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A recent fix in Singular makes computing a certain invariant of modular
cohomology rings of finite groups faster, but another recent fix in
Singular makes the p_group_cohomology package fail.

The new version p_group_cohomology-3.0.1 is supposed to cope with the
changes in Singular. I suggest to base it on top of #24735 and make it a
dependency for #25993 (which contains the above mentioned changes in
Singular).

While I was at it, I also improved more features of the package. Hence,
I propose to upgrade to p_group_cohomology-3.1.

[https://users.fmi.uni-jena.de/cohomology/p_group_cohomology-3.1.tar.xz
Upstream tarball v3.1]

URL: https://trac.sagemath.org/26001
Reported by: SimonKing
Ticket author(s): Simon King
Reviewer(s): Travis Scrimshaw, Dima Pasechnik

Note that self tests require `nose` which is optional only.

Also, the random seeds are not passed as integers, but as
`random.Random` instances, see https://networkx.github.io/documentation/
stable/release/release_2.2.html#improvements

Zipball: https://files.pythonhosted.org/packages/f3/f4/7e20ef40b11847819
1cec0b58c3192f822cace858c19505c7670961b76b2/networkx-2.2.zip

URL: https://trac.sagemath.org/26326
Reported by: tmonteil
Ticket author(s): Thierry Monteil, Dima Pasechnik
Reviewer(s): Volker Braun, Dima Pasechnik

#26326 : reorder creation of random graphs to avoid creating an empty one by bad luck on 32-bit systems.

Starting from somewhere around 8.5.beta the canonical labels given by
Sage and bliss are different on some instances
{{{
sage: G1 = Graph("Cr")
sage: G2 = Graph("C]")
sage: G1 == G2
False
sage: G1.is_isomorphic(G2) and G2.is_isomorphic(G1)
True
sage: G1.canonical_label(algorithm='bliss') == G1
True
sage: G1.canonical_label(algorithm='sage') == G2
True
}}}
That is `Cr` is canonical for bliss while `C]` is canonical for Sage...
More examples:
- 4 vertices: {{{C`}}} vs {{{CK}}}, {{{CR}}} vs {{{CL}}} and {{{Cr}}} vs
{{{C]}}}
- 5 vertices: {{{DGC}}} vs {{{D@O}}}, {{{DAK}}} vs {{{D@S}}}, {{{DC[}}}
vs {{{D@s}}}, {{{DIK}}} vs {{{DBW}}}, {{{DD[}}} vs {{{DBk}}}, {{{DDW}}}
vs {{{DBg}}}, {{{D`{}}} vs {{{DK{}}}, {{{DqK}}} vs {{{DLo}}}, {{{DMk}}}
vs {{{Dbk}}}, {{{DR{}}} vs {{{DL{}}}, {{{DR[}}} vs {{{DJk}}}, {{{Dr{}}}
vs {{{D]{}}}

As a consequence, when bliss is installed, we have the two following
doctest failures in `databases/sql_db.py`.
{{{
sage -t --long src/sage/databases/sql_db.py
**********************************************************************
File "src/sage/databases/sql_db.py", line 956, in
sage.databases.sql_db.SQLDatabase.__init__
Failed example:
    D.show('simon')
Expected:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    CK                   4                    2
    CL                   4                    3
    CN                   4                    4
    C]                   4                    4
    C^                   4                    5
    C~                   4                    6
Got:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    C`                   4                    2
    CR                   4                    3
    CN                   4                    4
    Cr                   4                    4
    C^                   4                    5
    C~                   4                    6
**********************************************************************
File "src/sage/databases/sql_db.py", line 1004, in
sage.databases.sql_db.SQLDatabase.__init__
Failed example:
    E.show('simon')
Expected:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    CK                   4                    2
    CL                   4                    3
    CN                   4                    4
    C]                   4                    4
    C^                   4                    5
    C~                   4                    6
Got:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    C`                   4                    2
    CR                   4                    3
    CN                   4                    4
    Cr                   4                    4
    C^                   4                    5
    C~                   4                    6
**********************************************************************
1 item had failures:
   2 of  26 in sage.databases.sql_db.SQLDatabase.__init__
    [288 tests, 2 failures, 1.59 s]
}}}

URL: https://trac.sagemath.org/26994
Reported by: vdelecroix
Ticket author(s): David Coudert
Reviewer(s): Volker Braun

On some patchbots, I see this:
{{{
sage -t --long src/sage/interfaces/gap.py
**********************************************************************
File "src/sage/interfaces/gap.py", line 1351, in
sage.interfaces.gap.Gap.help
Failed example:
    print(gap.help('SymmetricGroup', pager=False))
Expected:
    <BLANKLINE>
      50.1-... SymmetricGroup
    <BLANKLINE>
      ‣ SymmetricGroup( [filt, ]deg )
─────────────────────────────────── function
    ...
    <BLANKLINE>
Got:
    <BLANKLINE>
    <BLANKLINE>
      50.1-10 SymmetricGroup
    <BLANKLINE>
      > SymmetricGroup( [filt, ]deg )
----------------------------------- function
[..many more lines..]
}}}

This seems to be a matter of unicode output or not.

URL: https://trac.sagemath.org/26987
Reported by: jdemeyer
Ticket author(s): Erik Bray
Reviewer(s): Volker Braun

Trac #26676: Fix var() method for cryptominisat and picosat, which breaks solve_sat for boolean polynomial systems

When I used Sage7.2, I could easily solve my boolean equations with
solve_sat commands, and it's results were verified by the papers and
other tools, but when I upgraded my sage to version 8 (or later version)
I found that the new solve_sat solver (especially when we use
CryptoMiniSat as the SAT solver) doesn't work as correct as before. For
example, when I solve a system of equations via solve_sat which used
CryptoMiniSat as a SAT solver, I get different number of solutions in
different version of SageMath. I believe that there is something wrong
in newer version of SageMath because my previous experiences shows that
the older version's results were verified by the other tools and papers.
I hope someone could solve this problem.

See also the following thread on sage-devel:
https://groups.google.com/forum/?fromgroups#!topic/sage-
devel/2EhgHzGgUnQ

URL: https://trac.sagemath.org/26676
Reported by: gh-hadipourh
Ticket author(s): Thierry Monteil
Reviewer(s): Frédéric Chapoton

otherwise the output may be inconsistent on non-UTF-8 locales

See https://groups.google.com/d/msg/sage-release/MX-
SnQJh8EE/2vNChwf_CQAJ.

~~It looks like rpy2 picks up the systems R.~~

When a symbol has been overloaded, R's {{{help}}} doesn't pick the right
symbol.

URL: https://trac.sagemath.org/26791
Reported by: gh-timokau
Ticket author(s): Timo Kaufmann
Reviewer(s): Emmanuel Charpentier

As reported on [https://groups.google.com/d/msg/sage-
release/l635YEuT7Hs/WkHCnmWhAQAJ sage-release 8.3.beta3],

{{{
sage -tp --optional=sage,internet --logfile=logs/25501.log
src/sage/symbolic/integration/integral.py
src/sage/symbolic/integration/external.py
}}}

gives

{{{
**********************************************************************
File "src/sage/symbolic/integration/external.py", line 65, in
sage.symbolic.integration.external.mma_free_integrator
Failed example:
    mma_free_integrator(sin(x), x) # optional - internet
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
packages/sage/doctest/forker.py", line 572, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
packages/sage/doctest/forker.py", line 982, in compile_and_execute
        exec(compiled, globs)
      File "<doctest
sage.symbolic.integration.external.mma_free_integrator[1]>", line 1, in
<module>
        mma_free_integrator(sin(x), x) # optional - internet
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
packages/sage/symbolic/integration/external.py", line 97, in
mma_free_integrator
        page =
page[page.index('"inputForm"'):page.index('"outputForm"')]
    ValueError: substring not found
**********************************************************************

...

----------------------------------------------------------------------
sage -t src/sage/symbolic/integration/external.py  # 3 doctests failed
sage -t src/sage/symbolic/integration/integral.py  # 1 doctest failed
----------------------------------------------------------------------
}}}

It can be reproduced with:

{{{
sage: from sage.symbolic.integration.external import mma_free_integrator
sage: mma_free_integrator(sin(x), x)

...
ValueError: substring not found
}}}

URL: https://trac.sagemath.org/25501
Reported by: slabbe
Ticket author(s): Sébastien Labbé, Amaury Pouly
Reviewer(s): Frédéric Chapoton

URL: https://trac.sagemath.org/24562
Reported by: embray
Ticket author(s): Erik Bray
Reviewer(s): Frédéric Chapoton

* develop: (73 commits)
  Updated SageMath version to 8.6.beta1
  Fix tox testsuite for sage_bootstrap
  trac 26980 fix script for python3
  trac 26978 remove module finite_class from doc
  a little firework of typos
  remove FiniteCombinatorialClass after #13552
  remove some deprecated thing in combinat/partition
  remove deprecated things in combinat/integer_vector
  remove deprecated argument handling in symbolic integration
  remove deprecated interact decorator
  trac #26973: avoid .vertices() in graph_plot.py
  py3: fix doctests in Laurent polynomials
  py3: some minor fix fox traveling salesman
  trac 26953 : fallback for systems having only python3 command
  fix some fricas doctests for conversions of rings
  disable doctesting of these modules
  followup to #22626: adds a prerm script to the gap SPKG
  suppress "#I.." warnings
  Add the generic InfoWarning info class to the 'standard' GAP globals
  explicitly calling libgap.set_seed(0) for these tests allows consistent results for them
  ...

{{{
Traceback (most recent call last):
  File "/var/lib/buildbot/slave/sage_git/build/build/bin/sage-download-
file", line 28, in <module>
    run_safe()
  File "/var/lib/buildbot/slave/sage_git/build/build/bin/../sage_bootstr
ap/download/cmdline.py", line 119, in run_safe
    except StandardError as error:
NameError: name 'StandardError' is not defined
}}}

URL: https://trac.sagemath.org/26980
Reported by: vbraun
Ticket author(s): Frédéric Chapoton
Reviewer(s): Volker Braun

URL: https://trac.sagemath.org/26979
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

after #13552

URL: https://trac.sagemath.org/26978
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

after #13072

URL: https://trac.sagemath.org/26977
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

after #12453

URL: https://trac.sagemath.org/26976
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

after #12438

URL: https://trac.sagemath.org/26975
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

after #22636

URL: https://trac.sagemath.org/26974
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

URL: https://trac.sagemath.org/26973
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Frédéric Chapoton

URL: https://trac.sagemath.org/26972
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

by not sorting the connected components

URL: https://trac.sagemath.org/26971
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): David Coudert

`QQbar` and `AA` are very slow, to the point of often being unusable.
There are many reasons to that (see #18333), including computations
being triggered when they shouldn't, internal operations that construct
elements of large degree, and incomplete of caching in some places. Yet
the most visible issue by far is that, each time a new extension is
constructed internally, we try to optimize its representation using
PARI's `polredbest()`. This is bad, since `polredbest()` can easily take
days for moderately large extensions, and only made worse by other
issues that lead to lots of large extensions being created.

The reasons I can see to call `polredbest()` are:
* to limit the creation of isomorphic number fields (but with no
guarantee that we'll avoid it completely),
* to speed up subsequent computations in these number fields,
* and perhaps also, in simple cases, to make the elements more readable.
None of these is worth letting simple computations hang forever.

This ticket restricts the optimization step using `polredbest()` to
cases where (based on the size of the defining polynomial) it can be
expected to finish in reasonable time.

URL: https://trac.sagemath.org/15600
Reported by: mmezzarobba
Ticket author(s): Marc Mezzarobba
Reviewer(s): Vincent Delecroix