Sage-4.3.1.rc1 released!
Robert Miller
Sage-4.3.1.rc1 has been released (buyer beware! *). The source is here:
http://boxen.math.washington.edu/home/rlmill/sage-4.3.1.rc1.tar
Due to hardware issues, this is a source only release (at least for tonight).
After an intensive day of merging, Sage now has:
- OS X 10.6 support
- A massive number of bugfixes from Sage Days 19
- A new version of the Sage Notebook
- @parallel is much more robust, using fork now
- Improved parallel testing and release management tools
Note:
- wiki() is still/again broken
- This was pushed out the door more quickly than the typical rc, since
the Bug Hunters need a fresh release to base their patches on.
- (*)i.e. this has not yet been tested on the build farm
- We are now in feature freeze
The following tickets were merged:
#797: Mike Hansen: %timeit on command line doesn't recognize [1..10]
syntax [Reviewed by Jason Grout]
#2109: Mike Hansen: the maxima interface doesn't recognize a syntax
error [Reviewed by Karl-Dieter Crisman]
#3400: Robert Bradshaw: Elements of GL(n,R) should coerce properly to
matrices [Reviewed by Rob Beezer]
#3638: Robert Bradshaw: Vector equality coercion problems [Reviewed by
Mike Hansen]
#3964: Alex Ghitza, William Stein: projective space homs do not check
arguments sufficiently [Reviewed by John Cremona]
#4604: Bill Cauchois: Graphics() should work in 3d as a valid empty
object [Reviewed by Tim Dumol]
#4670: Kevin Stueve: prime_pi for input ~ 10^10 causes PariError
[Reviewed by Sebastian Pancratz]
#5496: Kevin Stueve: fix bugs in is_prime [Reviewed by Sebastian Pancratz]
#5666: William Stein: forming ideals in IntegerModRing_generic does
not work [Reviewed by Rob Beezer]
#6411: Mike Hansen: sdist makes sage unable to run without building
[Reviewed by Willem Jan Palenstijn]
#6657: John Cremona: EllipticCurve(..., j=...) shouldn't ignore field
argument if given. [Reviewed by Chris Wuthrich]
#6737: Arthur Gaer: change occurrences of "Pyrex" to "Cython"
[Reviewed by William Stein]
#6936: Jason Grout: Implement generic testing from #6343 for matrices
[Reviewed by Nicolas M. Thiéry]
#6960: William Stein: silly inconsistency in pari versus magma
interface [Reviewed by Robert Miller]
#6967: William Stein: @parallel -- dramatically improve by rewriting
with fork directly, using files, timeouts, controlling interfaces,
etc. [Reviewed by Robert Miller]
#7095: Craig Citro, John Palmieri, Francis Clarke, William Stein: os x
10.6 port [Reviewed by David Kirkby, Georg S. Weber]
#7152: Burcin Erocal: Segmentation fault with monomials() [Reviewed by
Willem Jan Palenstijn]
#7198: Michael Brickenstein, Burcin Erocal: Free Algebra Iteration
[Reviewed by Burcin Erocal, Mike Hansen]
#7440: Tim Dumol: optional valgrind-3.3.1 spkg doesn't build with
newer GCC's [Reviewed by David Kirkby]
#7472: Robert Marik: Taylor polynomial in two variables does not work
[Reviewed by Karl-Dieter Crisman]
#7543: Sebastien Labbe: Add S-adic to the word generator [Reviewed by
Vincent Delecroix]
#7576: Robert Miller: improvements to the prove_BSD function [Reviewed
by William Stein]
#7582: Burcin Erocal: Segfault in variety() over cyclotomicfield
[Reviewed by Willem Jan Palenstijn]
#7650: Mitesh Patel: Fix sagenb doctesting [Reviewed by Tim Dumol]
#7703: Robert Miller: S-units, S-class groups, and selmer groups of
etale algebras (and number fields) [Reviewed by John Cremona]
#7760: Mike Hansen: sage -merge fails silently when applying patches
with rejects [Reviewed by Craig Citro]
#7923: David Roe: signed int overflow in givaro elements' __pow__
method [Reviewed by Francis Clarke]
#7941: Robert Miller: sage -tp N should store times when some files
fail [Reviewed by Rob Beezer]
#7948: John Cremona, John Palmieri: fix docstring processing errors in
4.3.1.rc0 [Reviewed by John Palmieri, John Cremona]
#7959: Willem Jan Palenstijn: the docstring for the associated_primes
method on multivariate polynomial ideals is wrong [Reviewed by William
Stein]
#7961: Nils Bruin: Make recognition of runpath/develpath in editmodule
more robust [Reviewed by Tim Dumol]
#7967: Willem Palenstijn: DeprecationWarning for popen3 in hg_sage
[Reviewed by Tim Dumol]
#7968: William Stein: doctest failure in heegner.py (Sage-4.3.1.rc0)
[Reviewed by Craig Citro]
#7973: Arthur Gaer: Documentation for submitting a patch is overly
confusing [Reviewed by Minh Van Nguyen]
#7975: William Stein: remove dsage from sage [Reviewed by Robert Miller]
#7977: Minh Van Nguyen: explain how to use the MATH block and
automatic numbering with hash-dot [Reviewed by John Palmieri]
#7985: Bill Cauchois: fix doctest in base.pyx [Reviewed by Willem Jan
Palenstijn]
#7988: Willem Jan Palenstijn: add testcc and testcxx to hgignore in
scripts repo [Reviewed by Robert Miller]
#7994: Tim Dumol, William Stein: Upgrade sagenb to 0.6 [Reviewed by
Robert Miller]
#7801 Alex Leone: Notebook saves twice on exit [Reviewed by Tim Dumol]
#2779 Tim Dumol and Willem Palenstijn (ref. patch): Error
message for notebook server already running is misleading [Reviewed by
Willem Palenstijn and Tim Dumol]
#7835 Tim Dumol and Mitesh Patel (ref. patch): Preparsing on
server does not account for unicode text [Reviewed by Mitesh Patel and
Tim Dumol]
#7666 Mitesh Patel: Alphanumeric cell IDs, resize on Paste, ESC
ends introspection, JSLint for notebook_lib.js [Reviewed by Tim Dumol]
#7858 Mitesh Patel: Add Content-Type to JS and declare KEY_*
vars [Reviewed by Tim Dumol]
#7874 Mitesh Patel: jsMath.Process() interact controls' labels
[Reviewed by Tim Dumol]
#7863 Mitesh Patel: Declare vars, remove lint from auxilliary
JS files [Reviewed by Tim Dumol]
#7786 Tim Dumol and Mitesh Patel (ref. patch): Restructure
templates to idiomatic Jinja [Reviewed by Mitesh Patel and Tim Dumol]
#7847 Tim Dumol: Emptying the trash in Firefox 3.5.6 displays a
"Forbidden No referer found. Forbidden." page [Reviewed by Mitesh
Patel]
#7663 Mitesh Patel: Don't rstrip internal prompt in expect.py
[Reviewed by Tim Dumol]
#7648 Mitesh Patel: Issue with indentation of first line being
wrong [Reviewed by Tim Dumol]
#7937 Mitesh Patel: Add sass directory to MANIFEST.in [Reviewed
by Tim Dumol]
#7650 Mitesh Patel: Fix doctesting under sagenb [Reviewed by Tim Dumol]
--
Robert L. Miller
http://www.rlmiller.org/
Robert Miller
William Stein
>> http://boxen.math.washington.edu/home/rlmill/sage-4.3.1.rc1.tar
>
> Oops: http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1.tar
>
Also, note that you *must* do
chmod +x spkg/install
make test
because we forgot to make spkg/install executable.
William
Dima Pasechnik
releases?
It took 4+ hours here to download rc0...
Dag Sverre Seljebotn
> is it possible to make patches, instead/as well as posting full source
> releases?
> It took 4+ hours here to download rc0...
>
on boxen.math. rsync the rc1 file with a local copy of the rc0 tarball,
and have rsync deal with computing deltas etc.
If that works out well (I'm not sure how much compressed data would
change) then it's probably a method with lower maintenance overhead than
making patches.
Dag Sverre
William Stein
<da...@student.matnat.uio.no> wrote:
> Dima Pasechnik wrote:
>>
>> is it possible to make patches, instead/as well as posting full source
>> releases?
>> It took 4+ hours here to download rc0...
>>
We have a standard system for doing upgrades from say rc0 to rc1, etc,
which we usually use in such cases.
However, Robert Miller was *super tired* and didn't have time to set
that up in this case and post a link.
William
>
> One thing one could try out is to play with rsync over SSH to an account on
> boxen.math. rsync the rc1 file with a local copy of the rc0 tarball, and
> have rsync deal with computing deltas etc.
>
> If that works out well (I'm not sure how much compressed data would change)
> then it's probably a method with lower maintenance overhead than making
> patches.
>
> Dag Sverre
>
> --
> To post to this group, send an email to sage-...@googlegroups.com
> To unsubscribe from this group, send an email to
> sage-devel+...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/sage-devel
> URL: http://www.sagemath.org
>
>
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
Dima Pasechnik
diff -r DIR1 DIR2 >patch1
and putting patch1 up for download so hard to do?
Surely, a better way might be having the whole thing under a revision
control system allowing
(semi)anonymous pulls, than pulling an upgrade is trivial...
(well, I would be mighty surpised learning Sage is not under a
revision control system)
On Jan 19, 5:48 pm, Dag Sverre Seljebotn <da...@student.matnat.uio.no>
wrote:
Mike Hansen
> hmm, is running
> diff -r DIR1 DIR2 >patch1
> and putting patch1 up for download so hard to do?
>
> Surely, a better way might be having the whole thing under a revision
> control system allowing
> (semi)anonymous pulls, than pulling an upgrade is trivial...
> (well, I would be mighty surpised learning Sage is not under a
> revision control system)
The Sage library is under revision control. However, we don't put all
of our dependencies in revision control, and much of the download is
downloading those rather than the Sage library itself. We don't have
a public repository served over HTTP for the intermediate releases,
but the public repositories are update with each release.
--Mike
Robert Miller
> We have a standard system for doing upgrades from say rc0 to rc1, etc,
> which we usually use in such cases.
> However, Robert Miller was *super tired* and didn't have time to set
> that up in this case and post a link.
The main reason was the issues we were having with the hardware. It
was taking inordinate amounts of time to do the simplest things, like
"ls" and "cd". Especially "cp", which you might see interfering with
posting upgrade paths.
On Tue, Jan 19, 2010 at 2:59 AM, Dima Pasechnik <dim...@gmail.com> wrote:
> hmm, is running
> diff -r DIR1 DIR2 >patch1
> and putting patch1 up for download so hard to do?
To upgrade, change to your SAGE_ROOT directory, and type:
./sage -upgrade
http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1
There is also a binary available here, for the machines
{sage,geom,mod,boxen}.math:
http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1-x86_64-Linux.tar.gz
William Stein
> On Tue, Jan 19, 2010 at 2:49 AM, William Stein <wst...@gmail.com> wrote:
>> We have a standard system for doing upgrades from say rc0 to rc1, etc,
>> which we usually use in such cases.
>> However, Robert Miller was *super tired* and didn't have time to set
>> that up in this case and post a link.
>
> The main reason was the issues we were having with the hardware. It
> was taking inordinate amounts of time to do the simplest things, like
> "ls" and "cd". Especially "cp", which you might see interfering with
> posting upgrade paths.
And, lest anybody is worried, we have fixed these problems with the
hardware now :-)
William
>
> On Tue, Jan 19, 2010 at 2:59 AM, Dima Pasechnik <dim...@gmail.com> wrote:
>> hmm, is running
>> diff -r DIR1 DIR2 >patch1
>> and putting patch1 up for download so hard to do?
>
> To upgrade, change to your SAGE_ROOT directory, and type:
>
> ./sage -upgrade
> http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1
>
> There is also a binary available here, for the machines
> {sage,geom,mod,boxen}.math:
>
> http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1-x86_64-Linux.tar.gz
>
> --
> Robert L. Miller
> http://www.rlmiller.org/
>
John Cremona
sage -t devel/sage/sage/misc/sagedoc.py
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage-main/sage/misc/sagedoc.py", line 365:
sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
'variety', interact=False)
Expected:
True
Got:
False
John
2010/1/19 William Stein <wst...@gmail.com>:
John Cremona
> 4.3.1.rc1 built fine (64-bit ubuntu), one test failure:
>
> sage -t devel/sage/sage/misc/sagedoc.py
> **********************************************************************
> File "/home/jec/sage-4.3.1.rc1/devel/sage-main/sage/misc/sagedoc.py", line 365:
> sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
> 'variety', interact=False)
> Expected:
> True
> Got:
> False
>
> John
>
And on another 64-bit ubuntu machine, built fine and two failures --
the one above and also this:
jec@host-57-44%./sage -t devel/sage/sage/interfaces/sage0.py
sage -t "devel/sage/sage/interfaces/sage0.py"
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 445:
sage: F == sage0(F)._sage_()
Exception raised:
Traceback (most recent call last):
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_20[4]>", line 1, in <module>
F == sage0(F)._sage_()###line 445:
sage: F == sage0(F)._sage_()
File "/home/jec/sage-4.3.1.rc1/local/lib/python/site-packages/sage/interfaces/sage0.py",
line 455, in _sage_
return load(P._local_tmpfile())
File "sage_object.pyx", line 700, in
sage.structure.sage_object.load (sage/structure/sage_object.c:7521)
IOError: [Errno 2] No such file or directory:
'/home/jec/.sage//temp/host_57_44/32735//interface//tmp32735.sobj'
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 463:
sage: four_gcd(6)
Expected:
2
Got:
<BLANKLINE>
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 486:
sage: sage0(4).gcd
Expected:
<built-in method gcd of sage.rings.integer.Integer object at 0x...>
Got:
<BLANKLINE>
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 512:
sage: half = reduce_load_element(s); half
Expected:
1/2
Got:
<BLANKLINE>
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 544:
sage: sage0_version() == version()
Expected:
True
Got:
False
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 174:
sage: print "ignore this"; sage0.cputime() # random output
Exception raised:
Traceback (most recent call last):
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_3[2]>", line 1, in <module>
print "ignore this"; sage0.cputime() # random output###line 174:
sage: print "ignore this"; sage0.cputime() # random output
File "/home/jec/sage-4.3.1.rc1/local/lib/python/site-packages/sage/interfaces/sage0.py",
line 185, in cputime
return float(s)
ValueError: empty string for float()
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 176:
sage: sage0('factor(2^157-1)')
Expected:
852133201 * 60726444167 * 1654058017289 * 2134387368610417
Got:
<BLANKLINE>
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 178:
sage: print "ignore this"; sage0.cputime() # random output
Exception raised:
Traceback (most recent call last):
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_3[4]>", line 1, in <module>
print "ignore this"; sage0.cputime() # random output###line 178:
sage: print "ignore this"; sage0.cputime() # random output
File "/home/jec/sage-4.3.1.rc1/local/lib/python/site-packages/sage/interfaces/sage0.py",
line 185, in cputime
return float(s)
ValueError: invalid literal for float(): 852133201 * 60726444167 *
1654058017289 * 2134387368610417
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 192:
sage: len(t) > 100
Exception raised:
Traceback (most recent call last):
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_4[3]>", line 1, in <module>
len(t) > Integer(100)###line 192:
sage: len(t) > 100
TypeError: object of type 'float' has no len()
**********************************************************************
File "/home/jec/sage-4.3.1.rc1/devel/sage/sage/interfaces/sage0.py", line 194:
sage: 'gcd' in t
Exception raised:
Traceback (most recent call last):
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/jec/sage-4.3.1.rc1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_4[4]>", line 1, in <module>
'gcd' in t###line 194:
sage: 'gcd' in t
TypeError: argument of type 'float' is not iterable
**********************************************************************
7 items had failures:
Alex Ghitza
> 4.3.1.rc1 built fine (64-bit ubuntu), one test failure:
>
> sage -t devel/sage/sage/misc/sagedoc.py
> **********************************************************************
> File "/home/jec/sage-4.3.1.rc1/devel/sage-main/sage/misc/sagedoc.py", line 365:
> sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
> 'variety', interact=False)
> Expected:
> True
> Got:
> False
>
> John
>
Same report as John, on 32-bit and 64-bit archlinux with long tests.
Best,
Alex
--
Alex Ghitza -- Lecturer in Mathematics -- The University of Melbourne
-- Australia -- http://www.ms.unimelb.edu.au/~aghitza/
John H Palmieri
> 4.3.1.rc1 built fine (64-bit ubuntu), one test failure:
>
> sage -t devel/sage/sage/misc/sagedoc.py
> **********************************************************************
> File "/home/jec/sage-4.3.1.rc1/devel/sage-main/sage/misc/sagedoc.py", line 365:
> sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology',
> 'variety', interact=False)
> Expected:
> True
> Got:
> False
I bet this one is because of the non-ascii character mentioned in sage-
devel and being tracked at #7999: because of this, the reference
manual fails to build, so when the search function searches the
documentation, it doesn't find anything.
--
John
Robert Miller
> Sage-4.3.1.rc1 has been released.
I have fixed the tarball so you don't need to change permissions to build:
http://boxen.math.washington.edu/home/rlmill/sage-4.3.1.rc1.tar
You will likely need to apply the patch at #7999 in order for sage to start up.
Again, the upgrade directory is:
http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1
Note on the binaries! The binary posted yesterday was for sage.math
only! The other three machines have a different version of ubuntu on
them, so I'm building a binary for them right now. This one is for
sage.math (i.e. the machine identified as 128.208.160.191):
http://boxen.math.washington.edu/home/rlmill/release/sage-4.3.1.rc1-sage.math_only.tar.gz
John Cremona
> Hi John,
>
> On Wed, Jan 20, 2010 at 4:42 AM, John Cremona <john.c...@gmail.com> wrote:
>
> <SNIP>
>
>> And on another 64-bit ubuntu machine, built fine and two failures --
>> the one above and also this:
>>
>> jec@host-57-44%./sage -t devel/sage/sage/interfaces/sage0.py
>
> DOT_SAGE points to the directory HOME/.sage. Over time, that Sage
> directory accumulates heaps of stuff left behind by different versions
> of Sage. I recently ran into this doctest failure. So I first set
> DOT_SAGE to a different (empty) directory, say
>
> export DOT_SAGE=/tmp/mvngu/.sage
>
> and then ran doctest on devel/sage/sage/interfaces/sage0.py again.
> This time, all doctests in that file passed.
>
This worked for me. So it's certainly nothing which should delay
4.3.1, but it would still be nice to find a way of clearing up that
.sage directory!
John
> --
> Regards
> Minh Van Nguyen
Gonzalo Tornaria
No, that doesn't help.
What does help, to a certain extent is the following:
boxen$ tar xvf sage-4.3.1.rc1.tar
local$ tar xvf sage-4.3.1.rc0.tar
local$ mv sage-4.3.1.rc0 sage-4.3.1.rc1
local$ rsync -avP boxen:sage-4.3.1.rc1 .
[ ... I had about 97M transfer here IIRC ]
local$ tar cvf sage-4.3.1.rc1.tar sage-4.3.1
local$ rsync -avP boxen:sage-4.3.1.rc1.tar .
[ ... about 1M transfer IIRC ]
local$ md5sum sage-4.3.1.rc1.tar
32f20dbab7aeec8529085ec41bf61552 sage-4.3.1.rc1.tar
This is still way non-optimal, but a big savings anyway (100M transfer
vs. 267M normal download).
The reason it takes so long is because the .spkg files are bzipped --
rsync is baffled about them, so a tiny change in one spkg file ends up
transfering the whole spkg.
It would be *really* an advantage to recursively do the same with the
spkg files themselves, but you better use the same options for bzip!!
(maybe rsync the tree, then tar, then rsync the tar, then bzip, then
rsync the bzip).
Gonzalo
Robert Miller
> On Tue, Jan 19, 2010 at 12:28 AM, Robert Miller <r...@rlmiller.org> wrote:
>> Sage-4.3.1.rc1 has been released.
>
> only! The other three machines have a different version of ubuntu on
Here is a binary for {boxen, geom, mod}.math:
Recall you will need to apply #7999.