Sage 9.2.rc0 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 

f6250c2682 (tag: 9.2.rc0, trac/develop) Updated SageMath version to 9.2.rc0

8ff504da1c Trac #30629: Reject system libgc that breaks ECL build

8a0c61ce63 Trac #30654: Add fast matrix inverse for Hermitian positive-definite matrices

f448467a0d Trac #30653: add the Stieltjes continued fraction of a power series

6090756361 Trac #30645: Optimize `has_edge` of graph backend

458be0ad92 Trac #30642: modify HAVE_GC test in flint's spkg-configure.m4 to allow undefined HAVE_GC

908c661ae2 Trac #30638: internet doctest failing in arith/misc.py

08011764b2 Trac #30634: failing internet doctests using mathematica free

5f14e96183 Trac #30632: few easy internet doctests failures to fix

099c3ba98a Trac #30618: clean up pypolybori

4e66cfea78 Trac #30616: Replace use of `sage.misc.package.PackageNotFoundError` (2); lazy_import: Add keyword argument 'feature'

8a6a415df9 Trac #30614: Set size, font, and opacity for text3d in Three.js viewer

ef0ab126ca Trac #30607: Replace use of `sage.misc.package.PackageNotFoundError`, is_package_installed by features

e8631a7eac Trac #30606: sage.features.Feature.resolution: If SAGE_ROOT is available, recommend system packages

e2ed7d3f2d Trac #30461: Fully-commutative stable Grothendieck crystal

19001b58ff Trac #24802: berlekamp_massey: undefined behavior / silent invalid answer

608db74df2 Trac #30657: Fix up "sage -p"

cecf3dbc3b Trac #30701: integer expression expected in sage-env

91eac298eb Trac #30184: Support Python 3.9

a1810d570d Trac #30590: src/sage/cpython/debugimpl.c: remove python2 code

da3658c732 Trac #30675: Follow up to #30596: missing symbol in linking on gentoo with gcc10

a379746839 Trac #27749: is_globally_equivalent_to is not symmetric

219bd5401d Trac #24868: Neighbor method for quadratic forms

aedd032e4b Trac #30676: Follow up to #30563 too many quotes in maxima.py

1da6df404d (tag: 9.2.beta14) Updated SageMath version to 9.2.beta14

[Kwankyu Lee]

It would be nice to have

https://trac.sagemath.org/ticket/30418

in 9.2.rc1.

[Samuel Lelievre]

Volker Braun wrote:

>

> f6250c2682 (tag: 9.2.rc0, trac/develop) Updated SageMath version to 9.2.rc0

Thanks for this new release! I tried this:

- Sage 9.2.rc0 + #30589 (Use Python 3.9.0)

on two systems:

- Debian 10 buster

- macOS 10.14.6 Mojave with Homebrew

Things look good. Only two failures, as expected, see

- #30184 (Support Python 3.9)

Are there are already tickets for these?

See further down for the exact commands I ran.

Quality of life is improved with the ability to run bootstrap

in quiet mode, since #30533 and #30664 were merged;

many thanks to Michael Orlitzky and Matthias Koeppe.

I hope it can be even further improved, see below.

## Quality of life tickets

- "make distclean" should not run "./configure"

  https://trac.sagemath.org/ticket/29310

  needs branch

- Have configure run quiet if started by make in silent mode

  https://trac.sagemath.org/ticket/30258

  needs branch

- make V=0: Suppress "make --no-print-directory" lines for package builds

  https://trac.sagemath.org/ticket/30541

  needs branch

- Improve configure's recommendation message

  https://trac.sagemath.org/ticket/30624#comment:3

  needs work

## Debian 10 buster

From an existing installation on Debian 10 buster.

Apply 50389

```

$ git trac checkout 50389

```

Check we are based on 9.2.rc0

```

$ git log --oneline -3

6d3a0fa824 (HEAD -> t/30589/upgrade-python-3.9, trac/u/mkoeppe/upgrade-python-3.9) build/pkgs/python3: Update to 3.9.0

255d22ba66 build/pkgs/python3: Update to 3.9.0rc2

f6250c2682 (tag: 9.2.rc0, origin/develop, origin/HEAD, develop) Updated SageMath version to 9.2.rc0

```

Run make distclean, boostrap, configure, make, make testlong:

```

$ V=0 ; \

  MAKE='make -j1' ; \

  make -s V=0 distclean \

  &&  ./bootstrap \

  &&  ./configure --without-system-python --enable-download-from-upstream-url -q \

  &&  make -s V=0 \

  &&  make -s V=0 testlong

...

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

sage -t --long --random-seed=0 src/sage/functions/other.py  # 1 doctest failed

sage -t --long --random-seed=0 src/sage/rings/polynomial/pbori/randompoly.py  # 1 doctest failed

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

Total time for all tests: 13876.9 seconds

    cpu time: 12377.7 seconds

    cumulative wall time: 13454.8 seconds

```

## macOS 10.14.6 Mojave

From an existing installation on macOS 10.14.6 Mojave.

Apply 50389

```

$ git trac checkout 50389

```

Check we are based on 9.2.rc0

```

$ git log --oneline -3

6d3a0fa824 (HEAD -> t/30589/upgrade-python-3.9, trac/u/mkoeppe/upgrade-python-3.9) build/pkgs/python3: Update to 3.9.0

255d22ba66 build/pkgs/python3: Update to 3.9.0rc2

f6250c2682 (tag: 9.2.rc0, origin/develop, develop) Updated SageMath version to 9.2.rc0

```

Run make distclean, apply homebrew build env, boostrap, configure, make, make testlong:

```

$ V=0 ; \

  MAKE='make -j1' ; \

  make -s V=0 distclean \

  &&  source .homebrew-build-env

  &&  ./bootstrap \

  &&  ./configure --without-system-python --enable-download-from-upstream-url -q \

  &&  make -s V=0 \

  &&  make -s V=0 testlong

...

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

sage -t --long --warn-long 123.3 --random-seed=0 src/sage/functions/other.py  # 1 doctest failed

sage -t --long --warn-long 123.3 --random-seed=0 src/sage/rings/polynomial/pbori/randompoly.py  # 1 doctest failed

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

Total time for all tests: 22359.6 seconds

    cpu time: 16438.8 seconds

    cumulative wall time: 21763.6 seconds

make: *** [testlong] Error 1

```

[Clemens Heuberger]

In contrast to 9.2.beta14, on my Linux Mint 19.3 Tricia machine I get (after a
fresh build)

./sage -t -p --all --long --logfile=logs/ptestlong.log
Traceback (most recent call last):
File "/local/cheuberg/local/sage-9.2.rc0/src/bin/sage-runtests", line 181, in
<module>
DC = DocTestController(options, args)
File
"/local/cheuberg/local/sage-9.2.rc0/local/lib/python3.6/site-packages/sage/doctest/control.py",
line 371, in __init__
options.optional.update(system.name for system in package_systems())
File
"/local/cheuberg/local/sage-9.2.rc0/local/lib/python3.6/site-packages/sage/features/__init__.py",
line 376, in package_systems
proc = run('sage-guess-package-system', shell=True, capture_output=True,
text=True, check=True)
File "/usr/lib/python3.6/subprocess.py", line 423, in run
with Popen(*popenargs, **kwargs) as process:
TypeError: __init__() got an unexpected keyword argument 'capture_output'
Makefile:190: recipe for target 'ptestlong' failed


So apparently my system python3 is used which is Python 3.6.9. The option
capture_output has been introduced in python 3.7. The change introducing
capture_output might have been introduced in Trac #30606.






Am 06.10.20 um 23:22 schrieb Volker Braun:

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[Sébastien Labbé]

So apparently my system python3 is used which is Python 3.6.9. The option
capture_output has been introduced in python 3.7. The change introducing
capture_output might have been introduced in Trac #30606.

 

Oups, I did the review of #30606 on a machine with Python 3.8 installed (I installed python 3.8 since system python 3.6 was not supported on previous beta). Hopefully, it will be easy to fix in order to support python 3.6 which was the goal of https://trac.sagemath.org/ticket/30576

[Kenji Iohara]

I have did (first) built on my Mac OS 10.15.7 with Xcode 12, 

failed on compiling pynac even on zsh-mode:

[Thierry Dumont]

On Ubuntu 20-04 upgrading to 9.2 rc0 from the last beta version:

- compilation: ok.
- make ptestlong
----------------------------------------------------------------------
sage -t --long --warn-long 88.1 --random-seed=0
src/sage/interfaces/psage.py # 1 doctest failed
sage -t --long --warn-long 88.1 --random-seed=0
src/sage/quadratic_forms/quadratic_form__equivalence_testing.py # 1
doctest failed
----------------------------------------------------------------------

(1 doctest failed).

t.d.

[Dima Pasechnik]

On Wed, Oct 7, 2020 at 1:48 PM Kenji Iohara <simplye...@gmail.com> wrote:
>
> I have did (first) built on my Mac OS 10.15.7 with Xcode 12,
> failed on compiling pynac even on zsh-mode:

I presume you are using gmp from Homebrew;
before running ./configure and make, please run

source .homebrew-build-env

as described in
https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation

HTH
Dima

>
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>
> 2020/10/07 14:12、Sébastien Labbé <sla...@gmail.com>のメール:

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[Eric Gourgoulhon]

On Ubuntu 20.04 running on Intel Core i7-8665U + 32 GB RAM:

- incremental build (-j8) from 9.2.beta14 with system Python (=3.8.2): OK

- all tests from ptestlong passed, except for

sage -t --long --warn-long 74.5 --random-seed=0 src/sage/quadratic_forms/quadratic_form__equivalence_testing.py
**********************************************************************
File "src/sage/quadratic_forms/quadratic_form__equivalence_testing.py", line 90, in sage.quadratic_forms.quadratic_form__equivalence_testing.is_globally_equivalent_to
Failed example:
    Q.is_globally_equivalent_to(P)
Expected:
    False
Got:
    True
**********************************************************************
1 item had failures:
   1 of  21 in sage.quadratic_forms.quadratic_form__equivalence_testing.is_globally_equivalent_to
    [69 tests, 1 failure, 0.27 s]

This error is persistent (i.e. still occurs when the test is run standalone) and was not there in 9.2.beta14.

It has also been reported for this release with Ubuntu 20.04 in

https://groups.google.com/g/sage-release/c/0MnZQYItCYc/m/6ks32lnXAAAJ

Besides, the run of ptestlong generated the same Ubuntu crash reports regarding nauty and mwrank as those reported in

https://groups.google.com/g/sage-release/c/6RLsvBKi84I/m/PscGzDefCgAJ

Eric.

[Emmanuel Charpentier]

On Debian testing runninng on core i7 + 16 GB RAM, after upgrading 0.2.beta14 to 9.2.rc0 configured to use all available system packages, ptestlong results in one transient and five permanent failures, identical to those obtained on the same machine with 9.2.beta14 :

File	Result	P/T
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py	Killed due to abort	P
src/sage/tests/parigp.py	Timed out	T
src/sage/modules/fg_pid/fgp_module.py	3 doctests failed	P
src/doc/en/constructions/algebraic_geometry.rst	1 doctest failed	P
src/doc/en/developer/coding_in_other.rst	1 doctest failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P

Of note :

• ./configure --enable-download-from-upstream-url still suggested the installation of libnauty-dev notwithstanding the presence oflibnauty2-dev (already reported).

HTH,

​

[Kenji Iohara]

Thanks DIma, I could compile pynac with your indication. But there still is a problem with dochtml..

and here is its log file: 

[Sébastien Labbé]

Testing with few optional and external packages, I get:

Using --optional=4ti2,cbc,ccache,cryptominisat,database_jones_numfield,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,libnauty,lidia,lrslib,memlimit,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg

**********************************************************************
File "src/sage/databases/findstat.py", line 49, in sage.databases.findstat
Failed example:
    r = findstat([(m, m.number_of_nestings()) for n in range(6) for m in PM(2*n)]); r # optional -- internet
Expected:
    0: St000042oMp00116 (quality [100, 100])
    1: St000041 (quality [20, 100])
    ...
Got:
    The Combinatorial Statistic Finder (https://www.findstat.org/) provides a new collection:
        Cc0029: Lattices
    To use it with this interface, it has to be added to the dictionary
        _SupportedFindStatCollections in src/sage/databases/findstat.py
    of the SageMath distribution.  Please open a ticket on trac!
    0: St000042oMp00116 (quality [100, 100])
    1: St000041 (quality [20, 100])
    2: St000232oMp00115oMp00092 (quality [17, 70])
    3: St000233oMp00092 (quality [16, 100])
    4: St000496oMp00092 (quality [16, 100])
    5: St000123oMp00087oMp00058 (quality [13, 70])
    6: St000359oMp00087oMp00058 (quality [13, 70])
Killing test src/sage/databases/findstat.py
Killing test src/sage/sat/boolean_polynomials.py
Killing test src/sage/quadratic_forms/quadratic_form__neighbors.py
Killing test src/sage/interfaces/octave.py
Killing test src/sage/interfaces/fricas.py
Killing test src/sage/knots/gauss_code.py
Killing test src/sage/misc/repr.py
----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/lfunctions/sympow.py  # 4 doctests failed
sage -t --long --random-seed=0 src/doc/en/constructions/interface_issues.rst  # 1 doctest failed
Doctests interrupted: 2238/4211 files tested
----------------------------------------------------------------------

Above failures obtained before interruption are already tracked at https://trac.sagemath.org/ticket/25536

[Matthias Köppe]

Thanks for catching this. I have opened https://trac.sagemath.org/ticket/30740 for this.

> to sage-r...@googlegroups.com
> <mailto:sage-release+unsub...@googlegroups.com>.

[axio...@yahoo.de]

The findstat issue is already ready for review at https://trac.sagemath.org/ticket/30630.

[Eric Gourgoulhon]

Le mercredi 7 octobre 2020 à 16:40:16 UTC+2, Eric Gourgoulhon a écrit :

On Ubuntu 20.04 running on Intel Core i7-8665U + 32 GB RAM:

- incremental build (-j8) from 9.2.beta14 with system Python (=3.8.2): OK

- all tests from ptestlong passed, except for

sage -t --long --warn-long 74.5 --random-seed=0 src/sage/quadratic_forms/quadratic_form__equivalence_testing.py
**********************************************************************
File "src/sage/quadratic_forms/quadratic_form__equivalence_testing.py", line 90, in sage.quadratic_forms.quadratic_form__equivalence_testing.is_globally_equivalent_to
Failed example:
    Q.is_globally_equivalent_to(P)
Expected:
    False
Got:
    True
**********************************************************************
1 item had failures:
   1 of  21 in sage.quadratic_forms.quadratic_form__equivalence_testing.is_globally_equivalent_to
    [69 tests, 1 failure, 0.27 s]

This error is persistent (i.e. still occurs when the test is run standalone) and was not there in 9.2.beta14.

It has also been reported for this release with Ubuntu 20.04 in

https://groups.google.com/g/sage-release/c/0MnZQYItCYc/m/6ks32lnXAAAJ

This doctest failure is due to a bug in the system Pari (2.11.2 in Ubuntu 20.04); it has been fixed in Pari 2.11.4,  which is now shipped with Sage, cf. https://trac.sagemath.org/ticket/27749.