[sage-devel] sage-2.8.8

2007-10-21 Thread William Stein 

Hello,

I've released sage-2.8.8.  Get it at http://sagemath.org, as usual,
or just do sage -upgrade.

This release benefited hugely from work of Martin Albrecht, Michael
Abshoff, Craig Citro, Carl Witty, Mike Hansen, David Roe, John Voight,
and many other people.

 -- William

-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Fwd: singular build issue

2007-10-21 Thread William Stein 

Martin,


Your idea that Paul's build problem was caused by boost was right.
Maybe we can figure out a way to turn off using boost completely
by default for Singular.

Carl: Paul has some suggestions for changing how real numbers
print below.  What do you think?

 -- William

-- Forwarded message --
From: Paul Zimmermann
Date: Oct 21, 2007 1:25 AM
Subject: Re: singular build issue
To: William Stein [EMAIL PROTECTED]
Cc: sage-devel@googlegroups.com


 It looks like maybe there is an issue with the system-wide boost
 you have installed.

Thanks William. Moving /usr/include/boost to /usr/include/boost.old and
typing again make in SAGE_ROOT did it. You can recommend it to users who
encounter the same problem.

bash-3.00$ sage
--
| SAGE Version 2.8.7, Release Date: 2007-10-15   |
| Type notebook() for the GUI, and license() for information.|
--

Some feedback:

- in case one redefines DESTDIR in make install, one gets strange paths:
  $ make install -n DESTDIR=/usr/local/sage-2.8.7
  ...
  cp /usr/local/sage-2.8.7/usr/local/sage/sage /usr/local/sage-2.8.7/usr/bin/
  (I would expect at least 'usr' to disappear.)

- some f-p values are printed like integers, which may confuse the user
  (especially if one copies them with the mouse):
  sage: 2.0^46
  70368744177664.0
  sage: 2.0^47
  140737488355328
  I would expect '140737488355328.' or '1.40737488355328e14' in the 2nd case.
  By the way, typing 140737488355328.0 outputs itself, which is inconsistent,
  since 140737488355328.0-2.0^47 gives 0..

  Compare also:
  sage: 2.0^99
  633825300114115000
  sage: 2.0^100
  1.26765060022823e30

My 2 cents,
Paul



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: sage -upgrade and file corruption

2007-10-21 Thread Pablo De Napoli 

I'm currently working on ticket #329

My idea is adding to each .spkg file a .spkg.md5 file with the md5checksum
This should prevent file corruption.

I've already reimplemented the md5sum standard utility (from the
coreutils package) in python (using the md5 module), so that we
don't need to add an extra dependency to sage.

I still have to modify the logic of the scripts (sage-download-package, etc.)
so that they do the right thing.

Pablo




On 10/20/07, Timothy Clemans [EMAIL PROTECTED] wrote:

 Hi,

 I think I have done sage -upgrade a few times when William was in
 the process of uploading a new release. I think it would be helpful if
 Sage would check a file on sagemath that gave the latest release that
 had been completed uploaded. Another possibility might be that William
 would upload the files to directories that Sage doesn't look in and
 then move them over to the release directories after they have been
 completely uploaded.

 Timothy

 


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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread Jaap Spies 

William Stein wrote:
 Hello,
 
 I've released sage-2.8.8.  Get it at http://sagemath.org, as usual,
 or just do sage -upgrade.
 

There seems to be some typos in the test of gap.py

Jaap

[EMAIL PROTECTED] sage-2.8.8]$ ./sage -t  devel/sage-main/sage/interfaces/gap.py
sage -t  devel/sage-main/sage/interfaces/gap.py 
**
File gap.py, line 69:
 sage: R = gap.PolynomialRing('Rationals', 2); R
Expected:
 PolynomialRing(..., [ x, x_2 ])
Got:
 PolynomialRing(..., [ x_1, x_2 ])
**
File gap.py, line 71:
 sage: I = R.IndeterminatesOfPolynomialRing(); I
Expected:
 [ x, x_2 ]
Got:
 [ x_1, x_2 ]
**
File gap.py, line 86:
 sage: f = gap(str(g)); f
Expected:
 -x^5+x_2^2
Got:
 -x_1^5+x_2^2
**
1 items had failures:
3 of  22 in __main__.example_0
***Test Failed*** 3 failures.
For whitespace errors, see the file .doctest_gap.py
  [2.4 s]
exit code: 256

--
The following tests failed:


 sage -t  devel/sage-main/sage/interfaces/gap.py
Total time for all tests: 2.4 seconds
[EMAIL PROTECTED] sage-2.8.8]$


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[sage-devel] Re: Fwd: singular build issue

2007-10-21 Thread cwitty 

On Oct 21, 5:30 am, William Stein [EMAIL PROTECTED] wrote:
 Carl: Paul has some suggestions for changing how real numbers
 print below.  What do you think?

I have no particular opinion.  I've never dealt with floating-point
numbers in any computer algebra system other than Sage, so I don't
know what users might expect (and what they might find confusing).
When I worked on the floating-point printing, my goal was to fix a few
obviously broken things, but leave the output unchanged in non-
obviously-broken cases.

Carl Witty


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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread William Stein 

On 10/21/07, Jaap Spies [EMAIL PROTECTED] wrote:
 William Stein wrote:
  Hello,
 
  I've released sage-2.8.8.  Get it at http://sagemath.org, as usual,
  or just do sage -upgrade.
 

 There seems to be some typos in the test of gap.py

These are not typos.  The behavior of gap-4.4.10 changed from that
of gap-4.4.9, and the doctests reflect that change.  Evidently for
some reason your gap didn't get upgraded.   Try

   sage: !gap

to see what version of gap you now have.

Also, you may need to do
   sage: gap_reset_workspace()



 Jaap

 [EMAIL PROTECTED] sage-2.8.8]$ ./sage -t  
 devel/sage-main/sage/interfaces/gap.py
 sage -t  devel/sage-main/sage/interfaces/gap.py 
 **
 File gap.py, line 69:
  sage: R = gap.PolynomialRing('Rationals', 2); R
 Expected:
  PolynomialRing(..., [ x, x_2 ])
 Got:
  PolynomialRing(..., [ x_1, x_2 ])
 **
 File gap.py, line 71:
  sage: I = R.IndeterminatesOfPolynomialRing(); I
 Expected:
  [ x, x_2 ]
 Got:
  [ x_1, x_2 ]
 **
 File gap.py, line 86:
  sage: f = gap(str(g)); f
 Expected:
  -x^5+x_2^2
 Got:
  -x_1^5+x_2^2
 **
 1 items had failures:
 3 of  22 in __main__.example_0
 ***Test Failed*** 3 failures.
 For whitespace errors, see the file .doctest_gap.py
   [2.4 s]
 exit code: 256

 --
 The following tests failed:


  sage -t  devel/sage-main/sage/interfaces/gap.py
 Total time for all tests: 2.4 seconds
 [EMAIL PROTECTED] sage-2.8.8]$


 



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread cwitty 

On Oct 21, 9:34 am, William Stein [EMAIL PROTECTED] wrote:
 On 10/21/07, Jaap Spies [EMAIL PROTECTED] wrote:
  There seems to be some typos in the test of gap.py

 These are not typos.  The behavior of gap-4.4.10 changed from that
 of gap-4.4.9, and the doctests reflect that change.  Evidently for
 some reason your gap didn't get upgraded.   Try

sage: !gap

 to see what version of gap you now have.

Actually, I'm seeing the same problems as Jaap.

Here are some logs from a sage -gap session.

First, from an old install I haven't touched for a couple of weeks:
GAP4, Version: 4.4.9 of 6-Nov-2006, x86_64-unknown-linux-gnu-gcc
gap PolynomialRing(Rationals, 2);
PolynomialRing(..., [ x_1, x_2 ])

Next, from a clean 2.8.8 install:
GAP4, Version: 4.4.10 of 02-Oct-2007, i686-pc-linux-gnu-gcc
gap PolynomialRing(Rationals, 2);
PolynomialRing(..., [ x_1, x_2 ])

As far as I can tell, the behavior of GAP hasn't changed here.  (I
think we had a miscommunication last night... I was trying to report
that the gap.py doctest was failing with the latest code, after you
changed the doctest; but I didn't say that clearly.)

Carl


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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread Jaap Spies 

William Stein wrote:
 On 10/21/07, Jaap Spies [EMAIL PROTECTED] wrote:

 There seems to be some typos in the test of gap.py
 
 These are not typos.  The behavior of gap-4.4.10 changed from that
 of gap-4.4.9, and the doctests reflect that change.  Evidently for
 some reason your gap didn't get upgraded.   Try
 
sage: !gap
 

This is on a fresh install (but dito with the upgrade):

GAP4, Version: 4.4.10 of 02-Oct-2007, i686-pc-linux-gnu-gcc
gap

 to see what version of gap you now have.
 
 Also, you may need to do
sage: gap_reset_workspace()

That does not help. Same test failures.

Jaap



 [EMAIL PROTECTED] sage-2.8.8]$ ./sage -t  
 devel/sage-main/sage/interfaces/gap.py
 sage -t  devel/sage-main/sage/interfaces/gap.py 
 **
 File gap.py, line 69:
  sage: R = gap.PolynomialRing('Rationals', 2); R
 Expected:
  PolynomialRing(..., [ x, x_2 ])
 Got:
  PolynomialRing(..., [ x_1, x_2 ])
 **
 File gap.py, line 71:
  sage: I = R.IndeterminatesOfPolynomialRing(); I
 Expected:
  [ x, x_2 ]
 Got:
  [ x_1, x_2 ]
 **
 File gap.py, line 86:
  sage: f = gap(str(g)); f
 Expected:
  -x^5+x_2^2
 Got:
  -x_1^5+x_2^2
 **
 1 items had failures:
 3 of  22 in __main__.example_0
 ***Test Failed*** 3 failures.
 For whitespace errors, see the file .doctest_gap.py
   [2.4 s]
 exit code: 256

 --
 The following tests failed:


  sage -t  devel/sage-main/sage/interfaces/gap.py
 Total time for all tests: 2.4 seconds
 [EMAIL PROTECTED] sage-2.8.8]$


 
 


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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread Justin C. Walker 


On Oct 21, 2007, at 10:04 AM, William Stein wrote:


 I think I know what's going on.

 If you install the Gap optional packages, then reset the
 workspace you get the behavior I see.  If you don't install
 the optional packages you don't.  Thus one of the packages
 changes the print behavior of Gap.

 Indeed, here it is:

 gap LoadPackage(hap);
 Loading HAP 1.7.5gamma ...
 true
 gap PolynomialRing(Rationals,2);
 PolynomialRing(..., [ x, x_2 ])

I see the same problem as others have reported, but I have no  
optional packages installed.  If I run 'gap_console()', and then  
'LoadPackage(hap);', I get 'failed' as output.

'gap_console()' tells me it's version '4.4.10'.  'gap_reset_workspace 
()' seems to have no effect on the results.

This is a fresh install (not upgrade) of 2.8.8 on Mac OS X, 10.4.10,  
Core 2 Duo.

Justin


--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income

Experience is what you get
   when you don't get what you want.





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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread William Stein 

On 10/21/07, Justin C. Walker [EMAIL PROTECTED] wrote:
  gap LoadPackage(hap);
  Loading HAP 1.7.5gamma ...
  true
  gap PolynomialRing(Rationals,2);
  PolynomialRing(..., [ x, x_2 ])

 I see the same problem as others have reported, but I have no
 optional packages installed.  If I run 'gap_console()', and then
 'LoadPackage(hap);', I get 'failed' as output.

That's because hap is an optional package, and you don't have
it installed.

 'gap_console()' tells me it's version '4.4.10'.  'gap_reset_workspace
 ()' seems to have no effect on the results.

 This is a fresh install (not upgrade) of 2.8.8 on Mac OS X, 10.4.10,
 Core 2 Duo.

Do a sage -upgrade, and all your problems will be solved.

William

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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread cwitty 

On Oct 21, 10:36 am, Justin C. Walker [EMAIL PROTECTED] wrote:
 I see the same problem as others have reported, but I have no
 optional packages installed.  If I run 'gap_console()', and then
 'LoadPackage(hap);', I get 'failed' as output.

Yes, that's as expected.  For 2.8.8, William (accidentally) made it so
that the interface/gap.py doctests require the GAP optional packages.
So they worked for him (because he had the optional packages), but not
for most other people.

This has been fixed in 2.8.8.1 (just released a few minutes ago).  So
you can do sage -upgrade to get the fixed version.  Or you can just
do:

sage: hg_sage.pull()

followed by sage -b, and that should be a slightly faster way to get
the same fix.

Carl


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[sage-devel] [sage-forum] sage-2.8.8

2007-10-21 Thread Jaap Spies 


William Stein wrote:
 Hello,
 
 I've released sage-2.8.8.  Get it at http://sagemath.org, as usual,
 or just do sage -upgrade.
 

Another test failure in the upgraded sage-2.8.8.1 below

Jaap

[EMAIL PROTECTED] sage]#  sage -t  devel/sage-main/sage/numerical/test.py
sage -t  devel/sage-main/sage/numerical/test.py 
**
File test.py, line 9:
 : from scipy import linsolve
Exception raised:
 Traceback (most recent call last):
   File /usr/local/sage/local/lib/python2.5/doctest.py, line 1212, in 
__run
 compileflags, 1) in test.globs
   File doctest __main__.example_0[5], line 1, in module
 from scipy import linsolve###line 9:
 : from scipy import linsolve
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py, 
line 5, in module
 import umfpack
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/linsolve/umfpack/__init__.py,
 line 3, in module
 from umfpack import *
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/linsolve/umfpack/umfpack.py,
 line 11, in module
 import scipy.sparse as sp
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/sparse/__init__.py, 
line 5, in module
 from sparse import *
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/sparse/sparse.py, 
line 14, in module
 from scipy.sparse.sparsetools import cscmux, csrmux, \
 ImportError: cannot import name cscmux
**
File test.py, line 11:
 : from scipy import sparse
Exception raised:
 Traceback (most recent call last):
   File /usr/local/sage/local/lib/python2.5/doctest.py, line 1212, in 
__run
 compileflags, 1) in test.globs
   File doctest __main__.example_0[7], line 1, in module
 from scipy import sparse###line 11:
 : from scipy import sparse
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/sparse/__init__.py, 
line 5, in module
 from sparse import *
   File 
/usr/local/sage/local/lib/python2.5/site-packages/scipy/sparse/sparse.py, 
line 14, in module
 from scipy.sparse.sparsetools import cscmux, csrmux, \
 ImportError: cannot import name cscmux
**
1 items had failures:
2 of   8 in __main__.example_0
***Test Failed*** 2 failures.
For whitespace errors, see the file .doctest_test.py
  [3.0 s]
exit code: 256

--
The following tests failed:


 sage -t  devel/sage-main/sage/numerical/test.py
Total time for all tests: 3.0 seconds

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[sage-devel] Re: [sage-forum] sage-2.8.8

2007-10-21 Thread John Cremona 

Successfully upgraded to 2.8.8.1 on linux (Kubuntu 7.04):

sage --testall
(...)

All tests passed!
Total time for all tests: 1978.6 seconds


John Cremona

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[sage-devel] Re: [Fwd: back to permanents]

2007-10-21 Thread Jaap Spies 

Replying to my own message:

 Calculating the permanent of a 13 x 17 matrix with a 'band' of 4 1's
 over the main diagonal.


 
 Over ZZ:
 sage: time f(13,4)
 CPU times: user 3.98 s, sys: 0.07 s, total: 4.05 s
 Wall time: 4.08
  1596800
 

With a cython function generating the combinations I now have:

sage: time f(13,4)
CPU times: user 1.56 s, sys: 0.02 s, total: 1.58 s
Wall time: 1.62
  1596800

 
 Over QQ
 sage: time f(13,4)
 CPU times: user 8.39 s, sys: 0.09 s, total: 8.48 s
 Wall time: 8.56
  1596800


sage: time f(13,4)
CPU times: user 5.68 s, sys: 0.01 s, total: 5.69 s
Wall time: 5.72
  1596800

 My all C-program with ints based on gmp:
 [EMAIL PROTECTED] perm_gmp]$ time ./ds 13 4
 1596800 

 real0m0.328s
 user0m0.326s
 sys 0m0.003s
 [EMAIL PROTECTED] perm_gmp]$ 
 

More work to do!

Jaap


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[sage-devel] Re: sage -upgrade and file corruption

2007-10-21 Thread Pablo De Napoli 

My idea was actually the second one, so nothing has to be changed in
current sage packages.I don't see this as so painfull (as the

Debian is currently doing something similar for debian packages
(actually for each Debian package there are 3 sources files:
a .dsc file, with description and checksum, .diff.gz (the differencies
as a patch to pristine sources) and .orig.tar.gz (the pristine
sources)

I think that this good be a good model to follow.

But yes, perhaps is just having tar to report if the opeation of
unpacking was sucessfull or not.

Pablo

On 10/21/07, William Stein [EMAIL PROTECTED] wrote:

 On 10/21/07, Pablo De Napoli [EMAIL PROTECTED] wrote:
 
  I'm currently working on ticket #329
 
  My idea is adding to each .spkg file a .spkg.md5 file with the md5checksum
  This should prevent file corruption.

 Are you literally adding to each .spkg file.  If so,
 make sure this is completely automatic.  I.e., whenever anybody does
 sage -pkg directory-version
 the md5 file is created inside the resulting spkg.  What are you
 going to create the md5 hash of, by the way, given that the spkg
 doesn't exist when you create the md5 hash to add to the spkg?
 The alternative is that we have to have separate files
directory-version.spkg
 and
directory-version.spkg.md5
 and then whenever anybody ever wants to trade spkgs, they have
 to copy around, get, etc. 2 separate files. That would be painful
 in practice.

 Just out of curiosity, shouldn't tar report if the file it is
 unpacking is somehow corrupt?  Why do we need md5 hashes at all
 if the whole point is to determine whether or not a download of
 a .tar.bz2 file (an spkg) was corrupted or not?  Should we be
 able to get that information from tar during the extract process,
 or at least change how we make the tarball so that information
 is available.

 I really don't want to have to keep track of twice as many files
 if it isn't absolutely necessary.


 
  I've already reimplemented the md5sum standard utility (from the
  coreutils package) in python (using the md5 module), so that we
  don't need to add an extra dependency to sage.
 
  I still have to modify the logic of the scripts (sage-download-package, 
  etc.)
  so that they do the right thing.
 
  Pablo
 
 
 
 
  On 10/20/07, Timothy Clemans [EMAIL PROTECTED] wrote:
  
   Hi,
  
   I think I have done sage -upgrade a few times when William was in
   the process of uploading a new release. I think it would be helpful if
   Sage would check a file on sagemath that gave the latest release that
   had been completed uploaded. Another possibility might be that William
   would upload the files to directories that Sage doesn't look in and
   then move them over to the release directories after they have been
   completely uploaded.
  
   Timothy
  
   
  
 
  
 


 --
 William Stein
 Associate Professor of Mathematics
 University of Washington
 http://wstein.org

 


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