sage-5.0.beta5 released
Jeroen Demeyer
We're releasing Sage 5.0.beta5.
Source archive:
http://boxen.math.washington.edu/home/release/sage-5.0.beta5/sage-5.0.beta5.tar
Upgrade path:
http://boxen.math.washington.edu/home/release/sage-5.0.beta5/sage-5.0.beta5/
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 198 tickets in this release. For details, see
http://boxen.math.washington.edu/home/release/sage-5.0.beta5/tickets.html
Closed tickets:
#9162: cygwin/ARM:pynac.pyx use double precision special functions
instead of long double (REVISITED) [Reviewed by Burcin Erocal]
#10111: random_prime is badly documented. [Reviewed by Francis Clarke]
#11656: Imaginary part of symbolic variable disappears in
simplify_full() [Reviewed by Burcin Erocal]
#11842: substitute_function doesn't work as expected in many cases
[Reviewed by Burcin Erocal]
Merged in sage-5.0.beta5:
#4949: John Palmieri: Optionally build spkgs in $SAGE_BUILD_DIR
[Reviewed by Mariah Lenox, Leif Leonhardy, Maarten Derickx, Jeroen Demeyer]
#8983: Benjamin Jones: erf(0) should return 0 [Reviewed by Burcin
Erocal, Douglas McNeil]
#9362: Lukáš Lánský: Invalidate None as a vertex label. [Reviewed by
Paul Zimmermann]
#9714: Lukáš Lánský, Robert Miller: Graph(...,
format='incidence_matrix') doesn't work with graphs that have loops, but
G.incidence_matrix() does. So? [Reviewed by Nathann Cohen]
#10347: Christian Stump: Implementation of is_(skew_)symmetrizable for
matrices [Reviewed by Hugh Thomas]
#10670: Frédéric Chapoton, Florent Hivert: Mobius matrices of posets are
integer matrices [Reviewed by Florent Hivert, Nicolas M. Thiéry]
#11382: Florent Hivert: Speedup subposet and _vertex_to_element
[Reviewed by Nicolas M. Thiéry]
#11384: Volker Braun: Construct the complex of a fan [Reviewed by Andrey
Novoseltsev]
#11603: Rob Beezer: Deprecate eigenspaces for matrices over RDF/CDF
[Reviewed by Punarbasu Purkayastha]
#12025: William Stein: get doctest coverage of monoids/monoid.py to 100%
[Reviewed by Michael Orlitzky, Thierry Monteil, Karl-Dieter Crisman]
#12223: Jeroen Demeyer: the 'sage.rings.complex_mpc' optional extension
is broken in sage-4.8.alpha3 and over [Reviewed by François Bissey]
#12306: Nathann Cohen: Static sparse graphs for fast low-level
computations [Reviewed by David Coudert]
#12356: John Cremona, William Stein: many missing class number 2 orders
in CM j-invariant function over quadratic fields [Reviewed by John
Cremona, William Stein]
#12368: Jeroen Demeyer: Make "ratpoints" check whether
-fnested-functions is supported by the compiler [Reviewed by R. Andrew
Ohana]
#12423: Jeroen Demeyer: Numpy wrongly assumes that any non-i386 OS X
system is PowerPC [Reviewed by William Stein]
#12475: Sébastien Labbé: Define WordMorphism.__ne__ [Reviewed by Timo
Jolivet]
#12477: Nathann Cohen: Graph.relabel modifies the dictionary given as an
input [Reviewed by Nicolas M. Thiéry]
#12484: Nicolas M. Thiéry: CombinatorialFreeModule's: customizing the
order of terms in the output of elements [Reviewed by Florent Hivert]
#12488: Jeroen Demeyer: Make sage-make_devel_packages not fail if there
is nothing to commit [Reviewed by Volker Braun]
#12489: Nicolas M. Thiéry: Fix equality of combinatorial free module on
non totally ordered basis [Reviewed by Florent Hivert]
#12501: Jeroen Demeyer: Fix packages wanting to run autoconf [Reviewed
by Volker Braun]
#12506: William Stein: fix typo in debug() docstring [Reviewed by Aran
Carmon]
#12507: Benjamin Jones: Mark random symbolic expression doctests with
#random [Reviewed by Burcin Erocal]
#12511: Robert Bradshaw: Unable to take numeric powers of I [Reviewed by
Burcin Erocal]
#12517: William Stein: EllipticCurve(E.a_invariants()) doesn't work
[Reviewed by Robert Bradshaw]
#12522: Jeroen Demeyer: Check assignment of SAGE_ROOT in $SAGE_ROOT/sage
[Reviewed by Volker Braun]
#12530: Nicolas M. Thiéry: Improve the sage-combinat script to support
guards for developpers versions of Sage [Reviewed by Florent Hivert]
Nathann Cohen
Nathann
Justin C. Walker
On Feb 22, 2012, at 08:31 , Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta5.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.beta5/sage-5.0.beta5.tar
Built seemingly w/o problems on Mac OS X, 10.7.1 (Core i7) with "-j1". There were a few "syntax error" messages in the sympy and mpmath logs, but I can't tell if this is a problem. Testing, however, was not so good. I put the ptestlong.log file on
sage.math.washington.edu:~justin/logs/5.0-b5-ptestlong.log
for inspection. I'll put the build log there tomorrow, when I have a better internet connection.
I'll try the "-gcc" version next.
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.
-----------
Marshall Hampton
generated by matplotlib aren't displaying correctly if they are
filled. E.g.:
show(polygon([[0,0],[10,0],[10,1290],[0,1290]]))
does not do what it should.
-Marshall
On Feb 22, 10:31 am, Jeroen Demeyer <jdeme...@cage.ugent.be> wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta5.
>
> Source archive:
>
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.beta5/sage-5.0...
> 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 198 tickets in this release. For details, see
>
Jason Grout
> I'm having some graphics problems with all the 5.0 betas, polygons
> generated by matplotlib aren't displaying correctly if they are
> filled. E.g.:
>
> show(polygon([[0,0],[10,0],[10,1290],[0,1290]]))
>
> does not do what it should.
>
What happens, and what should it do?
Jason
Jason Grout
Wait, let me guess: the aspect ratio should be 'automatic', but instead
the aspect ratio is 1.
I think you are the second person to complain about this. Should we
change the aspect ratio to default to 'automatic'? I'm fine with that.
Jason
Marshall Hampton
had an interact I designed for some people that involved some rather
extreme values - the correct aspect ratio was about 0.0001, so it
looked totally broken with an aspect ratio of 1.
-Marshall
Jason Grout
> Yes, I guess that was it. It confused me a little at first because I
> had an interact I designed for some people that involved some rather
> extreme values - the correct aspect ratio was about 0.0001, so it
> looked totally broken with an aspect ratio of 1.
Should we change the default for polygon to 'automatic', then?
Jason
Marshall Hampton
don't have really strong feelings - this bit me in an extreme case,
usually I think people would be able to figure it out.
-Marshall
Andrey Novoseltsev
automatic can always be the default as the safest one, but it should
try to be 1 if it is reasonable (meaning that the ratio of sides does
not exceed some small value like 5). Many potential users of plots are
students and when they plot a circle, perpendicular lines, or a right
triangle, it may be quite confusing to have a non-1 aspect ratio...
Andrey
Marshall Hampton
your suggestion is good, although the optimal switching to automatic
ratio might be closer to 2 than 5.
-Marshall
kcrisman
On Feb 23, 11:51 pm, Andrey Novoseltsev <novos...@gmail.com> wrote:
> It seems that this automatic/1 issue appears again and again. Perhaps
> automatic can always be the default as the safest one, but it should
> try to be 1 if it is reasonable (meaning that the ratio of sides does
> not exceed some small value like 5). Many potential users of plots are
> students and when they plot a circle, perpendicular lines, or a right
> triangle, it may be quite confusing to have a non-1 aspect ratio...
>
ratio for polygons in the first place - so that *regular* polygons
would look regular. Anyone who wants a non-regular polygon is playing
with being destroyed by the government anyway... Oops, that's
Flatland, sorry.
kcrisman
in case...
When plotting (reviewing #9744), I get
sage: x,y = var('x,y')
sage: f(x,y) = x^2 + y^2 - 2
sage: implicit_plot(f, (-3, 3), (-3,
3),fill=True).show(aspect_ratio=1)
dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib
Referenced from: /usr/X11/bin/fc-list
Reason: Incompatible library version: fc-list requires version
14.0.0 or later, but libfreetype.6.dylib provides version 10.0.0
dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib
Referenced from: /usr/X11/bin/fc-list
Reason: Incompatible library version: fc-list requires version
14.0.0 or later, but libfreetype.6.dylib provides version 10.0.0
So somehow we are picking up the wrong library of libfreetype. I am
pretty sure that this has shown up in the past with respect to
"dyld" (maybe even I reported it) but anyway just putting it here for
reference.
- kcrisman
kcrisman
x,y = var('x,y')
? I'm reviewing #9744 and I'm seeing stuff that looks to be directly
contravening #2100, where we said that implicit and contour plots
*would* have default aspect ratio 1 (because that just tends to be the
most common use case).
In fact, this seems to be back in Sage 4.8... but it's okay in Sage
4.7.2. Could this be yet another side effect of #11963? I don't see
anywhere that contour plot aspect ratio is set other than where it
creates an empty Graphics() object...
Folks, anything that impacts plotting *has* to be looked at in the
live documentation - I've learned this the hard way.
- kcrisman
kcrisman
On Feb 24, 3:04 pm, kcrisman <kcris...@gmail.com> wrote:
> Jason, what's going on with
>
> x,y = var('x,y')
> contour_plot(x^2+y^2-2,(x,-1,1), (y,-1,1))
not fixed by #12222, because that only focused on shape primitives.
I've opened http://trac.sagemath.org/sage_trac/ticket/12581 as a
critical ticket, and am this close to making it a blocker.
- kcrisman
kcrisman
On Feb 24, 4:19 pm, kcrisman <kcris...@gmail.com> wrote:
> On Feb 24, 3:04 pm, kcrisman <kcris...@gmail.com> wrote:
>
> > Jason, what's going on with
>
> > x,y = var('x,y')
> > contour_plot(x^2+y^2-2,(x,-1,1), (y,-1,1))
>
>
doesn't break the summation aspect ratio handling, and comment on
whether it should be 1 or 1.0.
John Cremona
before. Build from scratch on 32-bit ubuntu, gcc 4.4.3. Only
numerical fuzz but still...
john@john-laptop%./sage -t --long -force_lib
"devel/sage/sage/stats/hmm/chmm.pyx"
sage -t --long -force_lib "devel/sage/sage/stats/hmm/chmm.pyx"
**********************************************************************
File "/home/john/sage-5.0.beta5/devel/sage/sage/stats/hmm/chmm.pyx", line 865:
sage: m.baum_welch([-2,-1,.1,0.1])
Expected:
(4.534646052182663, 7)
Got:
(4.534646052182662, 7)
**********************************************************************
File "/home/john/sage-5.0.beta5/devel/sage/sage/stats/hmm/chmm.pyx", line 867:
sage: m.log_likelihood([-2,-1,.1,0.1])
Expected:
4.534646052182663
Got:
4.534646052182662
**********************************************************************
1 items had failures:
2 of 21 in __main__.example_19
***Test Failed*** 2 failures.
For whitespace errors, see the file /home/john/.sage//tmp/chmm_19036.py
[2.7 s]
John
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>
William Stein
> Here's a test failure with beta5 which I don't think I have seen
> before. Build from scratch on 32-bit ubuntu, gcc 4.4.3. Only
> numerical fuzz but still...
It's an algorithm that involves tons of basic arithmetic with machine
doubles, which must be fast, but with no guarantee on any precision
(it's applied statistics after all).
I can post a patch to include some ...'s.
William
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
William Stein
> before. Build from scratch on 32-bit ubuntu, gcc 4.4.3. Only
> numerical fuzz but still...
Can you try (to review) this?
http://trac.sagemath.org/sage_trac/ticket/12594
--
John Cremona
> On Sun, Feb 26, 2012 at 7:29 AM, John Cremona <john.c...@gmail.com> wrote:
>> Here's a test failure with beta5 which I don't think I have seen
>> before. Build from scratch on 32-bit ubuntu, gcc 4.4.3. Only
>> numerical fuzz but still...
>
> Can you try (to review) this?
>
> http://trac.sagemath.org/sage_trac/ticket/12594
Done!
John
Kelvin Li
> We're releasing Sage 5.0.beta5.
4.6.2 in QEMU-KVM guest, running on Debian Wheezy host.
-- Kelvin