Sage 3.4.2.alpha0 released!

[mabshoff]

Hello folks,

here goes 3.4.2.alpha0. It does not contain all the fixes I wanted,
but I merged two large (200kb+) patches (#5610 and #5848) that touched
a lot of files and that were in danger of bitrotting. Since I
considered it pointless to force people to rebase potentially twice I
pulled them both into alpha0.

The source, upgrade bits and a sage.math-only binary should be
available in

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.2/

From here on the plan is to merge other reviewed patches (in case you
are bored, there are about 80 patches to review in trac), fix some
more issues and then get out rc0 on Sunday to have 3.4.2.final very
early next week. Coverage right now is at 69% and there is a doctest
patch for padics that brings that directory to 100% and gives us 2.1%
globally, so I definitely want that one merged. Another thing to
review and push hard are the pynac tickets and the not yet in trac
patch for the symbolics switch. Mike Hansen mentioned he could post
something today, so hopefully it will get reviewed until Sunday and
merged to give the code a good beating during 3.4.2.

If you have any patches in trac please make sure to check if they
apply to alpha0 since they will get bounced back if they fail to
merge.

Cheers,

Michael

Merged in Sage 3.4.2.alpha0:

#4809: Dan Drake, John Palmieri: the installation guide and
constructions guide should be CC licensed [Reviewed by John Palmieri,
Dan Drake]
#5111: Mike Hansen, Bill Page: axiom --> fricas [Reviewed by Carl
Witty]
#5130: R. Andrew Ohana: create a prime_pi function that doesn't just
compute len(prime_range(n) [Reviewed by Carl Witty, William Stein,
Michael Abshoff]
#5346: John Cremona: Some doctests in schemes/elliptic_curves/
ell_rational_field.py fail with optional database installed [Reviewed
by Michael Abshoff]
#5567: Wilfried Huss: bug in region_plot [Reviewed by Bill Cauchois]
#5595: Robert Bradshaw: minor dependancy checking glitch [Reviewed by
Carl Witty]
#5610: John Palmieri: LaTeX customization [Reviewed by Robert
Bradshaw, Rob Beezer]
#5627: Karl-Dieter Crisman: Trivial typo in quadratic_nonresidue
[Reviewed by Minh Van Nguyen]
#5704: John Cremona: Implementation of finding elliptic curves with
prescribed reduction over QQ [Reviewed by Robert Miller]
#5751: Dan Bump: cartan_type now a method rather than attribute in
weyl_characters.py [Reviewed by Anne Schilling]
#5795: Simon King: Improved performance of
MPolynomialRing_libsingular.__call__() [Reviewed by Martin Albrecht]
#5803: Robert Bradshaw: Upgrade Cython to 0.11.1 [Reviewed by William
Stein]
#5809: Alex Ghitza: schemes/generic/hypersurface.py is completely
broken [Reviewed by John Cremona]
#5815: Mitesh Patel, Jason Grout: Disable TinyMCE in the live
documentation [Reviewed by Jason Grout, Mitesh Patel]
#5821: Robert Bradshaw: preparser incorrectly handles backslash
operator inside strings (sometimes) [Reviewed by Carl Witty]
#5822: William Stein: cusps -- implement action of the Galois group on
cusps for congruence subgroups as on page 12 of Steven's "Arithmetic
on Modular Curves" [Reviewed by John Cremona]
#5836: Jason Grout: Make show() immediately show an image in the
notebook [Reviewed by William Stein]
#5848: John Palmieri: untabify Sage [Reviewed by Rob Beezer, Michael
Abshoff]
#5851: Chris Wuthrich: Convert 3 more elliptic curves files to ReST
and add to reference manual [Reviewed by John Cremona]
#5861: Michael Abshoff: Remove cocoa, four_ti_2, reduce and template
interfaces since they do not work/are broken [Reviewed by Michael
Abshoff]
#5863: John Palmieri: remove some files from sage/algebras [Reviewed
by William Stein]
#5871: William Stein: solaris x86 3.4.1 -- code_bounds.py fails some
plot doctests [Reviewed by Michael Abshoff]
#5876: John Cremona: Vast speedup in P1List construction [Reviewed by
William Stein, Robert Bradshaw]
#5886: William Stein: Bug in free module homomorphism creation
[Reviewed by Robert Bradshaw]

[John Cremona]

Successful build from source and all tests pass on both Suse 32-bit
and Ubuntu 64-bit.

John

2009/4/24 mabshoff <mabs...@googlemail.com>:

[Jaap Spies]

mabshoff wrote:
> Hello folks,
>
> here goes 3.4.2.alpha0. It does not contain all the fixes I wanted,
> but I merged two large (200kb+) patches (#5610 and #5848) that touched
> a lot of files and that were in danger of bitrotting. Since I
> considered it pointless to force people to rebase potentially twice I
> pulled them both into alpha0.
>
> The source, upgrade bits and a sage.math-only binary should be
> available in
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.2/
>

On Fedora 9, 32 bit, fresh build:

sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
**********************************************************************
File "/home/jaap/downloads/sage-3.4.2.alpha0/devel/sage/sage/matrix/matrix_symbolic_dense.pyx", line 413:
sage: M.determinant()
Expected:
4*x - 6
Got:
determinant(sage513)
**********************************************************************
1 items had failures:

On retry:

sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
**********************************************************************
File "/home/jaap/downloads/sage-3.4.2.alpha0/devel/sage/sage/matrix/matrix_symbolic_dense.pyx", line 214:
sage: -matrix(SR, 2, range(4))
Exception raised:
Traceback (most recent call last):
File "/home/jaap/downloads/sage-3.4.2.alpha0/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jaap/downloads/sage-3.4.2.alpha0/local/bin/sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
File "/home/jaap/downloads/sage-3.4.2.alpha0/local/bin/ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_11[2]>", line 1, in <module>
-matrix(SR, Integer(2), range(Integer(4)))###line 214:
sage: -matrix(SR, 2, range(4))
File "matrix0.pyx", line 1497, in sage.matrix.matrix0.Matrix.__repr__ (sage/matrix/matrix0.c:7963)
File "matrix0.pyx", line 1526, in sage.matrix.matrix0.Matrix.str (sage/matrix/matrix0.c:8252)
File "matrix0.pyx", line 172, in sage.matrix.matrix0.Matrix.list (sage/matrix/matrix0.c:2839)
File "matrix_symbolic_dense.pyx", line 349, in sage.matrix.matrix_symbolic_dense.Matrix_symbolic_dense._list (sage/matrix/matrix_symbolic_dense.c:4257)
File "matrix_symbolic_dense.pyx", line 123, in sage.matrix.matrix_symbolic_dense.Matrix_symbolic_dense.get_unsafe (sage/matrix/matrix_symbolic_dense.c:3011)
File "/home/jaap/downloads/sage-3.4.2.alpha0/local/lib/python2.5/site-packages/sage/calculus/calculus.py", line 10261, in
symbolic_expression_from_maxima_string
raise TypeError, "unable to make sense of Maxima expression '%s' in Sage"%s
TypeError: unable to make sense of Maxima expression '(-sage196)[1,1]' in Sage
**********************************************************************
1 items had failures:
1 of 3 in __main__.example_11
***Test Failed*** 1 failures.
For whitespace errors, see the file /home/jaap/downloads/sage-3.4.2.alpha0/tmp/.doctest_matrix_symbolic_dense.py
[204.6 s]
exit code: 1024

----------------------------------------------------------------------
The following tests failed:

sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
Total time for all tests: 204.6 seconds
[jaap@paix sage-3.4.2.alpha0]$

What is going on here? Can anyone reproduce this?

Jaap

[William Stein]

Can *you* reproduce it repeatedly?

William

[Jaap Spies]

William Stein wrote:
[...]

>
> Can *you* reproduce it repeatedly?
>

One again:

[jaap@paix sage-3.4.2.alpha0]$ ./sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"

File "/home/jaap/downloads/sage-3.4.2.alpha0/devel/sage/sage/matrix/matrix_symbolic_dense.pyx", line 413:
sage: M.determinant()
Expected:
4*x - 6
Got:
determinant(sage513)
**********************************************************************

2 items had failures:

1 of 3 in __main__.example_11

1 of 9 in __main__.example_18
***Test Failed*** 2 failures.

For whitespace errors, see the file /home/jaap/downloads/sage-3.4.2.alpha0/tmp/.doctest_matrix_symbolic_dense.py

[152.4 s]
exit code: 1024

----------------------------------------------------------------------
The following tests failed:

sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
Total time for all tests: 152.4 seconds
[jaap@paix sage-3.4.2.alpha0]$

Jaap

> William

[David Joyner]

Wow! I have stunning news (for me anyway):

This compiles perfectly *and passes all tests* on ubuntu 64bit 8.10
with a phenom chip.

This is the first time that has happened in more releases than I can remember!

Great job to everyone involed, which definitely includes Michael
Abshoff.

[Justin C. Walker]

On Apr 24, 2009, at 03:07 , mabshoff wrote:

> here goes 3.4.2.alpha0. It does not contain all the fixes I wanted,
> but I merged two large (200kb+) patches (#5610 and #5848) that touched
> a lot of files and that were in danger of bitrotting. Since I
> considered it pointless to force people to rebase potentially twice I
> pulled them both into alpha0.
>
> The source, upgrade bits and a sage.math-only binary should be
> available in
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.2/

Built as an upgrade (starting with 3.4.1.rc1 -> rc2 -> rc4) on Mac OS
X, 10.5.6, Dual Quad Xeon/Mac Pro2,1.

No problems in the build.

All tests passed!

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
My wife 'n kids 'n dogs are gone,
I can't get Jesus on the phone,
But Ol' Milwaukee's Best is my best friend.
-----------

[mabshoff]

On Apr 25, 5:53 am, David Joyner <wdjoy...@gmail.com> wrote:

Hi David,

> Wow! I have stunning news (for me anyway):
>
> This compiles perfectly *and passes all tests* on ubuntu 64bit 8.10
> with a phenom chip.

Well, give the trouble you have seen in the past with your specific
setup this clearly indicates clisp since that is the only real change
that made a difference. On some systems clisp 2.47 now completely
blows up when building, i.e. both current 32 and 64 bit Madriva
releases, where 2.46 did build, so I am glad we will be getting rid of
it. I am truly hoping ecl will act more stable, but our dependency on
Maxima will decrease with the switch to pynac anyways.

> This is the first time that has happened in more releases than I can remember!
>
> Great job to everyone involed, which definitely includes Michael
> Abshoff.

:)

Cheers,

Michael

[kcrisman]

Builds from scratch fine on OSX.4 on PPC G4. I do have a couple
random things which came out of it, but I assume these are known -
just in case, I post them:

1. I get this error message during the Sphinx run:

docstring of
sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.has_good_reduction_outside_S:
7: (ERROR/3) Unknown directive type "notes".

.. notes::

Primality of elements of S is not checked, and the output
is undefined if S is not a list or contains non-primes.

This only tests the given model, so should only be applied to
minimal models.

2. I get a lot of warnings like this during the Sphinx run:

WARNING: html_favicon is not an .ico file

3. I get this - maybe something wrong in this file:

sage/plot/plot3d/parametric_surface.pyx:203:20: cdef variable 'u'
declared after it is used

4. During cloning, I get a lot of this:

warning can't open dynamic library: libpari-gmp.dylib referenced
from: /Users/.../sage-3.4.2.alpha0/local/lib/libcsage.dylib (checking
for undefined symbols may be affected) (No such file or directory,
errno = 2)

Hope it helps,

- kcrisman

[mabshoff]

On Apr 25, 7:30 pm, kcrisman <kcris...@gmail.com> wrote:

Hi,

> Builds from scratch fine on OSX.4 on PPC G4.  I do have a couple
> random things which came out of it, but I assume these are known -
> just in case, I post them:
>
> 1. I get this error message during the Sphinx run:
>
> docstring of
> sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.has_good_reduction_outside_S:
> 7: (ERROR/3) Unknown directive type "notes".
>
> .. notes::
>
>     Primality of elements of S is not checked, and the output
>     is undefined if S is not a list or contains non-primes.
>
>     This only tests the given model, so should only be applied to
>     minimal models.

I did not see this - at least the build did not stop and exit. Can
anyone confirm this?

> 2. I get a lot of warnings like this during the Sphinx run:
>
> WARNING: html_favicon is not an .ico file

Pat opened a ticket and posted a patch a while ago - maybe someone
wants to review it? :)

> 3. I get this - maybe something wrong in this file:
>
> sage/plot/plot3d/parametric_surface.pyx:203:20: cdef variable 'u'
> declared after it is used

Hmm - no clue? Is that during the build?

> 4. During cloning, I get a lot of this:
>
> warning can't open dynamic library: libpari-gmp.dylib referenced
> from: /Users/.../sage-3.4.2.alpha0/local/lib/libcsage.dylib (checking
> for undefined symbols may be affected) (No such file or directory,
> errno = 2)

It is an annoyance with pari which provides two versions of pari, i.e.
one with and one without a statically linked gmp. Just ignore it - it
never seemed to bother me enough to fix this :)

> Hope it helps,
>
> - kcrisman

Cheers,

Michael

[Justin C. Walker]

On Apr 25, 2009, at 19:37 , mabshoff wrote:

>
>
>
> On Apr 25, 7:30 pm, kcrisman <kcris...@gmail.com> wrote:
>
> Hi,
>
>> Builds from scratch fine on OSX.4 on PPC G4. I do have a couple
>> random things which came out of it, but I assume these are known -
>> just in case, I post them:
>>
>> 1. I get this error message during the Sphinx run:
>>
>> docstring of
>> sage
>> .schemes
>> .elliptic_curves
>> .ell_rational_field
>> .EllipticCurve_rational_field.has_good_reduction_outside_S:
>> 7: (ERROR/3) Unknown directive type "notes".
>>
>> .. notes::
>>
>> Primality of elements of S is not checked, and the output
>> is undefined if S is not a list or contains non-primes.
>>
>> This only tests the given model, so should only be applied to
>> minimal models.
>
> I did not see this - at least the build did not stop and exit. Can
> anyone confirm this?

I did get this message when upgrading to 3.4.2.alpha0 on Mac OS X,
10.5.6.

>> 2. I get a lot of warnings like this during the Sphinx run:
>>
>> WARNING: html_favicon is not an .ico file
>
> Pat opened a ticket and posted a patch a while ago - maybe someone
> wants to review it? :)
>
>> 3. I get this - maybe something wrong in this file:
>>
>> sage/plot/plot3d/parametric_surface.pyx:203:20: cdef variable 'u'
>> declared after it is used
>
> Hmm - no clue? Is that during the build?

I got this as well, during the build, viz.:

gcc -L/Users/tmp/sage-3.4.1.rc1/local/lib -bundle -undefined
dynamic_lookup build/temp.macosx-10.3-i386-2.5/sage/plot/plot3d/
parametric_surface.o -L/Users/tmp/sage-3.4.1.rc1/local//lib -lcsage -
lstdc++ -lntl -o build/lib.macosx-10.3-i386-2.5/sage/plot/plot3d/
parametric_surface.so
building 'sage.rings.complex_double' extension

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------

I'm beginning to like the cut of his jibberish.
-----------

[Jaap Spies]

William Stein wrote:
> On Fri, Apr 24, 2009 at 4:00 PM, Jaap Spies <j.s...@hccnet.nl> wrote:
>> mabshoff wrote:
>>> Hello folks,
>>>
>>> here goes 3.4.2.alpha0. It does not contain all the fixes I wanted,
>>> but I merged two large (200kb+) patches (#5610 and #5848) that touched
>>> a lot of files and that were in danger of bitrotting. Since I
>>> considered it pointless to force people to rebase potentially twice I
>>> pulled them both into alpha0.
>>>
>>> The source, upgrade bits and a sage.math-only binary should be
>>> available in
>>>

>>> http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4..2/
>>>
[...]

--------------------
>> The following tests failed:
>>
>>
>> sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
>> Total time for all tests: 204.6 seconds
>> [jaap@paix sage-3.4.2.alpha0]$
>>
>>
>> What is going on here? Can anyone reproduce this?
>>
>>
>
> Can *you* reproduce it repeatedly?
>

On Fedora 10, 32 bit, fresh build:

[jaap@peace sage-3.4.2.alpha0]$ ./sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
**********************************************************************
File "/home/jaap/Download/sage-3.4.2.alpha0/devel/sage/sage/matrix/matrix_symbolic_dense.pyx", line 214:

sage: -matrix(SR, 2, range(4))
Exception raised:
Traceback (most recent call last):

File "/home/jaap/Download/sage-3.4.2.alpha0/local/bin/ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jaap/Download/sage-3.4.2.alpha0/local/bin/sagedoctest.py", line 38, in run_one_example

OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)

File "/home/jaap/Download/sage-3.4.2.alpha0/local/bin/ncadoctest.py", line 1172, in run_one_example

compileflags, 1) in test.globs
File "<doctest __main__.example_11[2]>", line 1, in <module>
-matrix(SR, Integer(2), range(Integer(4)))###line 214:
sage: -matrix(SR, 2, range(4))
File "matrix0.pyx", line 1497, in sage.matrix.matrix0.Matrix.__repr__ (sage/matrix/matrix0.c:7963)
File "matrix0.pyx", line 1526, in sage.matrix.matrix0.Matrix.str (sage/matrix/matrix0.c:8252)
File "matrix0.pyx", line 172, in sage.matrix.matrix0.Matrix.list (sage/matrix/matrix0.c:2839)
File "matrix_symbolic_dense.pyx", line 349, in sage.matrix.matrix_symbolic_dense.Matrix_symbolic_dense._list (sage/matrix/matrix_symbolic_dense.c:4257)
File "matrix_symbolic_dense.pyx", line 123, in sage.matrix.matrix_symbolic_dense.Matrix_symbolic_dense.get_unsafe (sage/matrix/matrix_symbolic_dense.c:3011)

File "/home/jaap/Download/sage-3.4.2.alpha0/local/lib/python2.5/site-packages/sage/calculus/calculus.py", line 10261, in

symbolic_expression_from_maxima_string
raise TypeError, "unable to make sense of Maxima expression '%s' in Sage"%s
TypeError: unable to make sense of Maxima expression '(-sage196)[1,1]' in Sage
**********************************************************************

File "/home/jaap/Download/sage-3.4.2.alpha0/devel/sage/sage/matrix/matrix_symbolic_dense.pyx", line 413:

sage: M.determinant()
Expected:
4*x - 6
Got:
determinant(sage513)
**********************************************************************

2 items had failures:

1 of 3 in __main__.example_11

1 of 9 in __main__.example_18

***Test Failed*** 2 failures.
For whitespace errors, see the file /home/jaap/Download/sage-3.4.2.alpha0/tmp/.doctest_matrix_symbolic_dense.py
[91.8 s]
exit code: 1024

----------------------------------------------------------------------
The following tests failed:

sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx"
Total time for all tests: 91.8 seconds
[jaap@peace sage-3.4.2.alpha0]$

Jaap