Sage 4.6.alpha2 released
Mitesh Patel
We've released Sage 4.6.alpha2.
Source archive:
http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha2.tar
Upgrade path:
http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha2/
Please build, test, and report! We'd love to hear about your
experiences with this release.
== Known problems ==
The full list of blockers is at
Feel free to comment, patch, and review.
== Next release ==
We'll merge into 4.6.alpha3 whichever of
Matplotlib
http://trac.sagemath.org/sage_trac/ticket/9221
NumPy and SciPy
http://trac.sagemath.org/sage_trac/ticket/9808
Cython
http://trac.sagemath.org/sage_trac/ticket/9828
Pynac
http://trac.sagemath.org/sage_trac/ticket/9901
SageNB
http://trac.sagemath.org/sage_trac/ticket/10036
is positively reviewed by 7 October 2010. After that, the 4.6 cycle
will be in feature freeze.
== Tickets ==
Closed:
#9675: Oriol Castejon: New package: Brian, a simulator for spiking
neural networks [Reviewed by Karl-Dieter Crisman]
#9857: Marshall Hampton: Upgrade biopython to version 1.55 (released
Augest 31, 2010) [Reviewed by Adam Webb]
Merged in sage-4.6.alpha2:
#1135: Luis Felipe Tabera Alonso: Error in preparsing generators,
QuadraticField [Reviewed by Nick Alexander]
#4446: Philippe Theveny, Alex Ghitza, Yann Laigle-Chapuy: New module
complex_mpc using lib mpc for complex multiprecision arithmetic
[Reviewed by William Stein, David Kirkby, Paul Zimmermann, Mitesh Patel]
#4836: Jeroen Demeyer: pari types getattr() function ugly and
inefficient [Reviewed by John Cremona]
#5739: Mike Hansen, Robert Bradshaw: changed from zeta(CDF(1)) go boom!
+ zeta of 1 return value be consistent in different rings [Reviewed by
Karl-Dieter Crisman, Robert Bradshaw, David Loeffler]
#6327: Jeroen Demeyer: Document PARI's ellpow() function for CM curves
[Reviewed by David Loeffler]
#6979: Yann Laigle-Chapuy: improve sparse matrix/vector product
[Reviewed by William Stein, Jason Grout, Rob Beezer]
#7741: Robert Bradshaw: Can't construct a rational fraction from a
symbolic one. [Reviewed by Florent Hivert, Burcin Erocal]
#7883: David Roe: Added some functionality to ideals [Reviewed by Robert
Bradshaw, David Loeffler]
#8054: Mike Hansen: roots(algorithm='numpy') does not work in arbitrary
precision [Reviewed by Paul Zimmermann]
#8228: Martin Albrecht, Hans Schönemann, Burcin Eröcal: Segfault in
libsingular [Reviewed by Martin Albrecht]
#8334: David Roe: Improvements to residue fields [Reviewed by David
Loeffler]
#8568: Burcin Erocal, Karl-Dieter Crisman: can not simplify derivative
of erf [Reviewed by Karl-Dieter Crisman, Burcin Erocal]
#8762: Johan Sebastian Rosenkilde Nielsen: the sparse=True flag is
horribly broken for GF(p)[x] [Reviewed by Yann Laigle-Chapuy]
#8825: Johan Grönqvist, Minh Van Nguyen: Improve documentation for
function norm [Reviewed by Minh Van Nguyen]
#8955: Martin Albrecht: random_matrix(GF(2),2,1) always returns all 1
matrix [Reviewed by Yann Laigle-Chapuy]
#9049: Andrey Novoseltsev: v4.4.1 bug in variety() over finite field
extensions of Q? [Reviewed by Burcin Erocal]
#9359: David Loeffler: Get number field coverage up to 100% [Reviewed by
Jeroen Demeyer]
#9383: Anna Haensch, David Loeffler: Add quadratic forms code to the
reference manual [Reviewed by Minh Van Nguyen]
#9420: Nathann Cohen: SubgraphSearch class instead of a method, digraphs
fixed [Reviewed by Dmitrii Pasechnik]
#9596: Marco Streng: is_totally_positive should give proven output
[Reviewed by David Loeffler]
#9619: Leonardo Sampaio: b-coloring of a graph [Reviewed by Nathann Cohen]
#9644: John Palmieri, Leif Leonhardy: Add error messages and update
documentation for spaces in $SAGE_ROOT [Reviewed by John Palmieri, David
Kirkby]
#9658: Jason Grout: mpz_clear->mpq_clear (typo) [Reviewed by Leif
Leonhardy]
#9701: Carl Witty: NumberFieldElement should have a conversion to float
[Reviewed by David Loeffler]
#9753: Jeroen Demeyer: Simplify NumberFieldIdeal.gens_reduced()
[Reviewed by David Loeffler]
#9755: Jason Bandlow: Symmetric Function coercion issue [Reviewed by
Mike Hansen]
#9764: William Stein, Jeroen Demeyer: Change hashing and printing for
NumberFieldIdeals [Reviewed by David Loeffler]
#9779: Ed Scheinerman: Grotzsch graph and Mycielski graphs [Reviewed by
Nathann Cohen]
#9780: David Kirkby: Check for static libraries libatlas.a, libcblas.a,
libf77blas and liblapack.a, so SAGE_ATLAS_LIB works [Reviewed by John
Palmieri]
#9814: David Roe: Improve creation time for p-adic elements [Reviewed by
David Harvey]
#9823: Robert Mařík: desolve_system is broken for a system of one
equation [Reviewed by David Joyner, Ryan Hinton]
#9835: Robert Marik: Make desolve more informative when solving BVP
[Reviewed by Karl-Dieter Crisman, Burcin Erocal, Marshall Hampton]
#9843: Alex Ghitza: modular/overconvergent/weightspace.py uses Maxima
because of symbolic variables [Reviewed by David Loeffler]
#9845: Jeroen Demeyer, Mike Hansen, William Stein: lcalc doesn't build
on cygwin due to missing time.h include [Reviewed by Leif Leonhardy]
#9856: Yann Laigle-Chapuy: improve `augment` method for sparse matrices
[Reviewed by Paul Zimmermann]
#9873: Ivan Andrus: Create Mac Application that people love to use
[Reviewed by Karl-Dieter Crisman, Jason Grout, John Palmieri]
#9876: Jeroen Demeyer: Building PARI/GP with SAGE_CHECK=yes fails on
32-bit big endian machines [Reviewed by John Palmieri, Leif Leonhardy]
#9898: Jeroen Demeyer: Clean up and add functions to
sage/libs/pari/decl.pxi [Reviewed by Leif Leonhardy]
#9915: Carl Witty: fixes for NZMATH/Sage interoperation [Reviewed by
Leif Leonhardy]
#9917: David Kirkby, Leif Leonhardy: ECL has too few arguments and two
many on file dpp.c [Reviewed by John Palmieri]
#9925: Nathann Cohen: Doctest error in sage/graphs/graph.py [Reviewed by
Dmitrii Pasechnik]
#9928: Jason Grout: vectors from numpy arrays don't always work
[Reviewed by Mike Hansen]
#9930: Nathann Cohen: Additional test in is_even_hole_free [Reviewed by
Dmitrii Pasechnik]
#9931: Jeroen Demeyer: Implement conversion from EllipticCurvePoint to
PARI [Reviewed by David Loeffler]
#9934: Volker Braun: Toric divisor class -> divisor lift should be
integral [Reviewed by Andrey Novoseltsev]
#9936: Minh Van Nguyen: add sage.symbolic.function_factory to the
reference manual [Reviewed by Niles Johnson]
#9938: Franco Saliola: GAP does not start if the path to the GAP
workspace file contains more than 82 characters [Reviewed by Sébastien
Labbé]
#9945: Robert Bradshaw: partial_fraction_decomposition broken for FpT
elements [Reviewed by Paul Zimmermann]
#9946: Francois Bissey, Alexander Dreyer: Parallel build of Singular
3-1-1-4-package fails in other cases [Reviewed by David Kirkby]
#9951: Leif Leonhardy: Missing package init file
'sage/tests/french_book/__init__.py' [Reviewed by Paul Zimmermann]
#9952: John Palmieri: make SAGE_CHECK work with SAGE_ATLAS_LIB [Reviewed
by David Kirkby, Leif Leonhardy]
#9961: Burcin Erocal, Robert Marik: Allow assumptions on the dependent
variable in desolve [Reviewed by Karl-Dieter Crisman, Robert Marik]
#9963: Volker Braun: non-nef divisors can have sections, too [Reviewed
by Andrey Novoseltsev]
#9966: Jason Grout: remove texttt from html.table output [Reviewed by
John Palmieri]
#9968: David Loeffler: Stop Dancing Links polluting the global namespace
[Reviewed by Nathann Cohen]
#9973: Jeroen Demeyer: Remove empty directories after PARI upgrade
[Reviewed by David Kirkby]
#10001: Jeroen Demeyer: Remove sage/schemes/elliptic_curves/sea.py
[Reviewed by John Cremona]
#10005: Andrey Novoseltsev: Update scheme overview [Reviewed by Volker
Braun]
#10016: Leif Leonhardy: R's spkg-install calls "sage -f ..." to install
the contained Rpy spkg [Reviewed by John Palmieri]
#10019: Yann Laigle-Chapuy: big performance issue with variance and std
[Reviewed by Mike Hansen]
#10021: Volker Braun: Empty LatticePolytope fails [Reviewed by Andrey
Novoseltsev]
#10022: Volker Braun: Cone.is_smooth() returns wrong answer [Reviewed by
Andrey Novoseltsev]
Marshall Hampton
from the known toric_divisor problem (#9926) on OS X. #9926 is solved
by #9798 which I can give a positive review as soon as someone
verifies its OK on Solaris.
-Marshall Hampton
On Sep 30, 8:58 pm, Mitesh Patel <qed...@gmail.com> wrote:
> Hi,
>
> We've released Sage 4.6.alpha2.
>
> Source archive:
>
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6...
> Please build, test, and report! We'd love to hear about your
> experiences with this release.
>
> == Known problems ==
>
> The full list of blockers is at
>
> Feel free to comment, patch, and review.
>
> == Next release ==
>
> We'll merge into 4.6.alpha3 whichever of
>
> Matplotlibhttp://trac.sagemath.org/sage_trac/ticket/9221
>
> NumPy and SciPyhttp://trac.sagemath.org/sage_trac/ticket/9808
>
> Cythonhttp://trac.sagemath.org/sage_trac/ticket/9828
>
> Pynachttp://trac.sagemath.org/sage_trac/ticket/9901
>
Dima Pasechnik
For the heck of it I tried to build Sage on iras @skynet, and got
a full-blown compiler crash in Pari. (might be a combination of an
unusual hardware
and a new compiler)
gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -O3 -g -
I. -I../src/headers -fPI
C -o krasner.o ../src/modules/krasner.c
../src/modules/krasner.c: In function 'GetRamifiedPol':
../src/modules/krasner.c:878:1: error: unrecognizable insn:
(insn:TI 7910 7861 7937 509 (parallel [
(set (reg:DI 134 f6)
(asm_operands:DI ("xma.hu %0 = %2, %3, f0
;;
xma.l %1 = %2, %3, f0") ("=&f") 0 [
(reg:DI 135 f7)
(reg/v:DI 130 f2 [orig:1756 pmodg ] [1756])
]
[
(asm_input:DI ("f") (null):0)
(asm_input:DI ("f") (null):0)
]
[] ../src/modules/krasner.c:878))
(set (reg:DI 135 f7)
(asm_operands:DI ("xma.hu %0 = %2, %3, f0
;;
xma.l %1 = %2, %3, f0") ("=f") 1 [
(reg:DI 135 f7)
(reg/v:DI 130 f2 [orig:1756 pmodg ] [1756])
]
[
(asm_input:DI ("f") (null):0)
(asm_input:DI ("f") (null):0)
]
[] ../src/modules/krasner.c:878))
]) -1 (nil))
../src/modules/krasner.c:878:1: internal compiler error: in
get_attr_first_insn, at config/ia64
/itanium2.md:1909
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[3]: *** [krasner.o] Error 1
make[3]: Leaving directory `/home/dima/sage/iras/sage-4.6.alpha2/spkg/
build/pari-2.4.3.svn-1257
7.p7/src/Olinux-ia64'
make[2]: *** [gp] Error 2
make[2]: Leaving directory `/home/dima/sage/iras/sage-4.6.alpha2/spkg/
build/pari-2.4.3.svn-1257
7.p7/src'
Error building GP
real 8m16.626s
user 8m2.656s
sys 0m5.008s
sage: An error occurred while installing pari-2.4.3.svn-12577.p7
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /home/dima/sage/iras/sage-4.6.alpha2/install.log. Describe your
computer, operating system,
etc.
dima@iras:~/sage/iras/sage-4.6.alpha2> gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.5.1/ia64-Linux-suse/libexec/gcc/
ia64-unknown-linux-gnu/4.5.1/lto-wrapper
Target: ia64-unknown-linux-gnu
Configured with: /usr/local/gcc-4.5.1/src/gcc-4.5.1/configure --enable-
languages=c,c++,fortran --with-gnu-as --with-as=/usr/local/
binutils-2.20.1/ia64-Linux-suse-gcc-4.4.3/bin/as --with-gnu-ld --with-
ld=/usr/local/binutils-2.20.1/ia64-Linux-suse-gcc-4.4.3/bin/ld --with-
gmp=/usr/local/gmp-5.0.1/ia64-Linux-suse-gcc-4.5.0 --with-mpfr=/usr/
local/mpfr-3.0.0/ia64-Linux-suse-gmp-5.0.1-gcc-4.5.0 --with-mpc=/usr/
local/mpc-0.8.2/ia64-Linux-suse-mpfr-3.0.0-gmp-5.0.1-gcc-4.5.0 --
prefix=/usr/local/gcc-4.5.1/ia64-Linux-suse
Thread model: posix
gcc version 4.5.1 (GCC)
On Oct 1, 9:58 am, Mitesh Patel <qed...@gmail.com> wrote:
> Hi,
>
> We've released Sage 4.6.alpha2.
>
> Source archive:
>
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6...
>
> experiences with this release.
>
> == Known problems ==
>
> The full list of blockers is at
>
> Feel free to comment, patch, and review.
>
> == Next release ==
>
> We'll merge into 4.6.alpha3 whichever of
>
>
> NumPy and SciPyhttp://trac.sagemath.org/sage_trac/ticket/9808
>
> Cythonhttp://trac.sagemath.org/sage_trac/ticket/9828
>
> Pynachttp://trac.sagemath.org/sage_trac/ticket/9901
>
Jeroen Demeyer
> Are we aiming for the release to work on ia64?
> For the heck of it I tried to build Sage on iras @skynet, and got
> a full-blown compiler crash in Pari. (might be a combination of an
> unusual hardware
> and a new compiler)
It is a bug in gcc, see http://trac.sagemath.org/sage_trac/ticket/9897
Justin C. Walker
On Sep 30, 2010, at 18:58 , Mitesh Patel wrote:
> Hi,
>
> We've released Sage 4.6.alpha2.
>
> Source archive:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha2.tar
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha2/
Built as an upgrade to 4.6.a0 on two 10.6.4 systems, w. no problems. Testing showed the following failures:
Dual Quad Xeon:
sage -t -long devel/sage/sage/algebras/all.py # 0 doctests failed
sage -t -long devel/sage/sage/misc/trace.py # 1 doctests failed
sage -t -long devel/sage/sage/plot/plot3d/base.pyx # 4 doctests failed
sage -t -long devel/sage/sage/schemes/generic/toric_divisor.py # 1 doctests failed
Core i7:
sage -t -long devel/sage/sage/misc/trace.py # 1 doctests failed
sage -t -long devel/sage/sage/schemes/generic/toric_divisor.py # 1 doctests failed
The logs are in sage.math.washington.edu:~justin/logs, as {xeon,i7}.4.6.a2.log.
--
Justin C. Walker
Curmudgeon-at-large
Director
Institute for the Absorption of Federal Funds
----
186,000 Miles per Second
Not just a good idea:
it's the law!
----
Mitesh Patel
> On Sep 30, 2010, at 18:58 , Mitesh Patel wrote:
> Built as an upgrade to 4.6.a0 on two 10.6.4 systems, w. no problems. Testing showed the following failures:
>
> Dual Quad Xeon:
These are [now]:
> sage -t -long devel/sage/sage/algebras/all.py # 0 doctests failed
http://trac.sagemath.org/sage_trac/ticket/9739 (probably)
> sage -t -long devel/sage/sage/misc/trace.py # 1 doctests failed
http://trac.sagemath.org/sage_trac/ticket/9446
> sage -t -long devel/sage/sage/plot/plot3d/base.pyx # 4 doctests failed
http://trac.sagemath.org/sage_trac/ticket/10059
> sage -t -long devel/sage/sage/schemes/generic/toric_divisor.py # 1 doctests failed
http://trac.sagemath.org/sage_trac/ticket/9926
François Bissey
>
> We've released Sage 4.6.alpha2.
>
> Source archive:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha
> 2.tar
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.6.alpha2/sage-4.6.alpha
> 2/
>
> Please build, test, and report! We'd love to hear about your
> experiences with this release.
>
> == Known problems ==
>
> The full list of blockers is at
>
> http://trac.sagemath.org/sage_trac/query?priority=blocker&group=status&grou
> pdesc=1&milestone=sage-4.6
>
> Feel free to comment, patch, and review.
>
> == Next release ==
>
> We'll merge into 4.6.alpha3 whichever of
>
> Matplotlib
> http://trac.sagemath.org/sage_trac/ticket/9221
>
> NumPy and SciPy
> http://trac.sagemath.org/sage_trac/ticket/9808
If this ticket depends on a positive review from me on linux-ppc I will at
best be just on schedule. I won't have access to hardware before the 6th
doing a build a test for the 7th will be very tight. My saving grace is that
my time zone is GMT+12.
Francois
John Cremona
The following tests failed:
sage -t -long devel/sage/sage/tensor/differential_forms.py # 1 doctests failed
sage -t -long
devel/sage/sage/rings/polynomial/polynomial_element.pyx # 1 doctests
failed
which are known (#10041, #10042). The patch at #10041 works for me.
John
> --
> You received this message because you are subscribed to the Google Groups "sage-release" group.
> To post to this group, send email to sage-r...@googlegroups.com.
> To unsubscribe from this group, send email to sage-release...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/sage-release?hl=en.
>
>
kcrisman
and the toric divisor one, and a known Maxima timeout due to tab-
completion. I also got the following non-repeating failure:
File "/Users/student/Desktop/sage-4.6.alpha2/devel/sage/sage/graphs/
graph.py", line 1346:
sage: if not g.is_forest():
cycle = g.is_even_hole_free(certificate = True)
if cycle.order() % Integer(2) == Integer(1):
print "Error !"
if not cycle.is_isomorphic(
graphs.CycleGraph(cycle.order())):
print "Error !"
Exception raised:
Traceback (most recent call last):
File "/Users/student/Desktop/sage-4.6.alpha2/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/Users/student/Desktop/sage-4.6.alpha2/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/Users/student/Desktop/sage-4.6.alpha2/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_6[8]>", line 1, in <module>
if not g.is_forest():###line 1346:
sage: if not g.is_forest():
File "/Users/student/Desktop/sage-4.6.alpha2/local/lib/python/
site-packages/sage/graphs/generic_graph.py", line 1823, in is_forest
for g in self.connected_components_subgraphs():
File "/Users/student/Desktop/sage-4.6.alpha2/local/lib/python/
site-packages/sage/graphs/generic_graph.py", line 3136, in
connected_components_subgraphs
list.append(self.subgraph(c, inplace=False))
File "/Users/student/Desktop/sage-4.6.alpha2/local/lib/python/
site-packages/sage/graphs/generic_graph.py", line 8170, in subgraph
edge_property=edge_property)
File "/Users/student/Desktop/sage-4.6.alpha2/local/lib/python/
site-packages/sage/graphs/generic_graph.py", line 8279, in
_subgraph_by_adding
G.add_vertices(vertices)
File "/Users/student/Desktop/sage-4.6.alpha2/local/lib/python/
site-packages/sage/graphs/bipartite_graph.py", line 534, in
add_vertices
raise RuntimeError("Partition must be specified (e.g.
left=True).")
RuntimeError: Partition must be specified (e.g. left=True).
Mitesh Patel
I've added a comment about this at
http://trac.sagemath.org/sage_trac/ticket/9925
which added the doctest above.
Dan Drake
> Hi,
>
> We've released Sage 4.6.alpha2.
Built and passed "ptestlong" tests on an Ubuntu Maverick 64-bit virtual
machine with 1 GB RAM. One tiny weirdness is that when I just did "make
ptestlong", at first I got a doctest failure related to the
documentation not being built -- so I did "make doc-html" and then the
failing doctest passed.
Also built and passed the same tests on a Ubuntu Lucid machine
(sagenb.kaist.ac.kr). 64-bit, 8 GB RAM.
Dan
--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------
Nathann Cohen
http://trac.sagemath.org/sage_trac/attachment/ticket/9422/trac_9422.patch
It is a way to rewrite is_forest without the computation of subgraphs,
and also improves the speed of is_forest. It would fix the doctest, as
it fails because of a call from is_forest to
conncted_components_subgraphs, but I have yet to find the "real
reason" out :-)
Nathann
Nathann Cohen
find in the code of the subgraph method :
if inplace or len(vertices)>0.05*self.order() or algorithm=="delete":
return self._subgraph_by_deleting(vertices=vertices, edges=edges,
inplace=inplace,
edge_property=edge_property)
else:
return self._subgraph_by_adding(vertices=vertices, edges=edges,
edge_property=edge_property)
And of course adding edges in a BipartiteGraph the way it is
implemented is a bad idea. When the best one can do with a class is
cast it to another one as soon as possible so as not to have any
problems later, there is something really wrong going on. I'l writing
a patch for that, and replacing the broken methods I find in
BipartiteGraph by exceptions.
Docstring :
http://trac.sagemath.org/sage_trac/attachment/ticket/9422/trac_9422.patch
Methods from BipartiteGraph that should not be taken from Graph or
generic_graph :
http://trac.sagemath.org/sage_trac/ticket/10068
The graph theory section could use a few reviews, by the way ^^;
Nathann