Sage 8.8.beta6 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 

9b91a096bd (tag: 8.8.beta6) Updated SageMath version to 8.8.beta6

ef24a11f75 Trac #27839: Remove some long() calls

e54ec9e6d9 Trac #27835: pyflakes cleanup in functions

b22dfb87bb Trac #27821: covering_design.py & design_catalog.py: Fix AttributeError

992d0a6d28 Trac #27802: polymake interface: Convert Python dicts to Perl hashes

bb7d45ebcf Trac #27738: Upgrade R to 3.6.0

c244c63497 Trac #27712: improve function field differentials to work over nested fields

9f9a4af799 Trac #27556: Move references in sage/schemes to master bibliography file

f8b9a2a717 Trac #27518: Implementation of Floyd-Warshall for all pair shortest distance

3e1cf317f4 Trac #27186: spkg-configure.m4 for libpng

1361286f04 Trac #26526: mutable poset: remove default for breaking ties in topological sort

34ac55769b Trac #26504: asymptotic ring substitute: allow modification of "internal" rules (as claimed in the docs)

f60793361a Trac #25091: Expose some normaliz features

eb31a82828 Trac #27304: Bug in factorization of simple symbolic expressions

5cbe9405ff Trac #27657: Simplify ideal generators in function field code

6c32357ace Trac #27644: Sage Jupyter Kernel vs EIN (Emacs Jupyter Interface)

4711a3e017 Trac #27830: py3: fix remaining doctests for groups/perm_gps

84cc7b8bb5 Trac #27815: more files in python3-known-passing.txt

7500f867f0 Trac #27814: Configure check for system "rw" library

fe1c495669 Trac #27812: py3: fix comparison of constants

925119dc61 Trac #27811: fix doctest with igraph

f655716380 Trac #27808: dispatch factorisation of univariate poly over number fields

2061b87d0b Trac #27783: 6 doctests failed in src/sage/databases/oeis.py with tag internet

6306f76deb Trac #27775: Fix some py3 doctests in src/sage/doctests

695d3d0ba0 Trac #27774: py3: fix various issues in cplex backend

5f7da089dd Trac #27654: py3 : Fix combinat/root_system/integrable_representations.py for python3.

a353731012 Trac #26189: Intersection of modular abelian varieties gives wrong answer

cf4c17f1f8 Trac #5548: fix that _hnf_mod segfaults sage completely

df404655c7 Trac #27810: small cleanup of fgp_module

39ef3e4498 Trac #27800: small cleaning for quaternion_algebra

a9f92c4fa6 Trac #27807: Polymake-jupymake interface: Fix polymake's error handling in Shell::Mock

77ce1617d9 Trac #27801: spkg-configure.m4 for ninja-build

05576b67b2 Trac #27799: AsymptoticRing.coefficients_of_generating_function: specify error term

446b735c50 Trac #27731: upgrade normaliz to 3.7.2, pynormaliz to 2.5

473a81be98 Trac #22704: Create a variant of the polymake interface using polymake's callable library (polymake::Main) via JuPyMake

bc19c41475 Trac #27045: Compute (degree bounded) minimal model of cdga's

d781a33ff5 Trac #24905: Upgrade polymake to version 3.4

8f5c3fc4c1 Trac #27681: GAP: Apparent problem with workspace initialization

baff1c42dd (tag: 8.8.beta5) Updated SageMath version to 8.8.beta5

[Timo Kaufmann]

There is no beta6 tag on github yet, is that still the canonical source?

[Dima Pasechnik]

neither trac, nor the usual places on github or gitlab have the branch!

On Wed, May 22, 2019 at 7:06 PM Timo Kaufmann <eisf...@gmail.com> wrote:
>
> There is no beta6 tag on github yet, is that still the canonical source?
>

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[Volker Braun]

Forgot, its up now!

On Wednesday, May 22, 2019 at 8:17:46 PM UTC+2, Dima Pasechnik wrote:

neither trac, nor the usual places on github or gitlab have the branch!

On Wed, May 22, 2019 at 7:06 PM Timo Kaufmann <eisf...@gmail.com> wrote:
>
> There is no beta6 tag on github yet, is that still the canonical source?
>
> --
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[Sébastien Labbé]

My first try at installing finishes with an error installing the (optional?) package pynormaliz

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package: pynormaliz-2.5
  log file: /home/slabbe/GitBox/sage/logs/pkgs/pynormaliz-2.5.log
  build directory: /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

The pynormaliz-2.5.log finishes with:

[...]

    runstatedir='${localstatedir}/run'
    sbindir='${exec_prefix}/sbin'
    sharedstatedir='${prefix}/com'
    sysconfdir='${prefix}/etc'
    target_alias=''

    ## ------------------- ##
    ## File substitutions. ##
    ## ------------------- ##

    SAGE_MAKE_DEPS=''

    ## ----------- ##
    ## confdefs.h. ##
    ## ----------- ##

    /* confdefs.h */
    #define PACKAGE_NAME "Sage"
    #define PACKAGE_TARNAME "sage"
    #define PACKAGE_VERSION "8.8.beta6"
    #define PACKAGE_STRING "Sage 8.8.beta6"
    #define PACKAGE_BUGREPORT "sage-dev....."
    #define PACKAGE_URL ""

    configure: exit 1
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-loTgzR/setup.py", line 102, in <module>
        cmdclass = {'build_ext': build_ext, 'test': TestCommand},
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/command/install.py", line 563, in run
        self.run_command('build')
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/command/build.py", line 127, in run
        self.run_command(cmd_name)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/tmp/pip-req-build-loTgzR/setup.py", line 63, in run
        subprocess.check_call(["sh", "configure"], env = my_env )
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/subprocess.py", line 190, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['sh', 'configure']' returned non-zero exit status 1
    Running setup.py install for PyNormaliz: finished with status 'error'
Cleaning up...
  Removing source in /tmp/pip-req-build-loTgzR
Removed build tracker '/tmp/pip-req-tracker-vrYyai'
Command "/home/slabbe/GitBox/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-loTgzR/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-avEj9i/install-record.txt --single-version-externally-managed --root /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5/inst --compile" failed with error code 1 in /tmp/pip-req-build-loTgzR/
Exception information:
Traceback (most recent call last):
  File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py", line 143, in main
    status = self.run(options, args)
  File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 366, in run
    use_user_site=options.use_user_site,
  File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs
    **kwargs
  File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 791, in install
    spinner=spinner,
  File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py", line 705, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command "/home/slabbe/GitBox/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-loTgzR/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-avEj9i/install-record.txt --single-version-externally-managed --root /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5/inst --compile" failed with error code 1 in /tmp/pip-req-build-loTgzR/
Error: installing with pip2 failed
********************************************************************************
Error installing pynormaliz-2.5
********************************************************************************

real    0m3.579s
user    0m1.256s
sys    0m0.208s
************************************************************************
Error installing package pynormaliz-2.5
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
  /home/slabbe/GitBox/sage/logs/pkgs/pynormaliz-2.5.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5' && '/home/slabbe/GitBox/sage/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

[Vincent Delecroix]

Could you check whether there is a config.log in

/home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5

and if so attach it.

Vincent

[Sébastien Labbé]

On Thursday, May 23, 2019 at 9:15:44 PM UTC+2, vdelecroix wrote:

Could you check whether there is a config.log in

/home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5

and if so attach it.

I am answering here: https://trac.sagemath.org/ticket/27731#comment:27

[darwin doppelganger]

SageMath version 8.8.beta6 builds successfully on my MacBook Pro, 10.14.4, Xcode 10.2.1

[Justin C. Walker]

> On May 22, 2019, at 10:45 , 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 of the develop branch on three macOS systems: 10.11.6 (mid 2015 MBP, Quad-core Core i7), 10.13.6 (2017 iMac Pro, 18-core Xeon W), 10.14.5 (2017 MBP, Quad-core Core i7). No problems with the build, all tests (‘ptestlong’) passed on all systems!

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!
----

[Steven Trogdon]

As far as I know this failure started with this beta.

sage -t --long src/sage/tests/gap_packages.py

**********************************************************************

File "src/sage/tests/gap_packages.py", line 137, in sage.tests.gap_packages.all_installed_packages

Failed example:

    all_installed_packages() == all_installed_packages(gap=gap)

Expected:

    True

Got:

    False

**********************************************************************

1 item had failures:

   1 of   4 in sage.tests.gap_packages.all_installed_packages

    [10 tests, 1 failure, 1.04 s]

For info:

sage: from sage.tests.gap_packages import all_installed_packages

sage: all_installed_packages()

('AtlasRep',

 'FactInt',

 'GAPDoc',

 'SmallGrp',

 'alnuth',

 'atlasrep',

 'autpgrp',

 'crisp',

 'ctbllib',

 'fga',

 'irredsol',

 'laguna',

 'polenta',

 'polycyclic',

 'primgrp',

 'resclasses',

 'sophus',

 'tomlib',

 'transgrp')

sage: all_installed_packages(gap=gap)

('FactInt',

 'GAPDoc',

 'SmallGrp',

 'alnuth',

 'atlasrep',

 'autpgrp',

 'crisp',

 'ctbllib',

 'fga',

 'irredsol',

 'laguna',

 'polenta',

 'polycyclic',

 'primgrp',

 'resclasses',

 'sophus',

 'tomlib',

 'transgrp')

ls ~/.gap/pkg/

AtlasRep

[François Bissey]

You have something in ~/.gap. See https://trac.sagemath.org/ticket/27681#comment:30

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[Steven Trogdon]

Found this also first on s-o-g. So should ~/.gap be empty or is a follow-up to https://trac.sagemath.org/ticket/27681 necessary?

On Friday, May 24, 2019 at 7:04:53 PM UTC-5, François Bissey wrote:

You have something in ~/.gap. See https://trac.sagemath.org/ticket/27681#comment:30

> To unsubscribe from this group and stop receiving emails from it, send an email to sage-r...@googlegroups.com.

[François Bissey]

We’ll want some kind of follow up. The test will fail if you have something in ~/.gap.
Not just on sage-on-gentoo.
The question is whether the pexpect interface should continue starting `gap` with the
“-r” option or not.

François

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[Sébastien Labbé]

Now that I managed to installed pynormaliz, I could run the doctests including the below optional/external ones:

Using --optional=4ti2,bliss,cbc,ccache,cmake,cryptominisat,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,mpir,ninja_build,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,qhull,rst2ipynb,sage,topcom

External software detected for doctesting: ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

I get:

----------------------------------------------------------------------
sage -t --long src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/combinat/species/library.py  # 1 doctest failed
sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed
----------------------------------------------------------------------

The usual ext_rep.py one is not reproducible. I can reproduce the other three files failures with:

sage -tp --long --optional=sage,optional,external src/sage/databases/oeis.py  src/sage/databases/findstat.py  src/sage/combinat/species/library.py  src/sage/combinat/designs/ext_rep.py 

find_stat.py failures are already tracked at https://trac.sagemath.org/ticket/25536

New failures are pasted below:

sage -t --long src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 1747, in sage.databases.oeis.OEISSequence.programs
Failed example:
    ee.programs()[0]                      # optional -- internet
Expected:
    '(PARI) { default(realprecision, 50080); x=exp(1); for (n=1, 50000, d=floor(x); x=(x-d)*10; write("b001113.txt", n, " ", d)); } \\\\ _Harry J. Smith_, Apr 15 2009'
Got:
    '(PARI) default(realprecision, 50080); x=exp(1); for (n=1, 50000, d=floor(x); x=(x-d)*10; write("b001113.txt", n, " ", d)); \\\\ _Harry J. Smith_, Apr 15 2009'

**********************************************************************
1 item had failures:

   1 of   7 in sage.databases.oeis.OEISSequence.programs
    5 webbrowser tests not run
    0 tests not run because we ran out of time
    [266 tests, 1 failure, 65.86 s]



sage -t --long src/sage/combinat/species/library.py
**********************************************************************
File "src/sage/combinat/species/library.py", line 64, in sage.combinat.species.library.SimpleGraphSpecies
Failed example:
    oeis(seq)[0]                              # optional -- internet
Expected:
    A006125: a(n) = 2^(n(n-1)/2).
Got:
    A006125: a(n) = 2^(n*(n-1)/2).

**********************************************************************
1 item had failures:

   1 of   9 in sage.combinat.species.library.SimpleGraphSpecies
    0 tests not run because we ran out of time
    [23 tests, 1 failure, 5.82 s]

[Sébastien Labbé]

On another machine (on which I did not updated sage since a long time), I get trouble with documentation:

[dochtml] OSError: /home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/graphs/generic_graph.py:docstring of sage.graphs.generic_graph.GenericGraph.longest_path:72: WARNING: Exception occurred in plotting generic_graph-1

which reappears even after make doc-clean.

The context is:

...

[dochtml] [graphs   ] dumping object inventory... fait
[dochtml] [graphs   ] build réussi, 108 warnings.
[dochtml] [graphs   ] The inventory files are in local/share/doc/sage/inventory/en/reference/graphs.
[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/runpy.py", line 174, in _run_module_as_main
[dochtml]     "__main__", fname, loader, pkg_name)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/runpy.py", line 72, in _run_code
[dochtml]     exec code in run_globals
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>
[dochtml]     main()
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 1730, in main
[dochtml]     builder()
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 351, in _wrapper
[dochtml]     getattr(get_builder(document), 'inventory')(*args, **kwds)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 547, in _wrapper
[dochtml]     build_many(build_ref_doc, L)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 288, in build_many
[dochtml]     ret = x.get(99999)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python2.7/multiprocessing/pool.py", line 572, in get
[dochtml]     raise self._value
[dochtml] OSError: /home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/graphs/generic_graph.py:docstring of sage.graphs.generic_graph.GenericGraph.longest_path:72: WARNING: Exception occurred in plotting generic_graph-1
Makefile:2048 : la recette pour la cible « doc-html » a échouée
make[3]: *** [doc-html] Erreur 1
make[3] : on quitte le répertoire « /home/slabbe/GitBox/sage/build/make »
Makefile:1860 : la recette pour la cible « all-start » a échouée
make[2]: *** [all-start] Erreur 2
make[2] : on quitte le répertoire « /home/slabbe/GitBox/sage/build/make »

real    1m11.623s
user    8m39.525s
sys    0m10.684s

[Thierry]

Hi,

for what is worth, https://trac.sagemath.org/ticket/27250 still prevents
my 32-bit patchbot to run. This is pretty important to be able to
maintain a constant pressure on such architectures, otherwise there is a
slow decay that then takes a long time to get fixed again.

Ciao,
Thierry

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[François Bissey]

Actually this is a little bit more complicated than what I thought. This test is likely to fail

on sage-on-gentoo and probably other distro.

atlasrep is a very naughty gap package that download data from the internet and

wants to put it in its installation directory. Which is a problem for a system wide install

where it belongs to root.

So I adopted some patches from debian to have the data downloaded and stored in

~/.gap. So what we see here in ~/.gap is not a package install but the result of

using atlasrep at any point. It is likely ~/.gap/pkg/AtlasRep will re-appear all by

itself during doctesting.

So we really need to improve on this situation.

1) does gap need to be run with "-r"

2) if it does what do we do about the fact that ~/.gap is skipped when using the pexpect interface.

Francois

> To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscribe@googlegroups.com.

[Steven Trogdon]

Yes, the two important folders on vanilla sage are

ls -al local/share/gap/pkg/atlasrep/data*

local/share/gap/pkg/atlasrep/datagens:

total 12

drwxr-xr-x 2 strogdon math 4096 Mar 30 20:09 .

drwxr-xr-x 9 strogdon math 4096 Mar 30 20:09 ..

-rw-r--r-- 1 strogdon math   70 Mar 30 20:05 dummy

local/share/gap/pkg/atlasrep/dataword:

total 12

drwxr-xr-x 2 strogdon math 4096 Mar 30 20:09 .

drwxr-xr-x 9 strogdon math 4096 Mar 30 20:09 ..

-rw-r--r-- 1 strogdon math   70 Mar 30 20:05 dummy

And the contents of dummy, in both folders, is:

This file is only for causing that the directory is created by `zoo'.

On Sunday, May 26, 2019 at 5:59:52 PM UTC-5, François Bissey wrote:

Actually this is a little bit more complicated than what I thought. This test is likely to fail

on sage-on-gentoo and probably other distro.

atlasrep is a very naughty gap package that download data from the internet and

wants to put it in its installation directory. Which is a problem for a system wide install

where it belongs to root.

So I adopted some patches from debian to have the data downloaded and stored in

~/.gap. So what we see here in ~/.gap is not a package install but the result of

using atlasrep at any point. It is likely ~/.gap/pkg/AtlasRep will re-appear all by

itself during doctesting.

So we really need to improve on this situation.

1) does gap need to be run with "-r"

2) if it does what do we do about the fact that ~/.gap is skipped when using the pexpect interface.

Francois

On Saturday, May 25, 2019 at 1:21:58 PM UTC+12, François Bissey wrote:

We’ll want some kind of follow up. The test will fail if you have something in ~/.gap.
Not just on sage-on-gentoo.
The question is whether the pexpect interface should continue starting `gap` with the
“-r” option or not.

François

[François Bissey]

I have actual data in one of them.
A little bit of testing show replacing
gap_cmd=“gap -r”
by
gap_cmd=“gap”
in interface/gap.py has no side effects on doctesting apart from letting
the doctest in question pass when ~/.gap is not empty.
I’ll open a ticket later.

François

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[Eric Gourgoulhon]

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

- python2:

  - incremental build (from 8.8.beta5, with -j16) completed, with Sphinx complaining during the doc build:

     formatargspec() is now deprecated.  Please use sphinx.util.inspect.Signature instead

  - all tests from ptestlong passed

- python3:

  - incremental build (from 8.8.beta5, with -j16) completed, with the same Sphinx deprecation warning as with python 2.

  - all tests from ptest-python3 passed

Eric.

[François Bissey]

This is now
https://trac.sagemath.org/ticket/27878

[E. Madison Bray]

The tests should make sure nothing in ~/.gap is ever loaded if at all possible (e.g. update the GAP interfaces to add an option to disable use of ~/.gap` when running the tests, for example)

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[François Bissey]

There is an actual option for that in the test. But in the current state it has
no effect when the expect interface to gap is selected since ~/.gap is already
ignored.

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