sage-5.4.beta1 released
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Jeroen Demeyer
Sep 11, 2012, 5:30:54 PM9/11/12
to sage-r...@googlegroups.com
Dear Sage lovers,
We're releasing Sage 5.4.beta1.
Source archive:
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1.tar
Upgrade path:
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1/
The source and upgrade path can also be found on the mirror network
(you might need to wait a while before the mirrors are synchronized):
http://www.sagemath.org/download-latest.html
Please build, test, and report! We'd love to hear about your
experiences with this release.
== Tickets ==
* We closed 58 tickets in this release. For details, see
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/tickets.html
Closed tickets:
#6003: Additions to Cholesky decomposition [Reviewed by Rob Beezer]
#9511: Upgrade Givaro to version 3.7.0 [Reviewed by Volker Braun]
#10153: Canonical generator matrices for linear codes and their
automorphism groups [Reviewed by Thomas Feulner]
#11718: Upgrade LinBox to version 1.1.7 [Reviewed by Volker Braun,
Martin Albrecht]
#13340: log scale plot fails if xmin > xmax [Reviewed by Punarbasu
Purkayastha]
Merged in sage-5.4.beta1:
#6654: Valentin Féray: New features in group algebra category [Reviewed
by Frédéric Chapoton]
#8899: Jason Bandlow, Chris Berg, Franco Saliola, Nicolas M. Thiéry:
Implement non commutative symmetric functions [Reviewed by Mike
Zabrocki, Franco Saliola, Mike Hansen]
#9906: Leif Leonhardy, Jeroen Demeyer: Move the RPy package outside of
the R package [Reviewed by Karl-Dieter Crisman, John Palmieri]
#12883: Paulo César Pereira de Andrade, Martin Albrecht: Update LinBox
to most recent upstream release [Reviewed by Volker Braun, Jeroen Demeyer]
#12972: John Cremona: Fix small bug in elliptic curve saturation
[Reviewed by Volker Braun]
#12994: R. Andrew Ohana: Serialization of setuptools targets in
spkg/standard/deps [Reviewed by Jeroen Demeyer]
#13145: David Roe: Sage's noncommutative rings don't always increment a
refcount [Reviewed by Martin Albrecht]
#13164: Paulo César Pereira de Andrade, Martin Albrecht, Jean-Pierre
Flori: Update Givaro to 3.7.1 [Reviewed by Volker Braun]
#13284: Alexander Dreyer: Some conversion between BooleanPolynomialRing
and QQ[.....] are missing [Reviewed by Charles Bouillaguet]
#13298: John Cremona: Update Cremona's table of elliptic curves to
270000 [Reviewed by R. Andrew Ohana]
#13327: Andrey Novoseltsev: Allow conversion of strings to iterated
polynomial rings [Reviewed by Frédéric Chapoton]
#13391: Daniel Bump: WeylCharacterRing improvement [Reviewed by Anne
Schilling]
#13395: Jeroen Demeyer: Fix upgrading with GCC [Reviewed by John Palmieri]
#13404: Nicolas M. Thiéry, Mike Zabrocki: Improved printing for
symmetric function bases and misc refactoring [Reviewed by Anne Schilling]
#13416: Jeroen Demeyer: Fix GAP dependencies [Reviewed by Volker Braun]
#13427: David Kirkby: Numerical noise causing sage/numerical/optimize.py
to fail on SPARC [Reviewed by Volker Braun]
#13428: Jeroen Demeyer: Race condition in R installation [Reviewed by
John Palmieri]
We're releasing Sage 5.4.beta1.
Source archive:
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1.tar
Upgrade path:
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1/
The source and upgrade path can also be found on the mirror network
(you might need to wait a while before the mirrors are synchronized):
http://www.sagemath.org/download-latest.html
Please build, test, and report! We'd love to hear about your
experiences with this release.
== Tickets ==
* We closed 58 tickets in this release. For details, see
http://boxen.math.washington.edu/home/release/sage-5.4.beta1/tickets.html
Closed tickets:
#6003: Additions to Cholesky decomposition [Reviewed by Rob Beezer]
#9511: Upgrade Givaro to version 3.7.0 [Reviewed by Volker Braun]
#10153: Canonical generator matrices for linear codes and their
automorphism groups [Reviewed by Thomas Feulner]
#11718: Upgrade LinBox to version 1.1.7 [Reviewed by Volker Braun,
Martin Albrecht]
#13340: log scale plot fails if xmin > xmax [Reviewed by Punarbasu
Purkayastha]
Merged in sage-5.4.beta1:
#6654: Valentin Féray: New features in group algebra category [Reviewed
by Frédéric Chapoton]
#8899: Jason Bandlow, Chris Berg, Franco Saliola, Nicolas M. Thiéry:
Implement non commutative symmetric functions [Reviewed by Mike
Zabrocki, Franco Saliola, Mike Hansen]
#9906: Leif Leonhardy, Jeroen Demeyer: Move the RPy package outside of
the R package [Reviewed by Karl-Dieter Crisman, John Palmieri]
#12883: Paulo César Pereira de Andrade, Martin Albrecht: Update LinBox
to most recent upstream release [Reviewed by Volker Braun, Jeroen Demeyer]
#12972: John Cremona: Fix small bug in elliptic curve saturation
[Reviewed by Volker Braun]
#12994: R. Andrew Ohana: Serialization of setuptools targets in
spkg/standard/deps [Reviewed by Jeroen Demeyer]
#13145: David Roe: Sage's noncommutative rings don't always increment a
refcount [Reviewed by Martin Albrecht]
#13164: Paulo César Pereira de Andrade, Martin Albrecht, Jean-Pierre
Flori: Update Givaro to 3.7.1 [Reviewed by Volker Braun]
#13284: Alexander Dreyer: Some conversion between BooleanPolynomialRing
and QQ[.....] are missing [Reviewed by Charles Bouillaguet]
#13298: John Cremona: Update Cremona's table of elliptic curves to
270000 [Reviewed by R. Andrew Ohana]
#13327: Andrey Novoseltsev: Allow conversion of strings to iterated
polynomial rings [Reviewed by Frédéric Chapoton]
#13391: Daniel Bump: WeylCharacterRing improvement [Reviewed by Anne
Schilling]
#13395: Jeroen Demeyer: Fix upgrading with GCC [Reviewed by John Palmieri]
#13404: Nicolas M. Thiéry, Mike Zabrocki: Improved printing for
symmetric function bases and misc refactoring [Reviewed by Anne Schilling]
#13416: Jeroen Demeyer: Fix GAP dependencies [Reviewed by Volker Braun]
#13427: David Kirkby: Numerical noise causing sage/numerical/optimize.py
to fail on SPARC [Reviewed by Volker Braun]
#13428: Jeroen Demeyer: Race condition in R installation [Reviewed by
John Palmieri]
Justin C. Walker
Sep 13, 2012, 7:38:24 PM9/13/12
to sage-r...@googlegroups.com
On Sep 11, 2012, at 14:30 , Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.4.beta1.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1.tar
Built w/o problems on Mac OS X, 10.7.4 (Quad core Core i7). All tests ('ptestlong') passed.
Justin
--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
I want to die, peacefully in my sleep, like my grandfather;
not screaming in terror, like his passengers.
P Purkayastha
Sep 18, 2012, 5:47:00 AM9/18/12
to sage-r...@googlegroups.com
Did you upgrade the installation from an older version, or did you compile the sage-5.4beta1 tarball? There shouldn't be any left over jsmath code in the 5.4beta1 sources.
In fact, here the following command does come up with some jsmath strings, but they are not really in the sage library:
cd SAGE_ROOT/devel/sage/sage
find -iname '*.py*' -exec grep -irnH jsmath {} \;
./server/notebook/cell.py
./server/notebook/worksheet.py
./server/notebook/tutorial.py
./server/notebook/run_notebook.py
./server/notebook/notebook.py
./geometry/point_collection.pyx
./server/notebook/worksheet.py
./server/notebook/tutorial.py
./server/notebook/run_notebook.py
./server/notebook/notebook.py
./geometry/point_collection.pyx
I am not sure what that notebook code is doing there. The last one is simply a single instance of jsmath in the docstring. It should be removed.
Dear Jeroen,
When starting sage-5.4.beta1 after compiling from source, I get the following error message on MacOs 10.6.8
----------------------------------------------------------------------
| Sage Version 5.4.beta1, Release Date: 2012-09-11 |
| Type "notebook()" for the browser-based notebook interface. |
| Type "help()" for help. |
----------------------------------------------------------------------
**********************************************************************
* *
* Warning: this is a prerelease version, and it may be unstable. *
* *
**********************************************************************
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/Applications/sage-5.4.beta1/<ipython console> in <module>()
/Applications/sage-5.4.beta1/local/lib/python2.7/site-packages/sage/misc/preparser.pyc in load(filename, globals, attach)
1657 else:
1658 # Preparse in memory only for speed.
-> 1659 exec(preparse_file(open(fpath).read()) + "\n", globals)
1660 elif fpath.endswith('.spyx') or fpath.endswith('.pyx'):
1661 import interpreter
/Applications/sage-5.4.beta1/<string> in <module>()
AttributeError: Latex instance has no attribute 'add_to_jsmath_avoid_list'
Is this a known issues?
Best,
Anne
Jeroen Demeyer
Sep 18, 2012, 6:08:25 AM9/18/12
to sage-r...@googlegroups.com
On 2012-09-18 11:47, P Purkayastha wrote:
> Did you upgrade the installation from an older version, or did you
> compile the sage-5.4beta1 tarball? There shouldn't be any left over
> jsmath code in the 5.4beta1 sources.
>
> In fact, here the following command does come up with some jsmath
> strings, but they are not really in the sage library:
>
> cd SAGE_ROOT/devel/sage/sage
> find -iname '*.py*' -exec grep -irnH jsmath {} \;
>
> ./server/notebook/cell.py
> ./server/notebook/worksheet.py
> ./server/notebook/tutorial.py
> ./server/notebook/run_notebook.py
> ./server/notebook/notebook.py
> ./geometry/point_collection.pyx
>
> I am not sure what that notebook code is doing there.
See http://trac.sagemath.org/sage_trac/ticket/11409
> Did you upgrade the installation from an older version, or did you
> compile the sage-5.4beta1 tarball? There shouldn't be any left over
> jsmath code in the 5.4beta1 sources.
>
> In fact, here the following command does come up with some jsmath
> strings, but they are not really in the sage library:
>
> cd SAGE_ROOT/devel/sage/sage
> find -iname '*.py*' -exec grep -irnH jsmath {} \;
>
> ./server/notebook/cell.py
> ./server/notebook/worksheet.py
> ./server/notebook/tutorial.py
> ./server/notebook/run_notebook.py
> ./server/notebook/notebook.py
> ./geometry/point_collection.pyx
>
> I am not sure what that notebook code is doing there.
Anne Schilling
Sep 19, 2012, 1:24:20 AM9/19/12
to sage-r...@googlegroups.com
I compiled sage-5.4.beta1 from a tarball.
Anne
Anne
John H Palmieri
Sep 19, 2012, 1:31:58 AM9/19/12
to sage-r...@googlegroups.com
Do you have an init.sage file with anything relevant in it?
--
John
Nicolas M. Thiery
Sep 19, 2012, 7:43:02 AM9/19/12
to sage-r...@googlegroups.com, Anne Schilling
Hi Anne,
On Mon, Sep 17, 2012 at 07:56:41AM -0700, Anne Schilling wrote:
> When starting sage-5.4.beta1 after compiling from source, I get the
> following error message on MacOs 10.6.8
>
> ----------------------------------------------------------------------
> | Sage Version 5.4.beta1, Release Date: 2012-09-11 |
> | Type "notebook()" for the browser-based notebook interface. |
> | Type "help()" for help. |
> ----------------------------------------------------------------------
> **********************************************************************
> * *
> * Warning: this is a prerelease version, and it may be unstable. *
> * *
> **********************************************************************
add_to_jsmath_avoid_list? If yes, does the error still occur if you
comment out that part?
Cheers,
Nicolas
--
Nicolas M. Thi�ry "Isil" <nth...@users.sf.net>
http://Nicolas.Thiery.name/
On Mon, Sep 17, 2012 at 07:56:41AM -0700, Anne Schilling wrote:
> When starting sage-5.4.beta1 after compiling from source, I get the
> following error message on MacOs 10.6.8
>
> ----------------------------------------------------------------------
> | Sage Version 5.4.beta1, Release Date: 2012-09-11 |
> | Type "notebook()" for the browser-based notebook interface. |
> | Type "help()" for help. |
> ----------------------------------------------------------------------
> **********************************************************************
> * *
> * Warning: this is a prerelease version, and it may be unstable. *
> * *
> **********************************************************************
> AttributeError: Latex instance has no attribute 'add_to_jsmath_avoid_list'
Just to make sure: does your .sage/init.sage mention
add_to_jsmath_avoid_list? If yes, does the error still occur if you
comment out that part?
Cheers,
Nicolas
--
Nicolas M. Thi�ry "Isil" <nth...@users.sf.net>
http://Nicolas.Thiery.name/
Nicolas M. Thiery
Sep 19, 2012, 10:53:12 AM9/19/12
to Anne Schilling, sage-r...@googlegroups.com
On Wed, Sep 19, 2012 at 07:41:22AM -0700, Anne Schilling wrote:
> Yes, indeed. I have the line
>
> latex.add_to_jsmath_avoid_list('\\begin{tikzpicture}')
>
> in my sage init file. When I remove this line it does not happen.
> But this never happened with previous versions of sage.
Ok, then I guess it's just that the function
latex.add_to_jsmath_avoid_list was removed in this new version of
Sage.
If this is confirmed, then I recommend that this function be
reinstated one way or the other in Sage 5.4 final, with a deprecation
warning. It's used quite often, and there might be spots left in the
doc/tutorials out there suggesting to use it (e.g. for graphviz
output, ...).
> Yes, indeed. I have the line
>
> latex.add_to_jsmath_avoid_list('\\begin{tikzpicture}')
>
> in my sage init file. When I remove this line it does not happen.
> But this never happened with previous versions of sage.
Ok, then I guess it's just that the function
latex.add_to_jsmath_avoid_list was removed in this new version of
Sage.
If this is confirmed, then I recommend that this function be
reinstated one way or the other in Sage 5.4 final, with a deprecation
warning. It's used quite often, and there might be spots left in the
doc/tutorials out there suggesting to use it (e.g. for graphviz
output, ...).
P Purkayastha
Sep 19, 2012, 11:05:10 AM9/19/12
to sage-r...@googlegroups.com, Anne Schilling, Nicolas M. Thiery
The move to mathjax has renamed this function. It is now
latex.add_to_mathjax_avoid_list
The same function, but different name to reflect the new math rendering system used.
Nicolas M. Thi�ry "Isil" <nth...@users.sf.net>
http://Nicolas.Thiery.name/
John H Palmieri
Sep 19, 2012, 11:34:37 AM9/19/12
to sage-r...@googlegroups.com, Anne Schilling, Nicolas M. Thiery
On Wednesday, September 19, 2012 7:53:19 AM UTC-7, Nicolas M. Thiéry wrote:
On Wed, Sep 19, 2012 at 07:41:22AM -0700, Anne Schilling wrote:
> Yes, indeed. I have the line
>
> latex.add_to_jsmath_avoid_list('\\begin{tikzpicture}')
>
> in my sage init file. When I remove this line it does not happen.
> But this never happened with previous versions of sage.
Ok, then I guess it's just that the function
latex.add_to_jsmath_avoid_list was removed in this new version of
Sage.
If this is confirmed, then I recommend that this function be
reinstated one way or the other in Sage 5.4 final, with a deprecation
warning. It's used quite often, and there might be spots left in the
doc/tutorials out there suggesting to use it (e.g. for graphviz
output, ...).
Dr. David Kirkby
Sep 19, 2012, 7:55:55 PM9/19/12
to sage-r...@googlegroups.com
On 11/09/2012 22:30, Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.4.beta1.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1.tar
>
> Merged in sage-5.4.beta1:
> Dear Sage lovers,
>
> We're releasing Sage 5.4.beta1.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.4.beta1/sage-5.4.beta1.tar
>
> #13427: David Kirkby: Numerical noise causing sage/numerical/optimize.py
> to fail on SPARC [Reviewed by Volker Braun]
I think trying 64-bit would be a bit pointless, as I know it is unstable there
due to the pynac bug.)
The patch #13427 has cured the numerical noise problem I had when building a
recent version of Sage on SPARC, and the other was due to a timeout, which I
avoided by setting SAGE_TIMEOUT_LONG (or whatever its called).
But still there are two failures on Solaris 10 SPARC, running on a dual
processor Sun Blade 2000.
----------------------------------------------------------------------
The temporary doctesting directory
/export/home/drkirkby/.sage/tmp/buzzard-29503
was not removed: it is not empty, presumably because doctests
failed or doctesting was interrupted.
----------------------------------------------------------------------
The following tests failed:
sage -t --long -force_lib devel/sage/sage/matrix/matrix_modn_dense.pyx
# 5 doctests failed
sage -t --long -force_lib
devel/sage/sage/matrix/matrix_modn_dense_template.pxi # 5 doctests failed
----------------------------------------------------------------------
Total time for all tests: 21324.3 seconds
Here are the errors in more detail.
**********************************************************************
File
"/export/home/drkirkby/sage-5.4.beta1/devel/sage-main/sage/matrix/matrix_modn_dense.pyx",
line 501:
sage: data, version = A._pickle()
Exception raised:
Traceback (most recent call last):
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_8[8]>", line 1, in <module>
data, version = A._pickle()###line 501:
sage: data, version = A._pickle()
File "matrix_modn_dense_template.pxi", line 638, in
sage.matrix.matrix_modn_dense_double.Matrix_modn_dense_template._pickle
(sage/matrix/matrix_modn_dense_double.cpp:6580)
sig_on()
RuntimeError: Bus error
**********************************************************************
File
"/export/home/drkirkby/sage-5.4.beta1/devel/sage-main/sage/matrix/matrix_modn_dense.pyx",
line 504:
sage: B == A
Expected:
True
Got:
False
**********************************************************************
File
"/export/home/drkirkby/sage-5.4.beta1/devel/sage-main/sage/matrix/matrix_modn_dense.pyx",
line 527:
sage: A._unpickle((8, False,
'\x00\x00\x00\x00\x00\x00\x02\x08\x00\x00\x00\x00\x00\x00\x01\x04'), 10)
Exception raised:
Traceback (most recent call last):
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_8[22]>", line 1, in <module>
A._unpickle((Integer(8), False,
'\x00\x00\x00\x00\x00\x00\x02\x08\x00\x00\x00\x00\x00\x00\x01\x04'),
Integer(10))###line 527:
sage: A._unpickle((8, False,
'\x00\x00\x00\x00\x00\x00\x02\x08\x00\x00\x00\x00\x00\x00\x01\x04'), 10)
File "matrix_modn_dense_template.pxi", line 726, in
sage.matrix.matrix_modn_dense_double.Matrix_modn_dense_template._unpickle
(sage/matrix/matrix_modn_dense_double.cpp:7004)
sig_on()
RuntimeError: Bus error
**********************************************************************
File
"/export/home/drkirkby/sage-5.4.beta1/devel/sage-main/sage/matrix/matrix_modn_dense.pyx",
line 528:
sage: A
Expected:
[520 260]
Got:
[259 5]
**********************************************************************
File
"/export/home/drkirkby/sage-5.4.beta1/devel/sage-main/sage/matrix/matrix_modn_dense.pyx",
line 537:
sage: loads(dumps(A)) == A
Exception raised:
Traceback (most recent call last):
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/export/home/drkirkby/sage-5.4.beta1/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_8[27]>", line 1, in <module>
loads(dumps(A)) == A###line 537:
sage: loads(dumps(A)) == A
File "sage_object.pyx", line 889, in sage.structure.sage_object.dumps
(sage/structure/sage_object.c:9855)
File "matrix0.pyx", line 1534, in sage.matrix.matrix0.Matrix.__reduce__
(sage/matrix/matrix0.c:7995)
data, version = self._pickle()
File "matrix_modn_dense_template.pxi", line 638, in
sage.matrix.matrix_modn_dense_double.Matrix_modn_dense_template._pickle
(sage/matrix/matrix_modn_dense_double.cpp:6580)
sig_on()
RuntimeError: Bus error
**********************************************************************
1 items had failures:
5 of 29 in __main__.example_8
***Test Failed*** 5 failures.
For whitespace errors, see the file
/export/home/drkirkby/.sage/tmp/buzzard-29503/matrix_modn_dense_11931.py
[12.6 s]
sage -t --long -force_lib devel/sage/sage/matrix/matrix_mod2_dense.pyx
[28.7 s]
--
Dr. David Kirkby Ph.D C.Eng MIET
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