[gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[Steven Trogdon]

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Hi everyone,

I performed the subject upgrade and I have one test that fails on my 32bit  
chroot that seems to be out of the ordinary. There is no problem with the test  
on amd64, at least here there isn't.

sage -t  -force_lib  
"devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py"
**********************************************************************
File  
"/usr/share/sage/devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py",  
line 315:
     sage: len(C.points())
Exception raised:
     Traceback (most recent call last):
       File "/usr/bin/ncadoctest.py", line 1231, in run_one_test
         self.run_one_example(test, example, filename, compileflags)
       File "/usr/bin/sagedoctest.py", line 38, in run_one_example
         OrigDocTestRunner.run_one_example(self, test, example, filename,  
compileflags)
       File "/usr/bin/ncadoctest.py", line 1172, in run_one_example
         compileflags, 1) in test.globs
       File "<doctest __main__.example_6[7]>", line 1, in <module>
         len(C.points())###line 315:
     sage: len(C.points())
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py",  
line 327, in points
         self.__points = self._points_fast_sqrt() # this is fast using Zech  
logarithms
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py",  
line 239, in _points_fast_sqrt
         points.append(self.point([x, v+sqrtD, one], check=True))
       File "/usr/lib/python2.6/site-packages/sage/schemes/generic/scheme.py",  
line 256, in point
         return self._point_class(self, v, check=check)
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py",  
line 208, in _point_class
         return self.__A._point_class(*args, **kwds)
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/generic/projective_space.py",  
line 561, in _point_class
         return morphism.SchemeMorphism_projective_coordinates_field(*args,  
**kwds)
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/generic/morphism.py", line 608,  
in __init__
         X.codomain()._check_satisfies_equations(v)
       File  
"/usr/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py",  
line 538, in _check_satisfies_equations
         raise TypeError, "Coordinates %s do not define a point on  
%s"%(list(v),self)
     TypeError: Coordinates [5*a + 6, 6*a + 4, 1] do not define a point on  
Hyperelliptic Curve over Finite Field in a of size 11^2 defined by y^2 + (x^2 +
  2)*y = x^5 + x + 10
**********************************************************************

When I enter into sage the lines in the test around the failing line (315)  
things seem to be OK. So perhaps there is something else in the test  
contributing to the failure. François suggested python as a culprit. Here is  
my configuration:

emerge -pv =dev-lang/python-2.6.5-r99

[ebuild   R   ] dev-lang/python-2.6.5-r99  USE="berkdb gdbm ipv6 ncurses  
readline sqlite ssl threads (wide-unicode) xml -build -doc -examples -tk  
-wininst" 0 kB [1]

Total: 1 package (1 reinstall), Size of downloads: 0 kB
Portage tree and overlays:
  [0] /usr/portage
  [1] /var/lib/layman/sage-on-gentoo

Steve


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Re: [gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[François Bissey]

> Hi everyone,
> 
> I performed the subject upgrade and I have one test that fails on my 32bit
> chroot that seems to be out of the ordinary. There is no problem with the
> test on amd64, at least here there isn't.
> 
> sage -t  -force_lib
> "devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py
> " **********************************************************************
> File
> "/usr/share/sage/devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic
> _finite_field.py", line 315:
>      sage: len(C.points())
> Exception raised:
>      Traceback (most recent call last):
>        File "/usr/bin/ncadoctest.py", line 1231, in run_one_test
>          self.run_one_example(test, example, filename, compileflags)
>        File "/usr/bin/sagedoctest.py", line 38, in run_one_example
>          OrigDocTestRunner.run_one_example(self, test, example, filename,
> compileflags)
>        File "/usr/bin/ncadoctest.py", line 1172, in run_one_example
>          compileflags, 1) in test.globs
>        File "<doctest __main__.example_6[7]>", line 1, in <module>
>          len(C.points())###line 315:
>      sage: len(C.points())
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/hyperel
> liptic_finite_field.py", line 327, in points
>          self.__points = self._points_fast_sqrt() # this is fast using Zech
> logarithms
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/hyperel
> liptic_finite_field.py", line 239, in _points_fast_sqrt
>          points.append(self.point([x, v+sqrtD, one], check=True))
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/generic/scheme.py", line
> 256, in point
>          return self._point_class(self, v, check=check)
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py"
> , line 208, in _point_class
>          return self.__A._point_class(*args, **kwds)
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/generic/projective_space.py"
> , line 561, in _point_class
>          return morphism.SchemeMorphism_projective_coordinates_field(*args,
> **kwds)
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/generic/morphism.py", line
> 608, in __init__
>          X.codomain()._check_satisfies_equations(v)
>        File
> "/usr/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py"
> , line 538, in _check_satisfies_equations
>          raise TypeError, "Coordinates %s do not define a point on
> %s"%(list(v),self)
>      TypeError: Coordinates [5*a + 6, 6*a + 4, 1] do not define a point on
> Hyperelliptic Curve over Finite Field in a of size 11^2 defined by y^2 +
> (x^2 + 2)*y = x^5 + x + 10
> **********************************************************************
> 
> When I enter into sage the lines in the test around the failing line (315)
> things seem to be OK. So perhaps there is something else in the test
> contributing to the failure. François suggested python as a culprit. Here
> is my configuration:
> 
Hi Steve,

just to be clear, when you enter the data of the test manually in sage there 
is no problems?
We already have one test like that, and there are a few reports of phantom
failing tests on sage-devel so it is possible.

Francois 

Re: [gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[Steven Trogdon]

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On 09/09/2010 03:47:27 AM, François Bissey wrote:

> Hi Steve,
> 
> just to be clear, when you enter the data of the test manually in sage there
> is no problems?
> We already have one test like that, and there are a few reports of phantom
> failing tests on sage-devel so it is possible.
> 
> Francois
> 

François ,

When the following

             sage: x = polygen(GF(121, 'a'))
             sage: C = HyperellipticCurve(x^5 + x - 1, x^2 + 2)
             sage: len(C.points())
             122

is entered manually I get the expected result. The last line of the sage input  
is where

  sage -t -force_lib  
"devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py"

fails. I downgraded to

sage-doc-4.5.2-r1
numpy-1.3.0-r2
scipy-0.7.2-r1
sage-4.5.2-r1

and the test passed. I then upgraded to the latest sage-doc, numpy, scipy and  
sage and the test passed, but only the first time. On subsequent tries the  
test has failed.

Steve






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Re: [gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[François Bissey]

> On 09/09/2010 03:47:27 AM, François Bissey wrote:
> > Hi Steve,
> > 
> > just to be clear, when you enter the data of the test manually in sage
> > there is no problems?
> > We already have one test like that, and there are a few reports of
> > phantom failing tests on sage-devel so it is possible.
> > 
> > Francois
> 
> François ,
> 
> When the following
> 
>              sage: x = polygen(GF(121, 'a'))
>              sage: C = HyperellipticCurve(x^5 + x - 1, x^2 + 2)
>              sage: len(C.points())
>              122
> 
> is entered manually I get the expected result. The last line of the sage
> input is where
> 
>   sage -t -force_lib
> "devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py
> "
> 
> fails. I downgraded to
> 
> sage-doc-4.5.2-r1
> numpy-1.3.0-r2
> scipy-0.7.2-r1
> sage-4.5.2-r1
> 
> and the test passed. I then upgraded to the latest sage-doc, numpy, scipy
> and sage and the test passed, but only the first time. On subsequent tries
> the test has failed.
> 
The important bit, I think, is that when you enter the data manually you get 
the expected results. There is quite possibly something wrong with the 
doctests framework. Some of it may come from the port to Gentoo, but
as I said there are other people in the sage community that wonder about 
the same thing.

We probably should enter that as a recorded issue on github, other people
may get it from time to time.

Francois

Re: [gentoo-science] [sage-on-gentoo] numpy-1.4.1/scipy-0.8.0

[Steven Trogdon]

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On 09/10/2010 05:47:10 AM, François Bissey wrote:
>> On 09/09/2010 03:47:27 AM, François Bissey wrote:
>> > Hi Steve,
>> >
>> > just to be clear, when you enter the data of the test manually in sage
>> > there is no problems?
>> > We already have one test like that, and there are a few reports of
>> > phantom failing tests on sage-devel so it is possible.
>> >
>> > Francois
>> 
>> François ,
>> 
>> When the following
>> 
>>              sage: x = polygen(GF(121, 'a'))
>>              sage: C = HyperellipticCurve(x^5 + x - 1, x^2 + 2)
>>              sage: len(C.points())
>>              122
>> 
>> is entered manually I get the expected result. The last line of the sage
>> input is where
>> 
>>   sage -t -force_lib
>> "devel/sage/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py
>> "
>> 
>> fails. I downgraded to
>> 
>> sage-doc-4.5.2-r1
>> numpy-1.3.0-r2
>> scipy-0.7.2-r1
>> sage-4.5.2-r1
>> 
>> and the test passed. I then upgraded to the latest sage-doc, numpy, scipy
>> and sage and the test passed, but only the first time. On subsequent tries
>> the test has failed.
>> 
> The important bit, I think, is that when you enter the data manually you get
> the expected results. There is quite possibly something wrong with the
> doctests framework. Some of it may come from the port to Gentoo, but
> as I said there are other people in the sage community that wonder about
> the same thing.
> 
> We probably should enter that as a recorded issue on github, other people
> may get it from time to time.
> 
> Francois
> 
Just an update. The subject test of this thread no longer fails here with  
sage-4.5.3?

Steve

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