Sage 9.2.beta2 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 

69d2b2da28 (HEAD -> develop, tag: 9.2.beta2, trac/develop) Updated SageMath version to 9.2.beta2

d5756d46d6 Trac #29785: Move Extension options from src/module_list.py to "distutils:" directives in the individual files (part 3: Get rid of uname_specific)

b4ca018c5a Trac #29778: Error in hypergeometric trace formula

fdfb55b9ea Trac #29772: convert some code in finitely generated groups to libgap

c819fd2dbe Trac #29767: Implement the Jucys-Murphy elements for the partition algebra

d402656175 Trac #29338: Reduction from dancing links instance to SAT instance

026ef51a8f Trac #29716: Splitting Algebras

54b9dba2fa Trac #29706: Move Extension options from src/module_list.py to "distutils:" directives in the individual files (part 1 - some packages without OptionalExtensions)

c721b2ac60 Trac #28945: clean _cmp_ in rational.pyx

9ae4ffbd67 Trac #20665: Remove code deprecated in #4492

409f2a2425 Trac #29904: Broken double description of hypercube

af55be1e4f Trac #29740: Bug in is_line_graph()

eded9859e4 Trac #29730: Update sympy to 1.6

bce6cdd075 Trac #29725: FriezePatterns

55af317183 Trac #29721: coxeter3: Add spkg-configure.m4, use coxeter/ prefix for includes, move OptionalExtension options to .pyx file directives

e92de388e7 Trac #29720: Move Extension options from src/module_list.py to "distutils:" directives in the individual files (part 2 - OptionalExtensions)

0d23704b3f Trac #29472: Modify doctest such that they work with pari >= 2.11.3 and pari < 2.11.3

bcb239a2af Trac #29316: Require ./configure before make

497f9cc79a Trac #28237: Implement Atkinson's algorithm for counting linear extensions of (tree) posets

f8dd963af5 Trac #27826: Remove calls to 'long(...)', etc.

e80494a1b5 Trac #26891: Upgrade to Nauty 2.7

9cf434b600 Trac #26029: polytopes_db_4d converted to new style package

67329430e0 Trac #25434: Path_Tableaux

0365026d8b Trac #23330: Broken typeset in pdf export of Jupyter notebook

c3dfbf52cc Trac #16351: Move RecursivelyEnumeratedSet_forest code to sage/sets/recursively_enumerated_set.pyx, remove deprecated classes SearchForest, TransitiveIdeal, TransitiveIdealGraded

5e331396a6 Trac #9792: kernel and inverse_image of (polynomial) ring homomorphisms

27d464f628 Trac #29859: Update palp to 2.11 (for GCC 10 compatibility)

e7e25c3a4a Trac #29836: normaliz backend isn't ready for generators

b4185c58d8 Trac #29866: closest_vector for IntegerLattice is broken

3f45a58101 Trac #29715: Radius computation for undirected graph using certificates

7038053065 Trac #29672: spkg-configure.m4 for palp

ec44755a19 Trac #29635: libsingular: fix broken degneglex term order

55dc3911cf Trac #29493: Failing tests when using system glpk

0527ee760d Trac #29345: replace bashisms in m4/sage_spkg_collect.m4, m4/sage_spkg_enable.m4, build/pkgs/*/spkg-configure.m4, src/bin/sage-env, build/make/Makefile.in

e8c2f50d19 Trac #29174: Remove autotools SPKG

7b7fee5dc2 Trac #29033: Support minimal system Python version 3.6 (for venv)

afedaa53c3 Trac #28856: Update to sphinx 3

b4708f056d Trac #28656: Incorrect behaviour of diff of an (hold) integral WRT its bounds.

880a2ad5c6 Trac #21264: Factoring and Irreducibility Related Methods in Skew Polynomials

a8e179b76a Trac #19448: Improvements to submodules

6f19ac97a4 Trac #14764: Let Mathematica free integration work with definite integrals

3b1997d3e1 Trac #29848: MR43: Force misc-clean to run after sagelib-clean

ac9b5ee901 Trac #29780: Still memory leaks with matrix operations over GF(2)

119b6d8c5a Trac #29042: Sort dictionaries for doctests independent of ipythons pretty print

1f46a09557 Trac #29818: segfault constructing matrix over field of characteristic 2

e2dcdeeabb (tag: 9.2.beta1) Updated SageMath version to 9.2.beta1

[Paul Masson]

Any reason Trac 29809 wasn't included in this release? It's blocking other tickets and future improvements.

[Matthias Köppe]

On Friday, June 26, 2020 at 2:36:15 PM UTC-7, Paul Masson wrote:

Any reason Trac 29809 wasn't included in this release? It's blocking other tickets and future improvements.

My guess is there is no particular reason other than a backlog of other positive-review tickets. https://trac.sagemath.org/query?milestone=sage-9.2&groupdesc=1&group=status&max=1500&col=id&col=summary&col=component&col=time&col=changetime&col=author&col=reviewer&col=keywords&desc=1&order=changetime

[Volker Braun]

Just overwhelmed with work the last couple of weeks; hopefully its going to be a bit closer to normal now ;-)

[Justin C. Walker]

> On Jun 26, 2020, at 12:06 , 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 fresh clones of the develop branch on each of three macOS systems: 10.13.6 (2017 iMac Pro, 18-core Xeon W); 10.14.6 (2017 MBP, Quad-core Core i7); and 10.15.5 (2019 MBP, 9 Core Core i9).

No problems with any of the builds, and all tests (‘ptestlong’) passed on each.

Justin

--
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!
----

[Thierry Dumont]

When upgrading from 9.1 to 9.2, building the doc:
1)

[reference] Sphinx v3.0.4 en cours d'exécution
[reference] WARNING: l'entrée html_static_path
'/usr/local/sage3/sage/src/doc/common/static' n'existe pas
[reference] WARNING: l'entrée html_static_path 'static' n'existe pas
[reference] WARNING: le fichier de favicon 'favicon.ico' n'existe pas
[reference] chargement de l'environnement pickled... échoué
[reference] échec : version non à jour de l’environnement de construction
...
[reference]
/usr/local/sage3/sage/src/doc/en/reference/references/index.rst:36:
WARNING: La citation [AAGMRZ2019] n'est pas référencée
[reference]
/usr/local/sage3/sage/src/doc/en/reference/references/index.rst:40:
WARNING: La citation [Ab1995] n'est pas référencée
... (a lot of messages like this)
[reference] build a réussi, 1327 warnings.
[reference] The inventory files are in
local/share/doc/sage/inventory/en/reference/references.

2)
Error building the documentation.
Traceback (most recent call last):
File "/usr/local/sage3/sage/local/lib/python3.7/runpy.py", line 193,
in _run_module_as_main
"__main__", mod_spec)
File "/usr/local/sage3/sage/local/lib/python3.7/runpy.py", line 85, in
_run_code
exec(code, run_globals)
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py",
line 2, in <module>
main()
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 1721, in main
builder()
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 328, in _wrapper
getattr(get_builder(document), 'inventory')(*args, **kwds)
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 551, in _wrapper
self._build_bibliography(lang, format, *args, **kwds)
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 528, in _build_bibliography
build_many(build_ref_doc, references)
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 281, in build_many
_build_many(target, args, processes=NUM_THREADS)
File
"/usr/local/sage3/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
line 283, in build_many
raise worker_exc.original_exception
OSError: WARNING: l'entrée html_static_path
'/usr/local/sage3/sage/src/doc/common/static' n'existe pas


* This is persisting, even after a "make doc-clean"
* Ubuntu 20-04.

But, as could be expected, sage starts.

Yours.
t.d.

[Emmanuel Charpentier]

Same snag when upgrading 9.1.beta1 to 9.1.beta2 on Debian testong running on core i7 + 16 GB RAM. make doc-clean doesn't work here either.

Trying make-distclean...

HTH,

[Emmanuel Charpentier]

Rebuilding afresh (after make-distclean) didn't work either. make fails with errors suspiciously similar to the first attempt during documentation building.

Enclosed are configuration and documentation building logs.

I'm stuck. Suggestions ?

[David Coudert]

same issue here on macOS after upgrading from beta1

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[Dima Pasechnik]

This appears to be issue Francophone...

I get neither these warnings about citations not being citations, a la
https://en.wikipedia.org/wiki/The_Treachery_of_Images#/media/File:MagrittePipe.jpg

nor an error.

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[Emmanuel Charpentier]

Dear Dima,

Le samedi 27 juin 2020 15:35:51 UTC+2, Dima Pasechnik a écrit :

This appears to be issue Francophone...

Sacrebleu merdalors !((C) Raymond Queneau)

Does that offer a hint ?

 

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[Jonathan Kliem]

Looks like the same problem we had on https://trac.sagemath.org/ticket/27122#comment:64

Are you compiling with CFLAGS containing `-march=native` or similiar?

Disabling `-march=native` for GAP solved the problem there.

Here is the corresponding commit (needs some modification of course, but it's only two lines):

https://git.sagemath.org/sage.git/commit/?h=234338ea6283549195c4b22fc84cb621fcb75c48&id=4c52d4d43794f807875739deb27a51d46836764c

I hope that helps.

Jonathan

P.S. The problem showed up all the sudden for centos-8 and linuxmint 19.3. Then also ubuntu bionic and ubuntu focal.

[Emmanuel Charpentier]

Le samedi 27 juin 2020 16:04:09 UTC+2, Jonathan Kliem a écrit :

Looks like the same problem we had on https://trac.sagemath.org/ticket/27122#comment:64

Are you compiling with CFLAGS containing `-march=native` or similiar?

I dunno : just doing "make distclean ; ./configure ; make".

I think I need handholding...

[Dima Pasechnik]

On Sat, Jun 27, 2020 at 2:47 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> Dear Dima,
>
> Le samedi 27 juin 2020 15:35:51 UTC+2, Dima Pasechnik a écrit :
>>
>> This appears to be issue Francophone...
>
>
> Sacrebleu merdalors !((C) Raymond Queneau)
>
> Does that offer a hint ?

again the same deja vu, no?

https://groups.google.com/d/msg/sage-release/xcGXMuHuEOw/KEA65NZqAAAJ

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[Antonio Rojas]

This happens with non-English locales. Warning messages are translated in sphinx 3, so sage's whitelist doesn't catch them, and they are treated as errors. Forcing the C locale works around the issue.

[Jonathan Kliem]

Never mind. Sorry about the confusion.

I didn't read the last line, because there was some french in it. I should have. I didn't realize that probably all docbuilding errors look alike except for the last line.

[Dima Pasechnik]

On Sat, Jun 27, 2020 at 4:19 PM Antonio Rojas <nqn...@gmail.com> wrote:
>
> This happens with non-English locales. Warning messages are translated in sphinx 3, so sage's whitelist doesn't catch them, and they are treated as errors. Forcing the C locale works around the issue.

yes, I can confirm this.
So if I set locale to a French one
by making sure I gave it available from locale
($ locale -a gives a list)

$ export LANG=fr_FR.utf8
and then

$ ./sage -docbuild reference html

suddenly gets very chatty, ending with an error from a WARNING

[reference] Sphinx v3.0.4 en cours d'exécution
[reference] WARNING: l'entrée html_static_path

'/home/dimpase/sage/src/doc/common/static' n'existe pas
...

OSError: WARNING: l'entrée html_static_path

'/home/dimpase/sage/src/doc/common/static' n'existe pas

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[Dima Pasechnik]

to fix this issue: https://trac.sagemath.org/ticket/30002

[Emmanuel Charpentier]

Yay ! " export LANG=C.UTF-8 ; make " *seems* to bulld the documentation.

Stay tuned.

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[Emmanuel Charpentier]

Le samedi 27 juin 2020 18:15:13 UTC+2, Emmanuel Charpentier a écrit :

Yay ! " export LANG=C.UTF-8 ; make " *seems* to bulld the documentation.

Well, that worked. With qualification :

After this (successful) build of the documentation, "make" in an environment where LANG is fr_FR.utf-8 fails. LANG=C.UTF-8 succeeds.

HTH

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, rebuilding 9.2.beta2 (see above and attached config.log) gives one (transient) timeout and three (permanent) failures (see attached chkerrs.txt):

File	Result	P/T
src/sage/tests/parigp.py	Timed out	T
src/sage/rings/complexarb.pyx	6 doctests failed	P
src/sage/tests/gappackages.py	1 doctest failed	P
src/sage/rings/realarb.pyx	2 doctests failed	P

The failures recorded for gap_packages are essentially cosmetic, and
have been reported before ; those reported for complex_arb seem
attributable to numerical noise ; those reported for real_arb seem
genuine (mathematical) failures.

HTH,

​

[Thierry Dumont]

I confirm, it worked for me too.

> <https://groups.google.com/d/msgid/sage-release/a38afb1f-a635-458d-a78d-b3999f632b7co%40googlegroups.com>.

>
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> <https://groups.google.com/d/msgid/sage-release/6118CF9C-8D7B-4CDE-A03D-84E70923EA11%40gmail.com>.

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[Sébastien Labbé]

Runing tests with few optional/external packages,

Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_numerical_backends_cplex,sage_numerical_backends_gurobi

I get:

----------------------------------------------------------------------
sage -t --long src/sage/combinat/quickref.py  # 1 doctest failed
sage -t --long src/sage/combinat/species/library.py  # 1 doctest failed
sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 17 doctests failed
sage -t --long src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Bad exit: 1
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,imagemagick,internet,latex,pandoc


Rerunning the failed tests, I get the same (except the timeout):

----------------------------------------------------------------------
sage -t --long src/sage/combinat/quickref.py  # 1 doctest failed
sage -t --long src/sage/combinat/species/library.py  # 1 doctest failed
sage -t --long src/sage/combinat/tutorial.py  # timeout in doctesting framework
sage -t --long src/sage/databases/findstat.py  # 17 doctests failed
sage -t --long src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Bad exit: 1
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: internet

Nothing new here that was not in 9.2.beta1

Follow up at https://trac.sagemath.org/ticket/25536

[Eric Gourgoulhon]

On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.2.beta1 after export LANG=C.UTF-8: OK
  - all tests from ptestlong passed

Eric.