Sage 9.6.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

43474c96d5 (tag: 9.6.beta6, trac/develop) Updated SageMath version to 9.6.beta6
f43e375fb5 Trac #33505: partial pep8 cleanup in arith/misc.py
8a3ece590f Trac #33502: various small details in code formatting
cbd71f5148 Trac #33491: fix usage of Matplotlib color maps
29f7b5ab37 Trac #33451: Change "hasattr(x, '__call__')" to "callable(x)" etc
5b015213e7 Trac #33122: add torsion_subgroup() method to AdditiveAbelianGroupWrapper
87a2e5724f Trac #32207: homebrew  llvm / clang - followup to #30835
9d867e2bc8 Trac #33541: some more precise unittest assert
fef33af293 Trac #33535: get rid of #py2 outside of explain_pickle
d88ed13837 Trac #33526: igraph, python_igraph: Upgrade, fix system package version check, fix dependencies
9906dcdaa6 Trac #33525: modernize coercion in monsky_washnitzer.py
2b4757d8a1 Trac #33524: fix indentation E111 in some pyx files
6adda63733 Trac #33518: crystals.TensorProduct does not respect super crystals
8aec9c744b Trac #33515: fix W391 in modular
26574b0f82 Trac #33512: Update python3 to 3.10.3
7a7956dd66 Trac #33511: more precise asserts in convex_sets
86b1833506 Trac #33504: sage.graphs, sage.numerical.mip: Remove unnecessary uses of set_binary, set_integer
822f4d0668 Trac #33501: Get rid of sqrt in spherical harmonics
438d5f8d8c Trac #33500: fix and activate pycodestyle E111
6d7ed571fd Trac #33498: Fix random order of cubic braid group elements
41a6910dae Trac #33496: Adjust doctest for interrupting large multiplication
e419b25d9d Trac #33495: Fix tests with networkx 2.7
2345381772 Trac #33494: bitset_intrinsics.h: Fix "expression result unused" warning
cedd9bbb57 Trac #33492: make sure "real" gcc is rejected on macOS
0444bcabf6 Trac #33482: Improve variable declaration and naming of localization of integral domains
fd656d14c5 Trac #33456: GH Actions: Re-add pyright check
53ca6151f2 Trac #32385: Compute the Bergman and augmented Bergman complex of a matroid
6dbf0930e7 Trac #30845: Fixes for the conda-for-Sage-developers installation method, add GH Actions workflow
95307a68b5 Trac #33522: pythran: Update to 0.11.0
3afe1c712a Trac #33440: sage.libs.singular: Do not fail if the Singular binary is not in PATH
3cc2873986 Trac #33437: Add Lehrer-Solomon symmetric function
6e77b3fd5b Trac #33416: Colormaps and contours for complex_plot
a636498287 Trac #33407: sage -t --installed
ff2baed67c Trac #33396: removing some useless ...: in the doc
dce5f06cf9 Trac #33233: sage -t --baseline-stats-path
f06a7f845e Trac #33170: Update doctests for compatibility with ipython 8.x
2fbf359176 Trac #33156: fix wrong results & huge slowdown due to broken caching in .multiplication_by_m()
b8d91ace4f Trac #33141: Fix doctests in sage_setup and sage_docbuild for sage-on-distribution
f30a4c8b06 Trac #32942: Introduce `align_latex` option that allows latex displays aligned left or centered
39de62bca0 Trac #32429: Typos
d79b00d98a Trac #30078: Check for duplicate hyperplanes in arrangements over any base ring
a633cce6f8 Trac #33532: Doctest failure when SAGE_LIB doesn't match `.../site-packages`
9873ee5a57 Trac #33361: configure: Handle the case of SAGE_LOCAL = a system directory with gcc better
dc311dcd82 Trac #32975: Improve doctest interaction with pytest
0e4f121222 Trac #33471: Add pictures to various 2d graphics manual pages
5b20998e56 Trac #33487: Package CyLP
df50acb8cc Trac #33477: Conversion problem between multivariate Laurent polynomial ring and its field of fraction
3c80055420 Trac #33475: deTeX document titles of sage documentation
5b872c9d08 Trac #30717: add "How to cite SageMath" to FAQ
a61c15ecd6 Trac #29631: spkg-configure.m4 for linbox
55a711e3d6 (tag: 9.6.beta5) Updated SageMath version to 9.6.beta5

[John H Palmieri]

I don't see it at any of the mirrors yet...

[Emmanuel Charpentier]

On >Debian testing running on core i5 + 8 GB RAM, upgrading 9.6.beta5 to 9.6.beta6 and running `ptestlong` passes wth no failure at all.

HTH,

[Emmanuel Charpentier]

FWIW, same result on Debian testing running on core i7 + 16 GB RAM.

HTH,

[G. M.-S.]

Thanks, Volker.

This is on Apple Silicon M1 Macs with Homebrew up to date.

For SageMath 9.6.beta6 plus #31924 and #33549 plus make pytest.

macOS 11.6.5 (Big Sur) with Xcode 13.2.1:  make ptestlong gives the usual:

----------------------------------------------------------------------
sage -t --long --warn-long 47.2 --random-seed=204316541266034313354224566486337275355 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed
----------------------------------------------------------------------

namely

**********************************************************************
File "src/sage/matrix/matrix_gf2e_dense.pyx", line 524, in sage.matrix.matrix_gf2e_dense.Matrix_gf2e_dense._multiply_karatsuba
Failed example:
    A._multiply_karatsuba(B) == A._multiply_classical(B)
Expected:
    True
Got:
    False
**********************************************************************

due to the fact that M4RIE fails on this configuration (see https://trac.sagemath.org/ticket/33212 and https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1). This could be an optimization bug in Xcode 13.2.1.

macOS 12.3 (Monterey) with Xcode 13.3:  make ptestlong gives every time 2 errors:

----------------------------------------------------------------------
sage -t --long --warn-long 25.3 --random-seed=214316356171001650843620063896143324610 src/sage/interfaces/expect.py  # 2 doctests failed
----------------------------------------------------------------------

namely

**********************************************************************
File "src/sage/interfaces/expect.py", line 914, in sage.interfaces.expect.Expect._eval_line
Failed example:
    singular.interrupt()
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/interfaces/expect.py", line 920, in sage.interfaces.expect.Expect._eval_line
Failed example:
    singular('2+3')
Expected:
    Singular crashed -- automatically restarting.
    5
Got:
    5
**********************************************************************

but they disappear when run alone.

On Monterey there were as usual several alerts "Pyhton quit unexpectedly", which were ignored.

Guillermo

[Emmanuel Charpentier]

On the same machine, but after installing pytest (with sage -i pytest), I get two permanent failures :

sage -t --long --warn-long 65.8 --random-seed=270444136495851075301247037545414794286 src/sage/tests/cmdline.py  # 1 doctest failed
sage -t --long --warn-long 65.8 --random-seed=270444136495851075301247037545414794286 src/sage/libs/giac/__init__.py  # Timed out

Reproducing the first one :

charpent@p-202-021:/usr/local/sage-9$ sage -t --long --warn-long 65.8 --random-seed=270444136495851075301247037545414794286 src/sage/tests/cmdline.py  # 1 doctest failed
Running doctests with ID 2022-03-28-15-03-04-43712df6.
Git branch: develop
Using --optional=debian,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib
Doctesting 1 file.
sage -t --long --warn-long 65.8 --random-seed=270444136495851075301247037545414794286 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 312, in sage.tests.cmdline.test_executable
Failed example:
    ret
Expected:
    0
Got:
    4
**********************************************************************
1 item had failures:
   1 of 218 in sage.tests.cmdline.test_executable
    [217 tests, 1 failure, 45.65 s]
----------------------------------------------------------------------
sage -t --long --warn-long 65.8 --random-seed=270444136495851075301247037545414794286 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 45.7 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 45.6 seconds
Features detected for doctesting: pandoc
============================= test session starts ==============================
platform linux -- Python 3.9.12, pytest-7.1.1, pluggy-1.0.0
rootdir: /usr/local/sage-9/src, configfile: tox.ini
collected 1 item                                                               

src/sage/tests/cmdline.py E                                              [100%]

==================================== ERRORS ====================================
______________________ ERROR at setup of test_executable _______________________
file /usr/local/sage-9/src/sage/tests/cmdline.py, line 61
  def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False, **kwds):
E       fixture 'args' not found
>       available fixtures: add_imports, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, doctest_namespace, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
>       use 'pytest --fixtures [testpath]' for help on them.

/usr/local/sage-9/src/sage/tests/cmdline.py:61
=========================== short test summary info ============================
ERROR src/sage/tests/cmdline.py::test_executable
=============================== 1 error in 0.01s ===============================

I can’t reproduce the second, which “never” returns>. Interrupting it after ~20 minutes, I get :

^CKilling test src/sage/libs/giac/__init__.py
----------------------------------------------------------------------
Doctests interrupted: 0/1 files tested
----------------------------------------------------------------------
Total time for all tests: 1164.9 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds
Features detected for doctesting: 
^CTraceback (most recent call last):
  File "/usr/local/sage-9/src/bin/sage-runtests", line 153, in <module>
    import pytest
  File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/pytest/__init__.py", line 7, in <module>
    from _pytest.cacheprovider import Cache
  File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/_pytest/cacheprovider.py", line 31, in <module>
    from _pytest.python import Module
  File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/_pytest/python.py", line 1156, in <module>
    class Metafunc:
  File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/_pytest/python.py", line 1204, in Metafunc
    ids: Optional[
  File "/usr/lib/python3.9/typing.py", line 274, in inner
    return cached(*args, **kwds)
  File "/usr/lib/python3.9/typing.py", line 354, in __getitem__
    return self._getitem(self, parameters)
  File "/usr/lib/python3.9/typing.py", line 479, in Optional
    return Union[arg, type(None)]
  File "/usr/lib/python3.9/typing.py", line 274, in inner
    return cached(*args, **kwds)
  File "/usr/lib/python3.9/typing.py", line 354, in __getitem__
    return self._getitem(self, parameters)
  File "/usr/lib/python3.9/typing.py", line 470, in Union
    return _UnionGenericAlias(self, parameters)
  File "/usr/lib/python3.9/typing.py", line 746, in __init__
    self.__parameters__ = _collect_type_vars(params)
  File "src/cysignals/signals.pyx", line 310, in cysignals.signals.python_check_interrupt
KeyboardInterrupt

HTH,

​

Le lundi 28 mars 2022 à 13:32:06 UTC+2, Emmanuel Charpentier a écrit :

[Emmanuel Charpentier]

On the second machine, I get only the first permanent failure ; testing `src/sage/libs/giac/__init__.py` terminates in 288.52s. Go figure...

HTH,

[Dima Pasechnik]

this seems to be https://trac.sagemath.org/ticket/33549
(pytest considers functions and classes named test_<...> as special.)

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[Emmanuel Charpentier]

Might be. But why the failure on one machine and not the other ??? On the machine where the tests completes :

charpent@zen-book-flip:~$ sage -pip list | grep pytest
pytest                        7.1.1

​

[Sébastien Labbé]

With Ubuntu 18.04, and running doctests with few optional/external packages, I get:

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

sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/geometry/polyhedron/base.py  # 1 doctest failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/graphs/graph.py  # 2 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/numerical/backends/glpk_backend.pyx  # 4 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/numerical/mip.pyx  # 8 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py  # 2 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,internet,latex,latex_package_tkz_graph,lualatex,nauty,octave,palp,pandoc,pdf2svg,pdflatex,pdftocairo,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx,xelatex


In the following four files, failures are related to the printing of "Long-step dual simplex will be used" in the output:

sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/geometry/polyhedron/base.py  # 1 doctest failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/numerical/backends/glpk_backend.pyx  # 4 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/numerical/mip.pyx  # 8 doctests failed
sage -t --long --random-seed=4345853567077574058850080858948729205 src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py  # 2 doctests failed

See below for typical failures.

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

sage -t --long --random-seed=232784267613452189426326653797934118933 src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py
**********************************************************************
File "src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py", line 38, in sage.tests.books.computational-mathematics-with-sagemath.lp_doctest
Failed example:
    p.solve() # abs tol 1e-10
Expected:
    8.8
Got:
    Long-step dual simplex will be used
    8.8
**********************************************************************
File "src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py", line 127, in sage.tests.books.computational-mathematics-with-sagemath.lp_doctest
Failed example:
    p.solve() # abs tol 1e-10
Expected:
    1.4199999999999999
Got:
    Long-step dual simplex will be used
    1.42

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

   2 of  69 in sage.tests.books.computational-mathematics-with-sagemath.lp_doctest
    0 tests not run because we ran out of time
    [68 tests, 2 failures, 0.07 s]
sage -t --long --random-seed=232784267613452189426326653797934118933 src/sage/numerical/backends/glpk_backend.pyx
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 1104, in sage.numerical.backends.glpk_backend.GLPKBackend.solve
Failed example:
    p.solve() # rel tol 100
Expected:
    1
Got:
    Long-step dual simplex will be used
    1.0
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 1111, in sage.numerical.backends.glpk_backend.GLPKBackend.solve
Failed example:
    p.solve() # rel tol 100
Expected:
    1
Got:
    Long-step dual simplex will be used
    5.0
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 1204, in sage.numerical.backends.glpk_backend.GLPKBackend.best_known_objective_bound
Failed example:
    p.solve() # rel tol 100
Expected:
    1.0
Got:
    Long-step dual simplex will be used
    1.0
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 1238, in sage.numerical.backends.glpk_backend.GLPKBackend.get_relative_objective_gap
Failed example:
    p.solve() # rel tol 100
Expected:
    1.0
Got:
    Long-step dual simplex will be used
    1.0
**********************************************************************
3 items had failures:
   1 of  11 in sage.numerical.backends.glpk_backend.GLPKBackend.best_known_objective_bound
   1 of  12 in sage.numerical.backends.glpk_backend.GLPKBackend.get_relative_objective_gap
   2 of  74 in sage.numerical.backends.glpk_backend.GLPKBackend.solve
    0 tests not run because we ran out of time
    [592 tests, 4 failures, 4.20 s]