Sage 8.1.beta8 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

a2e82e15a2 (HEAD -> develop, tag: 8.1.beta8, trac/develop) Updated SageMath version to 8.1.beta8

7dc7c74d76 Trac #23872: Singular expansion for implicitly defined function

71c53d6efc Trac #23844: GapElement.__contains__ (from libgap) should use the infix `in` from gap

03398aa3f4 Trac #23818: py3: hash for complex interval fields

756c0ec447 Trac #23671: hypergeometric motives

e7b4f77db7 Trac #22922: Faster implementation of LLT polynomials

8d71436074 Trac #20762: Several additional methods for SimplicialComplex

37b5b2cfd2 Trac #18236: support xz compressed tarballs

202fa8dd8c Trac #24020: Cygwin: misc test failures

a56746c985 Trac #23922: Upgrade eclib to compile with xcode 9

1472db0a6b Trac #23985: rst2ipynb causes doctest failures if pandoc is not installed

067b87c610 Trac #23983: dot2tex breaks docbuild

11c3bcca4e Trac #23979: Ignore failure in setrlimit on Cygwin

e96397a071 Trac #23973: doc build hangs on Cygwin

c249d236cb Trac #22461: Implement cython() using cythonize()

50670a7181 Trac #7516: bug in pickling quotient module over pid

fce8fd00d4 Trac #23997: installed_packages(False) gives wrong version for Python packages with patches

cbbbbc5307 Trac #23976: giacpy_sage causes doctest failures due to threading

a22a806a2d Trac #23975: sage-location: do not remove .pyc files

2c6ac6c343 Trac #23970: Simpler caching in ell_rational_field

cda826dfaf Trac #23966: Conversion from ZpFM to its fraction field incorrect

4bce0bfd2d Trac #23965: Coercion to fraction field is injective

c3b1b7780a Trac #23862: speed_up_left_and_right_key

a1b45bb7c4 Trac #23839: Fix reference manual index for partn_ref

1b74aa24b0 Trac #23634: A base class for integral quadratic forms seen as modules with a bilinear form.

9659a399eb Trac #18395: (moderate) Speedup in layout_spring

c4aef0e21f Trac #23962: rank() of elliptic curves should always consult Cremona database

78a2ebd287 Trac #23957: gmpy2 causes doctest failures

7d5784f2a9 Trac #23947: Reciprocal transformation and trace polynomial

e5cb49e05c Trac #23800: Add O method for Laurent series rings

0e98d937dc Trac #23963: py3: richcmp for function field ideals

380c526205 Trac #23951: fix rotate and conjugate in growth diagrams

639646985c Trac #23905: Avoid _element_constructor in Homset

a5eeff69d2 Trac #23949: py3 : some work on __cmp__ and richcmp

b580a4c279 Trac #23929: Upgrade to cypari2 version 1.1.3

894facd65a Trac #23912: parent() is slow for non-Elements

bda5b4d10b Trac #23925: Bulk fix of signal handling in symbolics

68cb85abe9 Trac #23713: Support SAGE_NUM_THREADS everywhere for parallellism

3c684b65ed Trac #23944: Q/Z

0d96592852 Trac #23932: differences in construction of PolynomialRing and LaurentPolynomialRing

35ffe56528 Trac #23915: include the inner_product_matrix in module comparison

da6237b58e Trac #23883: InheritComparisonClasscallMetaclass.__new__() does not work

2e522cf00a Trac #23865: disable a very long doctest in omega.py

b198ad5d04 Trac #23857: Implement conversion C++ <-> str

1a06cd5dd1 Trac #23815: Upgrade to Python 2.7.14

26a96021b2 Trac #23734: Implement iterator for generic permutations in Cython

5455b1ce78 Trac #23642: Factorization over some quotient rings incorrect

82260ab4ad Trac #23565: update arb to version 2.11.1

c3f620e7b7 Trac #23544: Upgrade PARI/GP to git master version

75daefe5ed Trac #23510: Fraction field of fixed modulus p-adic rings should have floating point type

f8b263fb53 Trac #23376: Equality testing of genera of quadratic forms over ZZ changes the genus and produces false results

b0c0f6749a Trac #22886: fix pxd header files

54ba5948be Trac #23429: Multivector fields and the Schouten-Nijenhuis bracket

c24da43be9 Trac #23131: Add computation of longest commons extensions in a word

c1c3197fc3 Trac #22720: AdditiveAbelianGroup([]).annihilator() fails.

294c389e84 Trac #18386: Doctests for: fix polylog evalf

cc613b1e98 (tag: 8.1.beta7) Updated SageMath version to 8.1.beta7

[Ralf Stephan]

Error downloading giacpy_sage-0.6.6.tar.gz

The servers only have the previous 0.6 version.

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[Ralf Stephan]

The package can be downloaded manually at http://webusers.imj-prg.fr/~frederic.han/xcas/giacpy/sage/giacpy_sage-0.6.6.tar.gz

That's the link given in https://trac.sagemath.org/ticket/23976

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM,  8.1beta8 + #24026 + #24006  + #23990 + #23923 passes ptestlong with no error whatsoever.

HTH,

--

Emmanuel Charpentier

[Justin C. Walker]

> On Oct 16, 2017, at 23:56 , 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

On macOS 10.11.6 (Quad-core Core i7): cloned the ‘develop’ branch, and built with no problems. Testing (‘ptestlong’) showed no failures!

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.
-----------

[Maarten Derickx]

On Tue, 17 Oct 2017 at 15:32 Ralf Stephan <gtr...@gmail.com> wrote:

Error downloading giacpy_sage-0.6.6.tar.gz

The servers only have the previous 0.6 version.

Note that the patchbots arando sage4 and quasar are failing to build for
the same reason (although rst2ipynb is the package whose most recent
version is missing for two of these patchbots). Is there a good reason for
not uploading the most recent packages to the mirrors at each beta release?

 

[Eric Gourgoulhon]

On Ubuntu 16.04 x86_64 Xeon E5-2623 + 16 GB RAM, from a fresh git clone + pull develop, parallel (-j16) build OK and ptestlong failed with two doctests:

sage -t --long --warn-long 46.0 src/sage/plot/point.py  # 1 doctest failed
sage -t --long --warn-long 46.0 src/doc/pt/tutorial/tour_plotting.rst  # 1 doctest failed

Both are due to the failure of Jmol to create some file in ~/.sage/temp/ :
This might be due to some race condition since both doctests are passed when run standalone.

Best wishes,

Eric.

[Eric Gourgoulhon]

PS: I noticed that "make ptestlong" created two files in the SAGE_ROOT directory:
- replay_pid28433.log
- hs_err_pid28433.log
The first one is empty and I am attaching the second one, where it is written "There is insufficient memory for the Java Runtime Environment to continue."

On the same computer (16 GB RAM), there was no such thing with versions <= 8.1.beta7.

Eric.

[Rich...@lozestech.com]

Under openSUSE Leap 42.2, on Intel i5-6300U, 8GB RAM, Sage8.1.beta8 compiled clean; 3 doctests failed (as usual on this machine):

----------------------------------------------------------------------
sage -t --long --warn-long 81.6 src/sage/interfaces/r.py  # 3 doctests failed
----------------------------------------------------------------------
Total time for all tests: 4331.8 seconds
    cpu time: 13577.0 seconds
    cumulative wall time: 16665.9 seconds

[Erik Bray]

Tried to build the Docker image but am getting the following test
failure consistently (which did not occur in 8.1.beta7 AFAIK):

File "/opt/sage/src/sage/misc/sageinspect.py", line 207, in
sage.misc.sageinspect._extract_embedded_position
Failed example:
print(open(_extract_embedded_position(inspect.getdoc(test_funct))[1]).read())
Exception raised:
Traceback (most recent call last):
File "/opt/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
line 515, in _run
self.compile_and_execute(example, compiler, test.globs)
File "/opt/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
line 885, in compile_and_execute
exec(compiled, globs)
File "<doctest
sage.misc.sageinspect._extract_embedded_position[4]>", line 1, in
<module>
print(open(_extract_embedded_position(inspect.getdoc(test_funct))[Integer(1)]).read())
IOError: [Errno 2] No such file or directory:
'/home/sage/.sage/temp/b282fa83da28/28678/spyx/.sage/temp/b282fa83da28/28678/spyx/_home_sage__sage_temp_b282fa83da28_28678_tmp_cyv3Wb_pyx/_home_sage__sage_temp_b282fa83da28_28678_tmp_cyv3Wb_pyx/.sage/temp/b282fa83da28/28678/spyx/_home_sage__sage_temp_b282fa83da28_28678_tmp_cyv3Wb_pyx/_home_sage__sage_temp_b282fa83da28_28678_tmp_cyv3Wb_pyx_0.pyx'

Any ideas? Looks odd...

[Jeroen Demeyer]

Just to be clear: is this the *only* failure or are you seeing several
similar failures (if so: please show them all).

[Erik Bray]

On Wed, Oct 18, 2017 at 4:59 PM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> Just to be clear: is this the *only* failure or are you seeing several
> similar failures (if so: please show them all).

(Assuming you're replying to me) No, just the one.

[Jeroen Demeyer]

On 2017-10-18 16:57, Erik Bray wrote:
> Any ideas? Looks odd...

Please try again with attached patch

[Erik Bray]

Thanks, but no need--I think I see the issue. If you happen to be
somewhere on the path of the cythonized file, then the "File" string
Cython produces ends up being relative to your current directory,
whereas _extract_embedded_position seems to assume the filename is
relative to the directory under SPYX_TMP.

The reason this happens in the Docker container is that it by default
starts out in /home/sage (the default user's home directory) and runs
the test suite from here as well, so the File string ends up being
relative to /home/sage instead.

It would probably be best if cython() change directory to target_dir
before calling cythonize() (or if there's some way to force cythonize
to output an absolute filename that might be good too, but I don't
know if there's an easy way to do this).

[Emmanuel Charpentier]

On another Debian testing running on core i5 + 8 GB RAM, the same binary (8.1beta8 + #24026 + #24006  + #23990 + #23923) passes ptestlong with no error whatsoever.

HTH,

--
Emmanuel Charpentier

[Emmanuel Charpentier]

On ONE of the two machines I've tested this, I have a similar happenstance :

charpent@p-202-021:/usr/local/sage-8$ git status
Sur la branche tst8-1
Fichiers non suivis:
  (utilisez "git add <fichier>..." pour inclure dans ce qui sera validé)

    hs_err_pid27411.log
    octave-workspace
    src/sage/libs/cypari2/

aucune modification ajoutée à la validation mais des fichiers non suivis sont présents (utilisez "git add" pour les suivre)

The presence of  is not new : it has already been reported ; I see it on all the machines I installed Sage on recently. No news...

HTH,

--
Emmanuel Charpentier

[François Bissey]

I got that in sage-on-gentoo as well. I meant to go after it but some work got 

in the way.

François

[Jeroen Demeyer]

On 2017-10-18 18:09, Erik Bray wrote:
> Thanks, but no need--I think I see the issue. If you happen to be
> somewhere on the path of the cythonized file, then the "File" string
> Cython produces ends up being relative to your current directory

I remember seeing this bug before...

[Jeroen Demeyer]

Could this be
https://github.com/cython/cython/issues/1375

[François Bissey]

> On 19/10/2017, at 08:54, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
>
> Could this be
> https://github.com/cython/cython/issues/1375

I am not sure, that ticket talk about truncation, we seem to suffer from some
limited form of recursive appending.
And I can confirm if I run the doctest somewhere else than my home directory
it passes.

François

[Dima Pasechnik]

I've tested this (with the necessary in the case of OSX 10.12) #12426+#23898 (thus, building with clang)
and got one persistent timeout here:

sage -t --long --warn-long 240.4 src/sage/rings/padics/padic_generic_element.pyx

Namely, it is this test, and it takes over 10 minutes on my (old and slow) Mac laptop if I just
run at sage prompt:

sage: R = Zp(17,10^6) ## line 2626 ##
sage: a = 17 * R.random_element() ## line 2627 ##
sage: b = a.exp() # should be rather fast ## line 2628 ##
------------------------------------------------------------------------

0 signals.so 0x000000010669932f print_backtrace + 63
1 signals.so 0x000000010669cb9c sigdie + 60
2 signals.so 0x000000010669caaf cysigs_signal_handler + 255
3 libsystem_platform.dylib 0x00007fffa670db3a _sigtramp + 26
4 ??? 0x8ba894b5e66ba4e9 0x0 + 10063456876335178985

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

[Erik Bray]

On Wed, Oct 18, 2017 at 9:54 PM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> Could this be
> https://github.com/cython/cython/issues/1375

Ah, I wasn't sure if that was a bug or a feature. In an case, it can
easily be worked around from the Sage side. Shall I open a ticket?

[Vincent Delecroix]

On a freshly compiled Sage on the quasar patchbot I got two doctet
failures in respectively schemes/elliptic_curves/heegner.py and
interfaces/qepcad.py.

sage -t --long src/sage/schemes/elliptic_curves/heegner.py
**********************************************************************
File "src/sage/schemes/elliptic_curves/heegner.py", line 6622, in
sage.schemes.elliptic_curves.heegner.heegner_index
Failed example:
E.heegner_index(-8)
Expected:

Traceback (most recent call last):

...
RuntimeError: ...
Got:
1.00000?
**********************************************************************


sage -t --long src/sage/interfaces/qepcad.py
**********************************************************************
File "src/sage/interfaces/qepcad.py", line 1566, in sage.interfaces.qepcad.?
Failed example:
_qepcad_atoms(qepcad('(E x)[a x + b > 0]', vars='(a,b,x)'))
# optional - qepcad
Expected:
{'a /= 0', 'b > 0'}
Got:
{'finish &'}
**********************************************************************


Complete report at

https://patchbot.sagemath.org/log/0/Ubuntu/16.04/x86_64/4.4.0-97-generic/quasar/2017-10-19%2022:05:36?short

Vincent

[John Cremona]

On 20 October 2017 at 08:00, Vincent Delecroix

<20100.d...@gmail.com> wrote:
> On a freshly compiled Sage on the quasar patchbot I got two doctet failures
> in respectively schemes/elliptic_curves/heegner.py and interfaces/qepcad.py.
>
> sage -t --long src/sage/schemes/elliptic_curves/heegner.py
> **********************************************************************
> File "src/sage/schemes/elliptic_curves/heegner.py", line 6622, in
> sage.schemes.elliptic_curves.heegner.heegner_index
> Failed example:
> E.heegner_index(-8)
> Expected:
> Traceback (most recent call last):
> ...
> RuntimeError: ...
> Got:
> 1.00000?
> **********************************************************************

I had this one too. On gcc version 5.4.0 20160609 (Ubuntu
5.4.0-6ubuntu1~16.04.4) . But not the second one below.

John

[Vincent Delecroix]

I opened a blocker ticket for the first issue

https://trac.sagemath.org/ticket/24075

For the second one, I already reported it previously (with another Sage
version) and it is due to a problem with the qepcad optional package.

Vincent

[Maarten Derickx]

I added #24075 to the known patchbot failures meta ticket at https://trac.sagemath.org/ticket/23832 . Do you have a ticket nr for the qepcad ticket for me?

[Maarten Derickx]

Please ignore the previous post, I found it in the mean time. For anyone interested, the qepcad issue can be found at https://trac.sagemath.org/ticket/22851