions. It's
> their specialty. We've written them many times.

In particular, since they see many such questions, they may have already
run across this particular license and figured out its compatibility.


Best,
Alex


--
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Lecturer in Mathematics -- The University of Melbourne -- Australia

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[sage-devel] Re: Report from useR! 2010

On Jul 30, 10:07 am, kcrisman <kcris...@gmail.com> wrote:

> The funniest thing was when I told them I had never taken a statistics
> course. There was spontaneous cheering! I don't know what that says
> about statistics education... but it certainly broke the ice :)

Probably that's all the Bayesians in the audience ...
the continued dominance of frequentist BS in service courses
for nonmajors (and undergraduate majors for that matter)
is a thorn in the side. Typical courses are worse than useless
from their (my) point of view. "w00t! Good for you! You don't
need that stuff anyway!" Well, anyway that's what I would
have said.

best

Robert Dodier

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[sage-devel] Re: Report from useR! 2010

On Jul 30, 6:39 pm, Harald Schilly <harald.schi...@gmail.com> wrote:
> On 30 Jul., 18:07, kcrisman <kcris...@gmail.com> wrote:
>
> > ... and once it's prominent on
> > the website
>
> +1, and as a variation on useR, I propose the name USageE ;)

Probably without the trailing "E".

Or "Sage BUG" ("Sage Bimonthly User Group")

I guess USage is better...

Sorry for my unqualified comment
Simon

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[sage-devel] Re: Report from useR! 2010

On 30 Jul., 18:07, kcrisman <kcris...@gmail.com> wrote:
> ... and once it's prominent on
> the website

+1, and as a variation on useR, I propose the name USageE ;)

H

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Re: [sage-devel] Help us test Cython?

On Fri, Jul 30, 2010 at 1:44 AM, Mitesh Patel <qed777@gmail.com> wrote:
> On 07/30/2010 01:54 AM, Craig Citro wrote:
>> So we're currently working on a long-overdue release of Cython with
>> all kinds of snazzy new features. However, our automated testing
>> system seems to keep turning up sporadic segfaults when running the
>> sage doctest suite. This is obviously bad, but we're having a hard
>> time reproducing this -- they seem to be *very* occasional failures
>> while starting up sage, and thus far the only consistent appearance
>> has been *within* our automated testing system (hudson). We've got a
>> pile of dumped cores, which have mostly led us to the conclusions that
>> (1) the problem occurs at a seemingly random point, so we should
>> suspect some sort of memory corruption, and (2) sage does a *whole*
>> lot of stuff when it starts up. ;)
>>
>> So we'd love to see if other people see these same failures. Anyone
>> want to try out the new cython? You can grab all the files you need
>> here:
>>
>>   http://sage.math.washington.edu/home/craigcitro/cython-0.13-beta/
>>
>> There's a new spkg and 6 patches against the sage library. You can add
>> the patches, sage -i the spkg, and then do a sage -ba, and voila! you
>> should have a sage running the bleeding edge cython. (If that doesn't
>> build, it means I forgot some patch somewhere -- there's a working
>> sage-4.4.4 with the new cython in /scratch/craigcitro/cy-work/fcubed
>> on sage.math if anyone wants to root around.)
>
> I haven't done any testing yet, but in order to get './sage -ba' to
> finish, I applied a seventh patch (attached), which I discovered with
>
> hg diff -R /scratch/craigcitro/cy-work/fcubed/devel/sage

Thanks! Yes, you'd probably need that too.

- Robert

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Re: [sage-devel] Any chance of access to OS X which defaults to 32-bit ?

On Thursday, July 29, 2010, Dr. David Kirkby <david.kirkby@onetel.net> wrote:
> Is there anyone that can provide me access to a OS X machine which defaults to building 32-bit executable, but can build 64-bit executables? Ideally a machine that has been used to compile 64-bit executables of Sage.
>

I have an Osx 10.5 intel Mac that I can get you remote access to,
which I think has the above property. This won't happen until I go
to CPUs though (Monday). Remind me!


> There's a lot of code in Sage which has something like this in it:
>
> if [ `uname` = "Darwin" -a "$SAGE64" = "yes" ]; then
>  # OS X 64-bit hacks on OS X
> fi
>
> In Numpy, there's a 64-bit hack which looks pretty alful to me.
>
> # numpy's distutils is buggy and runs a conftest without
> # taking CFLAGS into account. With 64 bit OSX this results
> # in *boom*
> if [ `uname` = "Darwin" -a "$SAGE64" = "yes" ]; then
>   echo "64 bit MacIntel: copying fake gcc"
>   rm $SAGE_LOCAL/bin/gcc
>   cp gcc_fake $SAGE_LOCAL/bin/gcc
>   chmod 755 $SAGE_LOCAL/bin/gcc
> fi
>
> then later this fake gcc gets deleted.
>
> if [ `uname` = "Darwin" -a "$SAGE64" = "yes" ]; then
>   echo "64 bit MacIntel: deleting fake gcc"
>   rm $SAGE_LOCAL/bin/gcc
> fi
>
>
> I think a much simpler solution is just to set
>
> CC="gcc -m64"
> export CC
>
> and that's it.
>
> No messing around with fake gccs. But I'd like access to an OS X machine which defaults to 32-bit, but can build 64-bit, in order that I can test this.
>
> Dave
>
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[sage-devel] Re: Report from useR! 2010

> Let's start users groups!  For the first year of Sage development,
> I actually was very active in the Boston (and San Diego) Python
> user groups, and gave a lot of talks about Sage.  Those people were
> great.  Maybe the time is right (and ripe).

I think the model would have to be different, of course, since most
current users of Sage aren't using it in the same way as a programmer
uses Python or a trader/statistician uses R, except some researchers
who are actively developing code. Particularly those using it
primarily for teaching likely wouldn't have the flexibility to pop off
to a monthly meeting to discuss something high-level. Keep in mind
that most R user groups have several *hundred* members, maybe a score
or two of whom show up in a given month.

But if we got three or four locations where a bimonthly Sage user
group (I can't think of a good acronym yet) would do well (Seattle...
where else?), that could work as a model, and once it's prominent on
the website and those are doing well, others may well ask for the same
thing - this happens with R a fair amount, I think. This could be a
separate thread if anyone is interested in discussing it further, and
the R user group people definitely are interested in talking about
it. See http://www.drewconway.com/zia/?p=2221 for a very informative
panel discussion on it, which also takes into account differences in
who is using R in different areas.

>
> > I hope this provides much food for thought!
>
> Many, many thanks for posting this.  I'm really glad you spoke at the
> R conference.

Thank John Verzani for raising the idea, and your tax dollars (via the
NSF and NIST) for making it possible! It was also a great experience
for me in terms of non-Sage pedagogy/advising issues, but that's not
relevant here.

The funniest thing was when I told them I had never taken a statistics
course. There was spontaneous cheering! I don't know what that says
about statistics education... but it certainly broke the ice :)

- kcrisman

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Re: [sage-devel] is this kind of license Sage-compatible?

On Friday, July 30, 2010, Dr. David Kirkby <david.kirkby@onetel.net> wrote:
> On 07/30/10 04:06 PM, Dima Pasechnik wrote:
>
> On Jul 29, 5:16 pm, William Stein<wst...@gmail.com>  wrote:
>
> On Thursday, July 29, 2010, Dima Pasechnik<dimp...@gmail.com>  wrote:
>
> I guess it boils down to whether "should" means "must" here, or not.
> Are there any means to decide, any precedents?
>
>
>
> (I can also contact authors and ask whether they might soften the
> language...)
>
>
> Yes and you should definitely write to the FSF.
>
>
>
> FSF - do you mean to write to<licensing@fsf.org>  asking this
> question about the legal meaning of "should"?
>
>
> I wonder how long their legal department would debate that one?
>
>
> I wrote to an author I know, no reply so far.
>

FSF regularly and promptly answer GPL compatibility questions. It's
their specialty. We've written them many times.

>
> That seems far more sensible.
>
>
> Dima
>
>
> I can appreciate an author would want acknowledging for their work. I think that is a big gripe many people have about the GPL v2.
>
> Dave
>
> --
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>

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http://wstein.org

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Re: [sage-devel] Re: is this kind of license Sage-compatible?

On 07/30/10 04:06 PM, Dima Pasechnik wrote:
> On Jul 29, 5:16 pm, William Stein<wst...@gmail.com> wrote:
>> On Thursday, July 29, 2010, Dima Pasechnik<dimp...@gmail.com> wrote:
>>> I guess it boils down to whether "should" means "must" here, or not.
>>> Are there any means to decide, any precedents?
>>
>>> (I can also contact authors and ask whether they might soften the
>>> language...)
>>
>> Yes and you should definitely write to the FSF.
>>
>
> FSF - do you mean to write to<licensing@fsf.org> asking this
> question about the legal meaning of "should"?

I wonder how long their legal department would debate that one?

> I wrote to an author I know, no reply so far.

That seems far more sensible.

> Dima

I can appreciate an author would want acknowledging for their work. I think that
is a big gripe many people have about the GPL v2.

Dave

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[sage-devel] Re: Groebner basis of Polynomials over integer

On Jul 30, 3:54 pm, Simon King <simon.k...@nuigalway.ie> wrote:
> Singular 3-1-1 did not solve the problem....

or at least, it did not solve all of it. The bug in liftstd has been
fixed in Singular 3-1-1.

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[sage-devel] Re: is this kind of license Sage-compatible?

On Jul 29, 5:16 pm, William Stein <wst...@gmail.com> wrote:
> On Thursday, July 29, 2010, Dima Pasechnik <dimp...@gmail.com> wrote:
> > I guess it boils down to whether "should" means "must" here, or not.
> > Are there any means to decide, any precedents?
>
> > (I can also contact authors and ask whether they might soften the
> > language...)
>
> Yes and you should definitely write to the FSF.
>

FSF - do you mean to write to <licensing@fsf.org> asking this
question about the legal meaning of "should"?

I wrote to an author I know, no reply so far.

Dima


> > Thanks,
> > Dima
>
> > On Jul 28, 9:43 pm, William Stein <wst...@gmail.com> wrote:
> >> On Wed, Jul 28, 2010 at 11:30 AM, David Joyner <wdjoy...@gmail.com> wrote:
> >> > On Wed, Jul 28, 2010 at 12:46 PM, William Stein <wst...@gmail.com> wrote:
> >> >> On Wed, Jul 28, 2010 at 8:52 AM, David Joyner <wdjoy...@gmail.com> wrote:
> >> >>> I think this is basically a modified BSD license, which is GPL compatible.
>
> >> >> It has an additional condition that is not in the GPL: "Any
> >> >> publication resulting from research that made use of
> >> >> this software should cite this document."  This might make it non-GPL
> >> >> compatible.
>
> >> > I view that as more of a request (as in "here is how to
> >> > cite DSDP...") than a legal requirement, but maybe I'm wrong.
>
> >> If it is a request, it's fine.  If it is a legal requirement, then it
> >> definitely renders the software GPL-incompatible.
> >> If it's a legal requirement, then it is kind of similar to the
> >> "advertising must explicitly cite this component" clause of the
> >> original non-GPL-compatible BSD license.
>
> >>  -- William
>
> >> >> William
>
> >> >>> On Wed, Jul 28, 2010 at 11:29 AM, Dima Pasechnik <dimp...@gmail.com> wrote:
> >> >>>>http://www.mcs.anl.gov/hs/software/DSDP/Copyright.txt
>
> >> >>>> (C) COPYRIGHT 2004 UNIVERSITY OF CHICAGO
>
> >> >>>> This program discloses material protectable under copyright laws of
> >> >>>> the United States.
> >> >>>> Permission to copy and modify this software and its documentation is
> >> >>>> hereby granted, provided that this notice is retained thereon and on
> >> >>>> all copies or
> >> >>>> modifications. The University of Chicago makes no representations as
> >> >>>> to the suitability
> >> >>>> and operability of this software for any purpose. It is provided "as
> >> >>>> is"; without
> >> >>>> express or implied warranty. Permission is hereby granted to use,
> >> >>>> reproduce, prepare
> >> >>>> derivative works, and to redistribute to others, so long as this
> >> >>>> original copyright notice
> >> >>>> is retained.  Any publication resulting from research that made use of
> >> >>>> this software
> >> >>>> should cite this document.
>
> >> >>>> [.... truncated - there is more stuff...]
>
> >> >>>> Thanks,
> >> >>>> Dima
>
> >> >>>> --
> >> >>>> To post to this group, send an email to sage-devel@googlegroups.com
> >> >>>> To unsubscribe from this group, send an email to sage-devel+unsubscribe@googlegroups.com
> >> >>>> For more options, visit this group athttp://groups.google.com/group/sage-devel
> >> >>>> URL:http://www.sagemath.org
>
> >> >>> --
> >> >>> To post to this group, send an email to sage-devel@googlegroups.com
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> >> >>> For more options, visit this group athttp://groups.google.com/group/sage-devel
> >> >>> URL:http://www.sagemath.org
>
> >> >> --
> >> >> William Stein
> >> >> Professor of Mathematics
> >> >> University of Washington
> >> >>http://wstein.org
>
> >> >> --
> >> >> To post to this group, send an email to sage-devel@googlegroups.com
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> >> >> URL:http://www.sagemath.org
>
> >> > --
> >> > To post to this group, send an email to sage-devel@googlegroups.com
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> >> > URL:http://www.sagemath.org
>
> >> --
> >> William Stein
> >> Professor of Mathematics
> >> University of Washingtonhttp://wstein.org
>
> > --
> > To post to this group, send an email to sage-devel@googlegroups.com
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> > URL:http://www.sagemath.org
>
> --
> William Stein
> Professor of Mathematics
> University of Washingtonhttp://wstein.org

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[sage-devel] Re: sage -clone failing with "...untrusted file/user..." message

it is a system-wide sage, right.

So I must be misreading what
devel/sage/doc/output/html/en/developer/walk_through.html#creating-a-
sandbox
is saying - I certainly know that I mostly can just do "cp -al ..." on
a sage installation to make a copy, but I just thought
this would be the right way.

On Jul 30, 5:52 pm, Willem Jan Palenstijn <w...@usecode.org> wrote:
> On Fri, Jul 30, 2010 at 07:47:17AM -0700, Dima Pasechnik wrote:
> > While this gets me past this particular message, it still does not do
> > the job:
>
> > guest@pasechnik1:/tmp/xx$ sage -clone xxx
> > Now cloning the current Sage library branch...
> > hg clone  sage sage-xxx
> > abort: Permission denied: sage-xxx
> > Error cloning
> > ....
> > -----
> > Is it trying to make a clone in-place rather than at the location I
> > want ?
>
> The sage library of which sage are you trying to clone? It looks like 'sage'
> might be a system-wide sage?
>
> -Willem Jan
>
>
>
> > On Jul 29, 9:48?pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
> > > Part 3, point #3 at
>
> > >http://hub.opensolaris.org/bin/view/Community+Group+on/2008080405
>
> > > says:
>
> > > "you can put a [trusted] section into your own .hgrc"
>
> > > Not a good solution universally, but maybe it will make a clone happen
> > > for you?
>
> > > On Jul 29, 8:11?am, Dima Pasechnik <dimp...@gmail.com> wrote:
>
> > > > I tried on couple of other systems, and got pretty much the same
> > > > problem.
> > > > All is needed is to be logged in as an ordinary user, different from
> > > > the one owning the sage
> > > > installation. The following is on my laptop (sage install owned by
> > > > dima, and logged in as guest)
>
> > > > guest@pasechnik1:~/test$ sage -clone test
> > > > Now cloning the current Sage library branch...
> > > > hg clone ?sage sage-test
> > > > Not trusting file /usr/local/src/sage/sage-4.5.1/devel/sage-main/.hg/
> > > > hgrc from untrusted user dima, group dima
> > > > abort: Permission denied: sage-test
> > > > Error cloning
> > > > ...
>
> > > > Dima
>
> > > > On Jul 28, 7:57?pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
>
> > > > > I just saw this yesterday. ?I had installed Sage from source as a
> > > > > normal user (myself), but then began messing around while in a shell
> > > > > as root (oops). ?If I recall right, the first thing I did was
>
> > > > > hg qinit
>
> > > > > and then as a result several files had their ownership change to root
> > > > > and I started to see the "Not trusting..." message. ?When I restored a
> > > > > few files to the right ownership (fncache ?being one) all was well and
> > > > > the message went away.
>
> > > > > Maybe poke around in ?devel/sage/.hg ?and see who owns what?
>
> > > > > Rob
>
> > > > > On Jul 28, 5:07?am, Dima Pasechnik <dimp...@gmail.com> wrote:
>
> > > > > > Dear all,
> > > > > > any idea what to do with this:
>
> > > > > > dima@sage:/scratch/dima$ sage -clone testcvxopt
> > > > > > Now cloning the current Sage library branch...
> > > > > > hg clone ?sage sage-testcvxopt
> > > > > > Not trusting file /usr/local/sage/devel/sage-main/.hg/hgrc from
> > > > > > untrusted user mvngu, group mvngu
> > > > > > abort: Permission denied: sage-testcvxopt
> > > > > > Error cloning
>
> > > > > > real ? ?0m0.091s
> > > > > > user ? ?0m0.070s
> > > > > > sys ? ? 0m0.010s
> > > > > > dima@sage:/scratch/dima$
>
> > > > > > Thanks,
> > > > > > Dima
>
> > --
> > To post to this group, send an email to sage-devel@googlegroups.com
> > To unsubscribe from this group, send an email to sage-devel+unsubscribe@googlegroups.com
> > For more options, visit this group athttp://groups.google.com/group/sage-devel
> > URL:http://www.sagemath.org

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[sage-devel] Re: Groebner basis of Polynomials over integer

I just saw that Singular has a disclaimer:
> ring R = integer, (x,y), dp;
// ** You are using coefficient rings which are not fields.
// ** Please note that only limited functionality is available
// ** for these coefficients.
// **
// ** The following commands are meant to work:
// ** - basic polynomial arithmetic
// ** - std
// ** - syz
// ** - lift
// ** - reduce

So, they do not claim that slimgb works over the integers.

Anyway, it's annoying.

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[sage-devel] Re: Groebner basis of Polynomials over integer

On Jul 30, 3:02 pm, Simon King <simon.k...@nuigalway.ie> wrote:
> The Singular version in Sage is 3-1-0, but the most recent Singular
> version is 3-1-1. I think there is some new singular-spkg lying
> around, and so I'll soon be able to tell whether Singular 3-1-1 still
> has these problems.

Singular 3-1-1 did not solve the problem. So, I'll report upstream.

Cheers,
Simon

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Re: [sage-devel] Re: sage -clone failing with "...untrusted file/user..." message

On Fri, Jul 30, 2010 at 07:47:17AM -0700, Dima Pasechnik wrote:
> While this gets me past this particular message, it still does not do
> the job:
>
> guest@pasechnik1:/tmp/xx$ sage -clone xxx
> Now cloning the current Sage library branch...
> hg clone sage sage-xxx
> abort: Permission denied: sage-xxx
> Error cloning
> ....
> -----
> Is it trying to make a clone in-place rather than at the location I
> want ?

The sage library of which sage are you trying to clone? It looks like 'sage'
might be a system-wide sage?

-Willem Jan



> On Jul 29, 9:48?pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
> > Part 3, point #3 at
> >
> > http://hub.opensolaris.org/bin/view/Community+Group+on/2008080405
> >
> > says:
> >
> > "you can put a [trusted] section into your own .hgrc"
> >
> > Not a good solution universally, but maybe it will make a clone happen
> > for you?
> >
> > On Jul 29, 8:11?am, Dima Pasechnik <dimp...@gmail.com> wrote:
> >
> >
> >
> > > I tried on couple of other systems, and got pretty much the same
> > > problem.
> > > All is needed is to be logged in as an ordinary user, different from
> > > the one owning the sage
> > > installation. The following is on my laptop (sage install owned by
> > > dima, and logged in as guest)
> >
> > > guest@pasechnik1:~/test$ sage -clone test
> > > Now cloning the current Sage library branch...
> > > hg clone ?sage sage-test
> > > Not trusting file /usr/local/src/sage/sage-4.5.1/devel/sage-main/.hg/
> > > hgrc from untrusted user dima, group dima
> > > abort: Permission denied: sage-test
> > > Error cloning
> > > ...
> >
> > > Dima
> >
> > > On Jul 28, 7:57?pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
> >
> > > > I just saw this yesterday. ?I had installed Sage from source as a
> > > > normal user (myself), but then began messing around while in a shell
> > > > as root (oops). ?If I recall right, the first thing I did was
> >
> > > > hg qinit
> >
> > > > and then as a result several files had their ownership change to root
> > > > and I started to see the "Not trusting..." message. ?When I restored a
> > > > few files to the right ownership (fncache ?being one) all was well and
> > > > the message went away.
> >
> > > > Maybe poke around in ?devel/sage/.hg ?and see who owns what?
> >
> > > > Rob
> >
> > > > On Jul 28, 5:07?am, Dima Pasechnik <dimp...@gmail.com> wrote:
> >
> > > > > Dear all,
> > > > > any idea what to do with this:
> >
> > > > > dima@sage:/scratch/dima$ sage -clone testcvxopt
> > > > > Now cloning the current Sage library branch...
> > > > > hg clone ?sage sage-testcvxopt
> > > > > Not trusting file /usr/local/sage/devel/sage-main/.hg/hgrc from
> > > > > untrusted user mvngu, group mvngu
> > > > > abort: Permission denied: sage-testcvxopt
> > > > > Error cloning
> >
> > > > > real ? ?0m0.091s
> > > > > user ? ?0m0.070s
> > > > > sys ? ? 0m0.010s
> > > > > dima@sage:/scratch/dima$
> >
> > > > > Thanks,
> > > > > Dima
>
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[sage-devel] Re: sage -clone failing with "...untrusted file/user..." message

While this gets me past this particular message, it still does not do
the job:

guest@pasechnik1:/tmp/xx$ sage -clone xxx
Now cloning the current Sage library branch...
hg clone sage sage-xxx
abort: Permission denied: sage-xxx
Error cloning
....
-----
Is it trying to make a clone in-place rather than at the location I
want ?

Thanks,
Dima

On Jul 29, 9:48 pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
> Part 3, point #3 at
>
> http://hub.opensolaris.org/bin/view/Community+Group+on/2008080405
>
> says:
>
> "you can put a [trusted] section into your own .hgrc"
>
> Not a good solution universally, but maybe it will make a clone happen
> for you?
>
> On Jul 29, 8:11 am, Dima Pasechnik <dimp...@gmail.com> wrote:
>
>
>
> > I tried on couple of other systems, and got pretty much the same
> > problem.
> > All is needed is to be logged in as an ordinary user, different from
> > the one owning the sage
> > installation. The following is on my laptop (sage install owned by
> > dima, and logged in as guest)
>
> > guest@pasechnik1:~/test$ sage -clone test
> > Now cloning the current Sage library branch...
> > hg clone  sage sage-test
> > Not trusting file /usr/local/src/sage/sage-4.5.1/devel/sage-main/.hg/
> > hgrc from untrusted user dima, group dima
> > abort: Permission denied: sage-test
> > Error cloning
> > ...
>
> > Dima
>
> > On Jul 28, 7:57 pm, Rob Beezer <goo...@beezer.cotse.net> wrote:
>
> > > I just saw this yesterday.  I had installed Sage from source as a
> > > normal user (myself), but then began messing around while in a shell
> > > as root (oops).  If I recall right, the first thing I did was
>
> > > hg qinit
>
> > > and then as a result several files had their ownership change to root
> > > and I started to see the "Not trusting..." message.  When I restored a
> > > few files to the right ownership (fncache  being one) all was well and
> > > the message went away.
>
> > > Maybe poke around in  devel/sage/.hg  and see who owns what?
>
> > > Rob
>
> > > On Jul 28, 5:07 am, Dima Pasechnik <dimp...@gmail.com> wrote:
>
> > > > Dear all,
> > > > any idea what to do with this:
>
> > > > dima@sage:/scratch/dima$ sage -clone testcvxopt
> > > > Now cloning the current Sage library branch...
> > > > hg clone  sage sage-testcvxopt
> > > > Not trusting file /usr/local/sage/devel/sage-main/.hg/hgrc from
> > > > untrusted user mvngu, group mvngu
> > > > abort: Permission denied: sage-testcvxopt
> > > > Error cloning
>
> > > > real    0m0.091s
> > > > user    0m0.070s
> > > > sys     0m0.010s
> > > > dima@sage:/scratch/dima$
>
> > > > Thanks,
> > > > Dima

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[sage-devel] Re: Groebner basis of Polynomials over integer

PS:

On Jul 30, 2:58 pm, Simon King <simon.k...@nuigalway.ie> wrote:
> I see three probably independent bugs, two of them in Singular. So, I
> will also report upstream.

The Singular version in Sage is 3-1-0, but the most recent Singular
version is 3-1-1. I think there is some new singular-spkg lying
around, and so I'll soon be able to tell whether Singular 3-1-1 still
has these problems.

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[sage-devel] Re: Groebner basis of Polynomials over integer

On Jul 30, 1:51 pm, Simon King <simon.k...@nuigalway.ie> wrote:
> I just arrived in my office, I am now doing some tests, also involving
> other computer algebra systems. I'll report back when I opened a trac
> ticket for this.

The trac ticket is at http://trac.sagemath.org/sage_trac/ticket/9645

I see three probably independent bugs, two of them in Singular. So, I
will also report upstream.

Cheers,
Simon

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[sage-devel] Re: Groebner basis of Polynomials over integer

Hi Dusan,

On Jul 30, 12:58 pm, Dušan Orlović <duleorlo...@gmail.com> wrote:
> Hi Simon, thanks for replying,
> your example: y*I.0 -2*y^3*I.1 -x*I.2  is x*y^2  which lies in ideal [x*y^3,
> 2*x^2 + x*y, 3*x*y,
> 2*y^2]  as  y * (3*x*y) - x * (2*y^2) = x*y^2, so it has to be reduced to
> zero. Am I right?

Yes. I wrote "y*I.0 -2*y^3*I.1 -x*I.2" in order to demonstrate that we
really have an element of the ideal that is not reduced to zero, in
order to assert that the answer you expected was not a Groebner basis
in degree reverse lexicographic order (and x>y, by the way).

> Please tell me which command should I use to avoid bugs.
> Is it the parameter (algorithm='toy:buchberger2')  ?

As the name says, 'toy:...' is a toy, hardly useful for any serious
computation. And, as I demonstrated in my previous post, the answer
given with toy:buchberger and toy:buchberger2 and (surprisingly)
libsingular:slimgb are wrong.

It is hard to say how to avoid bugs. Groebner bases over the integers
are relatively new in Singular (hence, also new in Sage), and
therefore it does not surprise me that there are still a couple of
bugs to discover.

But I don't know where the bug is actually located. Theoretically, it
could also be in "reduce".

The best way to avoid bugs? Well, one should never blindly trust any
computer algebra system. Doing a verification by hand (as you did) is
certainly a good approach, as long as the examples are small enough.

I just arrived in my office, I am now doing some tests, also involving
other computer algebra systems. I'll report back when I opened a trac
ticket for this.

Cheers,
Simon

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[sage-devel] Re: multivariate power series with rmpoly

On Jul 30, 7:36 am, mario <mario.pern...@gmail.com> wrote:
>
> I have not tried using other rings; can you give me an example to try?
>
Sure! The patch works over any commutative ring that sage supports;
here are a couple:

sage: M.<a,b,c,d> = MPowerSeriesRing(GF(11),4); M
Multivariate Power Series Ring in a, b, c, d over Finite Field of size
11
sage: p = 3 + a + 7*b + 2*c^2 - 5*a^2*d - b^4 - 5*c*d^3 + 5*c^5 - c^8
+ 2*a^5*b^2*c^2 + M(0).O(10)
sage: %time p^(-30);

sage: P.<x,y,z> = PolynomialRing(ZZ,3); P
Multivariate Polynomial Ring in x, y, z over Integer Ring
sage: H.<f,g,h,k> = MPowerSeriesRing(P,4); H
Multivariate Power Series Ring in f, g, h, k over Multivariate
Polynomial Ring in x, y, z over Integer Ring
sage: q = 1 + H(-x*y - y^2 - 4*y*z + 3*z^2 + 1)*h + H(x*y + 3*x*z +
y)*k + H(-x^2 + y^2 + x*z - 2*z^2 + z)*f + H(-x*y + 4*x*z - z^2 +
2*x)*h*k + H(-y^2 + 2*z^2 + 12*y - 1)*f*g*h^2 + H(-x*y - 12*z^2 -
y)*f^2*g^2 + H(1 + 6*z)*f*k^3 + H(0).O(5)
sage: %time q^(-1);


Also, it might make more sense to compare your code with sage's
multivariate polynomial arithmetic directly; the multivariate power
series patch is mostly just a wrapper for the polynomial arithmetic,
and I haven't (yet) made any attempt to optimize it. Here are the
commands to construct some relevant polynomial rings:

sage: Q.<x,y,z,w,v> = PolynomialRing(GF(7),5); Q
Multivariate Polynomial Ring in x, y, z, w, v over Finite Field of
size 7
sage: R.<a,b,c> = PolynomialRing(RR,3); R
Multivariate Polynomial Ring in a, b, c over Real Field with 53 bits
of precision

-Niles


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Re: [sage-devel] Re: Groebner basis of Polynomials over integer

Hi Simon, thanks for replying,
your example: y*I.0 -2*y^3*I.1 -x*I.2  is x*y^2  which lies in ideal [x*y^3, 2*x^2 + x*y, 3*x*y,
2*y^2]  as  y * (3*x*y) - x * (2*y^2) = x*y^2, so it has to be reduced to zero. Am I right?
Please tell me which command should I use to avoid bugs.
Is it the parameter (algorithm='toy:buchberger2')  ?
Bye,


On Fri, Jul 30, 2010 at 1:07 PM, Simon King <simon.king@nuigalway.ie> wrote:
PS:

On 30 Jul., 12:57, Simon King <simon.k...@nuigalway.ie> wrote:
> No, you are wrong. Your expected answer is definitely not correct,

But certainly there is something wrong in Singular/libsingular (which
by default is used in Sage to compute Gröbner bases) as well:

sage:
(I.groebner_basis(algorithm='toy:buchberger2')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='toy:buchberger')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='singular:std')*R).interreduced_basis()
[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='libsingular:std')*R).interreduced_basis()
[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='libsingular:slimgb')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]

So, it looks like both toy:buchberger and toy:buchberger2 and slimgb
coincide - and they are in majority. But again, they are wrong:

sage: (y*I.0 -2*y^3*I.1 -x*I.
2).reduce(I.groebner_basis(algorithm='libsingular:slimgb'))
x*y^2

So, this will actually be several bug reports to Singular.

Thank you for pointing us to this!
Simon

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[sage-devel] Re: multivariate power series with rmpoly

On Jul 30, 8:35 am, Niles <nil...@gmail.com> wrote:
> Hi, I think both the links are pointing to the same patch, which I've
> been working on recently--thanks for taking a look!  To get the patch
> from trac to work, I think you need to use mercurial; there are some
> instructions in the sage developer guide, but in case you don't feel
> like going through all that I've put the two files online at
>
> http://www.math.uga.edu/~njohnson/sage-code/multi_power_series_ring.py
>
> and
>
> http://www.math.uga.edu/~njohnson/sage-code/multi_power_series_ring_e...
>
> It should work to just read them into a sage session, but let me know
> if you have trouble.  The times for your code look great!  If I
> understand correctly, the left column is from the trac patch, the
> middle is your code in python, and the right is your code modified to
> run in sage.  I suspect that if you run all the tests on the same
> machine, the timings for your code will look even better, but maybe
> you could let us know if that's not the case.  Could your code extend
> to work over other base rings?
>
> For those interested, the email link from Mario's first post contains
> timing comparisons between the trac patch and magma, with the general
> conclusion that the trac patch performs better than Magma in several
> cases, especially when the total degree is larger than a few hundred.
>

Thank you for putting the files online! I have updated the benchmark
table using the trac patch code

(time in seconds)
trac rmpoly.py rmpoly.sage expression
3.72 0.58 1.24 (1 + 2*a + 3*b + 4*d +
L(0).O(16))^-5
0.03 0.01 0.01 (1 + a^3 + b^3 + c^4 +
d^4 + L(0).O(15))^-20
0.33 0.07 0.12 (-1/6*b^6*d^14 -
1/9*a^4*b^10*c^4*d^12 +...+L(0).O(50))^20
14.3 0.52 1.21 (1 + 1/2*a + 3*b +
4*a*b + ... + Z(0).O(30))^-20
0.10 0.001 0.002
(1+a^14*b^9+8/3*a^22*b^11-...+Z(0).O(51))^-20
2.28 0.39 1.03 (1 + a + b + a*b +
a^2 + b^2 + Z(0).O(30))^-20
3.38 0.40 1.09 (1 + a + 2*b - a*b +
3*a^2 - b^2 + Z(0).O(30))^-20
3.77 0.41 1.10 (1+a+12*b-10*a*b
+13*a^2-7*b^2+Z(0).O(30))^-20

I have not tried using other rings; can you give me an example to try?

> On 30 Jul., 01:03, Bill Hart <goodwillh...@googlemail.com> wrote:
> I'm curious how you are getting good timings in Pure python? Is it a
> new/clever algorithm? How does it fare for longer power series? Are
> there even good algorithms that are asymptotically fast for these
> sorts of problems? And can some of these be reduced to ordinary
> multivariate polynomial computations?

In rmpoly Poly inherits from dict, in which the key is an integer
packed exponent;
a polynomial p has a precision p.rp.bits_exp; each variable
has bits_exp bits, so the maximum power of a variable is 2^(bits_exp)
- 1 .
There is an extra bit for each variable, used to detect overflow.
The values of the dict are the coefficients.
Packed exponents save memory, which helps with big polynomials. The
product of two monomials
is given by the sum of the packed exponents. The division is given by
the difference
of the packed exponents and a mask operation (see
http://code.google.com/p/rmpoly/wiki/Internals).
With 'grlex' ordering there is an extra variable carrying the total
degree, used in truncations based on
the total degree.
No clever algorithm is used; packed exponents have been used before,
see
e.g. the article by M. Monagan, R. Pearce 'Polynomial multiplication
and division using heap'
available online.
Since Python has fast dicts and integers with arbitrary size, it
performs well with the product of
polynomials and series.
I suppose that the Sage version of rmpoly is slower because the Sage
Integer is slower than Python
integer for sums, and that a cython version of rmpoly would be as fast
as the Python version.

Mario


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[sage-devel] Re: Groebner basis of Polynomials over integer

PS:

On 30 Jul., 12:57, Simon King <simon.k...@nuigalway.ie> wrote:
> No, you are wrong. Your expected answer is definitely not correct,

But certainly there is something wrong in Singular/libsingular (which
by default is used in Sage to compute Gröbner bases) as well:

sage:
(I.groebner_basis(algorithm='toy:buchberger2')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='toy:buchberger')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='singular:std')*R).interreduced_basis()
[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='libsingular:std')*R).interreduced_basis()
[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
sage:
(I.groebner_basis(algorithm='libsingular:slimgb')*R).interreduced_basis()
[2*x^2 + x*y, 3*x*y, 2*y^2]

So, it looks like both toy:buchberger and toy:buchberger2 and slimgb
coincide - and they are in majority. But again, they are wrong:

sage: (y*I.0 -2*y^3*I.1 -x*I.
2).reduce(I.groebner_basis(algorithm='libsingular:slimgb'))
x*y^2

So, this will actually be several bug reports to Singular.

Thank you for pointing us to this!
Simon

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[sage-devel] Re: Groebner basis of Polynomials over integer

Hi Dule,

On 30 Jul., 12:03, DuleOrlovic <duleorlo...@gmail.com> wrote:
>...
>  [x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
> ... this is wrong result.
> Right one is  [x*y^3, 2*x^2 + x*y, 3*x*y, 2*y^2]

No, you are wrong. Your expected answer is definitely not correct,
since it does not reduce all elements of I to zero:
sage: R.<x,y>=PolynomialRing(ZZ,2)
sage: I=R*(4*x^2*y^2+2*x*y^3+3*x*y,2*x^2+x*y,2*y^2)
sage: (y*I.0 -2*y^3*I.1 -x*I.2).reduce([x*y^3, 2*x^2 + x*y, 3*x*y,
2*y^2])
x*y^2

On the contrary, the answer of Sage reduces all elements of your
expected result to zero:
sage: G = I.groebner_basis(); G
[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
sage: [g.reduce(G) for g in [x*y^3, 2*x^2 + x*y, 3*x*y, 2*y^2]]
[0, 0, 0, 0]

So, if any of the two answers is correct then it is G -- provided that
all elements of G belong to I.

Here might indeed be a problem. I am using singular's liftstd:
sage: r = singular(R)
sage: i = singular(I)
sage: singular.eval('matrix m')
'matrix m;'
sage: singular.eval('liftstd(%s,m)'%i.name())
'_[1]=2*y^2\n_[2]=-3*x*y\n_[3]=2*x^2+x*y\n_[4]=x*y^2\n_[5]=x^2*y'
sage: singular('m')
0,-1, 0,y, -3*x-y,
0,2*y^2,1,-2*y^3,2*y^3+5*y,
1,0, 0,-x, -x-2*y

So, singular yields the elements of G in opposite order (up to sign),
which is fine.

However, there indeed seems to be something wrong, because multiplying
i with the matrix m should result in the returned Gröbner basis:
sage: i.matrix()*singular('m')
2*y^2,-3*x*y,2*x^2+x*y,x*y^2,-12*x^3*y^2-6*x^2*y^3+x^2*y-4*y^3
So, the last polynomial is not as expected.

I'll file a bug report to singular.

You are certainly aware that the Gröbner basis crucially depends on
the choice of a term ordering. What ordering did you use? G is a
degrevlex Gröbner basis:
sage: R.term_order()
Degree reverse lexicographic term order

Cheers,
Simon

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[sage-devel] Groebner basis of Polynomials over integer

Hi,
when I type example below...

R.<x,y>=PolynomialRing(ZZ,2)
I=R*(4*x^2*y^2+2*x*y^3+3*x*y,2*x^2+x*y,2*y^2)
I.groebner_basis()

[x^2*y, x*y^2, 2*x^2 + x*y, 3*x*y, 2*y^2]
... this is wrong result.
Right one is [x*y^3, 2*x^2 + x*y, 3*x*y, 2*y^2] (from the book, and
calculating by hand).
How can I find the bug?

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Re: [sage-devel] Help us test Cython?

# HG changeset patch
# User Mitesh Patel <qed777@gmail.com>
# Date 1280479098 25200
# Node ID 82cbd7d1972a74357d6cebda757f42e6a58fde64
# Parent 41eae77c6bd6d1fb54827a96c1a019c036904a46
Update CYTHON_INCLUDE_DIRS

diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -464,7 +464,11 @@ class sage_build_ext(build_ext):
###### Dependency checking
#############################################

-CYTHON_INCLUDE_DIRS=[ SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/' ]
+#CYTHON_INCLUDE_DIRS=[ SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/' ]
+CYTHON_INCLUDE_DIRS=[
+ SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/',
+ SAGE_LOCAL + '/lib/python/site-packages/Cython/Includes/Deprecated/'
+]

# matches any dependency
import re
On 07/30/2010 01:54 AM, Craig Citro wrote:
> So we're currently working on a long-overdue release of Cython with
> all kinds of snazzy new features. However, our automated testing
> system seems to keep turning up sporadic segfaults when running the
> sage doctest suite. This is obviously bad, but we're having a hard
> time reproducing this -- they seem to be *very* occasional failures
> while starting up sage, and thus far the only consistent appearance
> has been *within* our automated testing system (hudson). We've got a
> pile of dumped cores, which have mostly led us to the conclusions that
> (1) the problem occurs at a seemingly random point, so we should
> suspect some sort of memory corruption, and (2) sage does a *whole*
> lot of stuff when it starts up. ;)
>
> So we'd love to see if other people see these same failures. Anyone
> want to try out the new cython? You can grab all the files you need
> here:
>
> http://sage.math.washington.edu/home/craigcitro/cython-0.13-beta/
>
> There's a new spkg and 6 patches against the sage library. You can add
> the patches, sage -i the spkg, and then do a sage -ba, and voila! you
> should have a sage running the bleeding edge cython. (If that doesn't
> build, it means I forgot some patch somewhere -- there's a working
> sage-4.4.4 with the new cython in /scratch/craigcitro/cy-work/fcubed
> on sage.math if anyone wants to root around.)

I haven't done any testing yet, but in order to get './sage -ba' to
finish, I applied a seventh patch (attached), which I discovered with

hg diff -R /scratch/craigcitro/cy-work/fcubed/devel/sage

> After that, run the full test suite as many times as you're willing,
> hopefully with and without parallel doctesting (i.e. sage -tp). Then
> let us know what you turn up -- lots of random failures, or does
> everything pass? Points for machines we can ssh into and generated
> core files (ulimit -c unlimited), and even more points for anyone
> seeing consistent/repeatable failures. I'd also be very interested of
> reports that you've run the test suite N times with no failures.

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[sage-devel] Re: Semicolons in doctests

> i.e. the following produces no output:
> sage: 42;
>
> However, in doctests, it *does* produce output, the same line in a
> doctest would give:
> **********************************************************************
> File "/home/jdemeyer/printtest.sage", line 6:
>     sage: 42;
> Expected nothing
> Got:
>     42

I'm not familiar with the doctests, but the python language grammar
says the following:

simple_stmt: small_stmt (';' small_stmt)* [';'] NEWLINE

from: http://docs.python.org/release/2.6.5/reference/grammar.html

I hope that's helpful to you. A Sage guru must know. ;-)

Don

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[sage-devel] Semicolons in doctests

Hello sage-devel,

When a line in Sage ends with a semicolon, the output gets suppressed,
i.e. the following produces no output:
sage: 42;

However, in doctests, it *does* produce output, the same line in a
doctest would give:
**********************************************************************
File "/home/jdemeyer/printtest.sage", line 6:
sage: 42;
Expected nothing
Got:
42
**********************************************************************

Is this a bug, a feature? I tried Googling and searching on
sagemath.org, but found nothing relevant to this...


Jeroen.

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