Sage 8.2.rc1 released

[Volker Braun]

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

fb9f38a4ae (tag: 8.2.rc1) Updated SageMath version to 8.2.rc1

97a9c3fe1a Trac #25025: Fix jmol package in Cygwin

1fe5f21b49 Trac #25021: Update the jmol SPKG with DESTDIR support

c67129c035 Trac #25055: Upgrade openssl to 1.1.0h

f756e2ebe9 Trac #21828: Use MemoryAllocator in generic graphs; fixes crash

e5c848a64c (tag: 8.2.rc0) Updated SageMath version to 8.2.rc0

[Justin C. Walker]

> On Mar 31, 2018, at 15:39 , Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

Built from a fresh clone/update of the develop branch on macOS 10.11.6 (Quad-core Core i7) w/o problems, and all tests (‘testing’) passed!

Justin

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Director
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--------
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Well, except the weasel."
- Homer J Simpson
--------

[Ralf Stephan]

Builds fine with clang-5 on OpenSuSE but not with the new clang-6.0.0 due to gfan. I opened

https://trac.sagemath.org/ticket/25072

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[Ralf Stephan]

Testing on OpenSuSE fails because of https://trac.sagemath.org/ticket/24920

So, still no working patchbots with that system.

[Emmanuel Charpentier]

On Debian testing running on Core i7 + 16 GB RAM, builds and passes ptestlong without errors whatsoever.

However, I get 648 (!) logs of errors related to Java in $SAGE_ROOT (see enclosed tarball). This might be specific to my machine. ATM, I haven't the slightest clue...

HTH,

--

Emmanuel Charpentier

[Emmanuel Charpentier]

Important : I forgot to specifu that's for Sage 8.2rc1 + Trac#24585 (positively reviewed) + Trac#24969 (needs review ; my tperusal of ptestlong before pushing it didn't show anything abnormal).

--

Emmanuel Charpentier

[François Bissey]

Would https://trac.sagemath.org/ticket/25026 look helpful? sun.audio missing?

[Emmanuel Charpentier]

Nope.

make ptestlong now gives me two failures :

----------------------------------------------------------------------

sage -t --long src/sage/parallel/map_reduce.py  # 3 doctests failed

sage -t --long src/sage/coding/linear_code.py  # Timed out

----------------------------------------------------------------------

which turn out to be transient (i. e. tests pass when ran standalone).

And I still get 648 Java-related errors, which seem to be pretty similar tl those already reported...

Do you care for formal reporting in your original ticket ?

--

Emmanuel Charpentier

[Emmanuel Charpentier]

And, BTW, one cannot plot using jmol from the terminal :

charpent@asus16-ec:~$ sage

SageMath version 8.2.rc1, Release Date: 2018-03-31

sage: plot3d(lambda x,y:x^2+y^2, (-2,2), (2,2))

---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

<ipython-input-1-e082d582023f> in <module>()

----> 1 plot3d(lambda x,y:x**Integer(2)+y**Integer(2), (-Integer(2),Integer(2)), (Integer(2),Integer(2)))

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/plot/plot3d/plot3d.pyc in plot3d(f, urange, vrange, adaptive, transformation, **kwds)

   1073         u=fast_float_arg(0)

   1074         v=fast_float_arg(1)

-> 1075         P=parametric_plot3d.parametric_plot3d((u,v,f), urange, vrange, **kwds)

   1076     P.frame_aspect_ratio([1.0,1.0,0.5])

   1077     return P

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/plot/plot3d/parametric_plot3d.pyc in parametric_plot3d(f, urange, vrange, plot_points, boundary_style, **kwds)

   1007         if plot_points == "automatic":

   1008             plot_points = [40, 40]

-> 1009         G = _parametric_plot3d_surface(f, urange, vrange, plot_points=plot_points, boundary_style=boundary_style, **kwds)

   1010     G._set_extra_kwds(kwds)

   1011     return G

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/plot/plot3d/parametric_plot3d.pyc in _parametric_plot3d_surface(f, urange, vrange, plot_points, boundary_style, **kwds)

   1120     """

   1121     from sage.plot.misc import setup_for_eval_on_grid

-> 1122     g, ranges = setup_for_eval_on_grid(f, [urange, vrange], plot_points)

   1123     urange = srange(*ranges[0], include_endpoint=True)

   1124     vrange = srange(*ranges[1], include_endpoint=True)

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/plot/misc.pyc in setup_for_eval_on_grid(funcs, ranges, plot_points, return_vars)

    134     range_steps = [abs(range[1] - range[0])/(p-1) for range, p in zip(ranges, plot_points)]

    135     if min(range_steps) == float(0):

--> 136         raise ValueError("plot start point and end point must be different")

    137 

    138     options={}

ValueError: plot start point and end point must be different

sage: plot3d(lambda x,y:x^2+y^2, (-2,2), (-2,2))

---------------------------------------------------------------------------

RuntimeError                              Traceback (most recent call last)

<ipython-input-2-b8b9618a6cbb> in <module>()

----> 1 plot3d(lambda x,y:x**Integer(2)+y**Integer(2), (-Integer(2),Integer(2)), (-Integer(2),Integer(2)))

/usr/local/sage-8/local/lib/python2.7/site-packages/IPython/core/displayhook.pyc in __call__(self, result)

    244             self.start_displayhook()

    245             self.write_output_prompt()

--> 246             format_dict, md_dict = self.compute_format_data(result)

    247             self.update_user_ns(result)

    248             self.fill_exec_result(result)

/usr/local/sage-8/local/lib/python2.7/site-packages/IPython/core/displayhook.pyc in compute_format_data(self, result)

    148 

    149         """

--> 150         return self.shell.display_formatter.format(result)

    151 

    152     # This can be set to True by the write_output_prompt method in a subclass

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/repl/display/formatter.pyc in format(self, obj, include, exclude)

    200         """

    201         # First, use Sage rich output if there is any

--> 202         sage_format, sage_metadata = self.dm.displayhook(obj)

    203         assert PLAIN_TEXT in sage_format, 'plain text is always present'

    204         if not set(sage_format.keys()).issubset(self.default_mime()):

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.pyc in displayhook(self, obj)

    806         self._backend.set_underscore_variable(obj)

    807         plain_text, rich_output = self._rich_output_formatter(obj, dict())

--> 808         return self._backend.displayhook(plain_text, rich_output)

    809 

    810     def display_immediately(self, obj, **rich_repr_kwds):

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/repl/rich_output/backend_ipython.pyc in displayhook(self, plain_text, rich_output)

    264             return ({u'text/plain': msg}, {})

    265         elif isinstance(rich_output, OutputSceneJmol):

--> 266             msg = self.launch_jmol(rich_output, plain_text.text.get_unicode())

    267             return ({u'text/plain': msg}, {})

    268         elif isinstance(rich_output, OutputSceneWavefront):

/usr/local/sage-8/local/lib/python2.7/site-packages/sage/repl/rich_output/backend_ipython.pyc in launch_jmol(self, output_jmol, plain_text)

    367         jdata = JmolData()

    368         if not jdata.is_jvm_available() and not DOCTEST_MODE:

--> 369             raise RuntimeError('jmol cannot run, no suitable java version found')

    370         launch_script = output_jmol.launch_script_filename()

    371         from sage.env import SAGE_LOCAL

RuntimeError: jmol cannot run, no suitable java version found

sage: 

Doubleplus ungood...

--

Emmanuel Charpentier

[Emmanuel Charpentier]

It seems more complicated (and hopefully more local) than that : see my comments in François'  ticket.

--

Emmanuel Charpentier

[Emmanuel Charpentier]

A couple more data points, currently observed on Debian testing, using Debian's packaging(s) of Java (one can switch from one to the other via update-java-alternatives)  :

• with Java 8 (current in stable) :
  
• both the current jmol engine and the newer proposed by Trac#25026 work as expected ;
• running ptestlong suceeds with no anomalies
• with Java 9 (current in testing) :
  
• both the current and newer jmol engine fail ;
• ptestlong may result in tran,sient failures and leaves a huge bunch of Java VM-related failure logs in $SAGE_ROOT.

I have no clues about other platforms or distributions.

HTH,

--

Emmanuel Charpentier

[Samuel Lelièvre]

2018-04-01 21:39 GMT+02:00 Emmanuel Charpentier <emanuel.c...@gmail.com>:
>
> A couple more data points, currently observed on Debian testing, using Debian's packaging(s) of Java (one can switch from one to the other via update-java-alternatives)  :
>
> with Java 8 (current in stable) :
>
> both the current jmol engine and the newer proposed by Trac#25026 work as expected ;
> running ptestlong suceeds with no anomalies
>
> with Java 9 (current in testing) :
>
> both the current and newer jmol engine fail ;
> ptestlong may result in tran,sient failures and leaves a huge bunch of Java VM-related failure logs in $SAGE_ROOT.
>
> I have no clues about other platforms or distributions.

Under macOS 10.10.5, whether in SageMath 8.2.beta8, SageMath 8.2.rc0, SageMath 8.2.rc1,

    plot3d(lambda x, y: x^2 + y^2, (-2, 2), (-2, 2))

works fine, launching Jmol as expected.

[Justin C. Walker]

> On Apr 1, 2018, at 09:40 , Emmanuel Charpentier <emanuel.c...@gmail.com> wrote:
>
> And, BTW, one cannot plot using jmol from the terminal :
> charpent@asus16-ec:~$ sage
> SageMath version 8.2.rc1, Release Date: 2018-03-31
> sage: plot3d(lambda x,y:x^2+y^2, (-2,2), (2,2))
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)

[snip]...

> ValueError: plot start point and end point must be different
> sage: plot3d(lambda x,y:x^2+y^2, (-2,2), (-2,2))
> ---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call last)
> <ipython-input-2-b8b9618a6cbb> in <module>()

[snip]...

> RuntimeError: jmol cannot run, no suitable java version found
> sage:

Another datapoint:
On macOS 10.11.6, sage-8.2.rc1, I got the same results (same ValueError for the first, same RuntimeError for the second).

This is my java setup:

java 9.0.1
Java(TM) SE Runtime Environment (build 9.0.1+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.1+11, mixed mode)

Justin

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[Eric Gourgoulhon]

Since we have entered the 8.2.rc cycle, may I ask about the status of the (blocker) ticket #24484 (broken export of Jupyter notebooks  to any format) ?
Without it, many users might complain (it was working fine in Sage 8.1).

Eric.

[Volker Braun]

I don't have time to work on this atm; if nobody fixes it it won't get fixed...

[Samuel Lelièvre]

I would also like to advocate getting the following tickets in Sage 8.2:

- #21022: version information in sage.__version__

  https://trac.sagemath.org/ticket/21022

  (long awaited by downstream projects, such as flipper)

- #25050: Allow braid computation for more links

  https://trac.sagemath.org/ticket/25050

  (fixes a cornercase computation of Seifert circles of knots/ links)

Samuel

[Jeroen Demeyer]

On 2018-04-02 18:18, Samuel Lelièvre wrote:
> I would also like to advocate getting the following tickets in Sage 8.2:

I nominate https://trac.sagemath.org/ticket/25047

It's really trivial but convenient for Python 3 development.

[Samuel Lelièvre]

+1

By the way, is there a similar ticket to provide

    sage --jupyter

in such a way that you can

    sage --jupyter kernelspec list

or

    sage --jupyter kernelspec install /path/to/some_jupyter_kernel

etc?

Samuel

 

[Emmanuel Charpentier]

Since we are nominating last-minute additions to 8.2, I have a plea for Trac#24585 (positively reviewed : eases the installation of the R jupyter kernel, which is a nice interface for stats-oriented work) and Trac#24969 (upgrade to latest R : innocuous, needs review, my perusal of ptestlong before pushing it didn't show anything abnormal on Debian).

--

Emmanuel Charpentier

[Simon King]

I tried to send that message before (using slrn), but since it didn't
show up within 30 minutes, I am trying again.

Giac fails to build.

Setting:
$ uname -a
Linux king-C70-B 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/issue
Ubuntu 16.04.4 LTS \n \l

Before that, it used to work in some beta branch (don't recall exactly
which one). Then I installed tkinter, did sage -f python2, and "make
start" (which was rebuilding large portions of Sage, of course). It
still worked. However, I could imagine that it is related to installing
tkinter, as Jeroen told me that people have reported it before, but it
couldn't be reproduced.

The giac log is attached at #25076 (although that ticket's topic is not
related with giac).

Best regards,
Simon

[Simon King]

On 2018-03-31, Volker Braun <vbrau...@gmail.com> wrote:

Giac fails to build.

Machine:

$ uname -a
Linux king-C70-B 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/issue
Ubuntu 16.04.4 LTS

The log is attached at #25076.

Cheers,
Simon

[François Bissey]

Broken libpng, we have seen this before in this cycle.
Search on sage-devel.
./sage -f libpng
should fix this.

François

[Eric Gourgoulhon]

On Ubuntu 16.04 x86_64 Xeon E5-2623 + 16 GB RAM, from a fresh git clone, parallel (-j16) build OK and make ptestlong reported some transient errors due to "Jmol failed to create file" in 4 files + a new transient (i.e. passed when run standalone) error:

sage -t --long --warn-long 46.2 src/sage/sets/totally_ordered_finite_set.py
**********************************************************************
File "src/sage/sets/totally_ordered_finite_set.py", line 218, in sage.sets.totally_ordered_finite_set.TotallyOrderedFiniteSet
Failed example:
    for e in [1,'a',(0, 0)]:
        f = A(e)
        l = (e == f,
             cmp(e,f) == cmp(type(e),type(f)),
             cmp(f,e) == cmp(type(f),type(e)))
        print(l)
Expected:
    (False, True, True)
    (False, True, True)
    (False, True, True)
Got:
    (False, False, False)
    (False, True, True)
    (False, True, True)
**********************************************************************
1 item had failures:
   1 of  29 in sage.sets.totally_ordered_finite_set.TotallyOrderedFiniteSet

All these errors disappear when the doctests are run standalone.

Eric.

Le dimanche 1 avril 2018 00:39:14 UTC+2, Volker Braun a écrit :

[Erik Bray]

I'll see if I can work on finishing it, and hopefully we can get that
in the next "rc". If it is in fact a blocker it should be treated as
such.

The raft of "last minute" issue requests for 8.2 appearing in this
thread indicates to me once again the problems with Sage's release
scheduling, or lack thereof. Without more communication / planning of
Sage releases no one really "knows" for sure when a Sage release is
imminent until some commit happens to get tagged "rc". *Then* it
becomes a panic of "oh, those issues I haven't been working on
(because I was busy with other things, etc.) are suddenly higher
priority", because otherwise they won't be in a final release until
after the next 3+ month development cycle.

I think this can be mitigated significantly simply by having a rough,
but published release cycle (say, one every 3 months), with cutoff
dates for non-critical issues, and reminders (to this list) of those
cutoff dates so that any people can have a chance to advocate for
and/or complete work that they hope to see in the release *before* we
start tagging things as "release candidates".

Best,
E

[Eric Gourgoulhon]

Le mardi 3 avril 2018 12:17:20 UTC+2, Erik Bray a écrit :

On Mon, Apr 2, 2018 at 11:09 AM, Eric Gourgoulhon
<egourg...@gmail.com> wrote:
> Since we have entered the 8.2.rc cycle, may I ask about the status of the
> (blocker) ticket #24484 (broken export of Jupyter notebooks  to any format)
> ?
> Without it, many users might complain (it was working fine in Sage 8.1).

I'll see if I can work on finishing it, and hopefully we can get that
in the next "rc".  

OK thanks! Sorry I cannot do it myself. Needless to say, I volunteer to review it.
 

I think this can be mitigated significantly simply by having a rough,
but published release cycle (say, one every 3 months), with cutoff
dates for non-critical issues, and reminders (to this list) of those
cutoff dates so that any people can have a chance to advocate for
and/or complete work that they hope to see in the release *before* we
start tagging things as "release candidates".

+1

Best wishes,

Eric.

[Samuel Lelièvre]

+1 too

Volker, another ticket that would be very nice to have in 8.2 is

- #25082: Fix symbolic power of matrix

  https://trac.sagemath.org/ticket/25082

It just got positive review (thanks Frédéric!).

[Erik Bray]

I am consistently getting this failure in
src/sage/sets/totally_ordered_finite_set.py when running the tests on
Cygwin, even when I just run

./sage -t src/sage/sets/totally_ordered_finite_set.py

directly. I don't recall ever seeing such a failure previously.

Still getting the failure from https://trac.sagemath.org/ticket/24986
as well but that's to be expected since it isn't fixed yet :)

> Le dimanche 1 avril 2018 00:39:14 UTC+2, Volker Braun a écrit :
>>
>> As always, you can get the latest beta version from the "develop" git
>> branch. Alternatively, the self-contained source tarball is at
>> http://www.sagemath.org/download-latest.html
>>
>> fb9f38a4ae (tag: 8.2.rc1) Updated SageMath version to 8.2.rc1
>> 97a9c3fe1a Trac #25025: Fix jmol package in Cygwin
>> 1fe5f21b49 Trac #25021: Update the jmol SPKG with DESTDIR support
>> c67129c035 Trac #25055: Upgrade openssl to 1.1.0h
>> f756e2ebe9 Trac #21828: Use MemoryAllocator in generic graphs; fixes crash
>> e5c848a64c (tag: 8.2.rc0) Updated SageMath version to 8.2.rc0
>>

[Erik Bray]

Oh, I just realized this is fixed by https://trac.sagemath.org/ticket/25077

[Emmanuel Charpentier]

FWIW, Trac#24969 has been given positive review (thjanks, Dima !).

--

Emmanuel Charpentier