Sage 9.5.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 

 6ec717a56d (trac/develop, tag: 9.5.beta6) Updated SageMath version to 9.5.beta6

fda367752b Trac #32724: Replace "... is SR" by isinstance(..., sage.rings.abc.SymbolicRing) to handle symbolic subrings

470c171913 Trac #32650: sage.misc.latex: Replace have_... functions by Features

741cb457a8 Trac #32602: Magma interface throws segfault

ad454f613b Trac #32587: upgrade gsl to version 2.7

f4f555cc95 Trac #32508: Eliminate use of __init__.py files for supplying package docstrings

29a9c27e35 Trac #32836: Work around clobbering of PATH on initialization of libsingular from system singular

b3ce5f4843 Trac #32061: New SPKG for GNU gengetopt

813c94ef62 Trac #32818: TypeError raised after a successful doctest when pytest is installed

d3a570f495 Trac #32732: sage.geometry: More # optional for test with examples that need sage.combinat, sage.rings.number_field, sage.plot

a44476579f Trac #32424: Upgrade to OpenBLAS 0.3.18 and make Sage fat binaries portable

4327983ea8 Trac #32817: Fix two tests failing at random

a3b4810595 Trac #31527: spkg-configure.m4 for polymake

8cbffb96aa Trac #32799: Explicitly set MPMATH_SAGE env variable

ef03d4459c Trac #32794: sage.functions.log.log: Move to sage.misc.functional

ec8a1b8b32 Trac #32793: removing another wave of py2 / py3 doctest tags

e148e86743 Trac #32790: fix E713 and E714 in modular/

3fddb00aa4 Trac #32719: sage.rings.abc: Add documentation/tests as done in sage.geometry.abc

607c4688e9 Trac #32306: int overflow in multiplicities computations in strongly_regular_graph

b4bb35e070 Trac #32751: Reinstallation of dependencies of setuptools_scm fails with packaging-related packages

c15692220a Trac #32783: random doctest failure in src/sage/graphs/generic_graph.py

9d06a54f0c Trac #32781: SAGE_CHECK='warn' is broken

a35e2c5c98 Trac #32776: split convex set methods of polyhedra into base1.py

32cfd6ff5a Trac #32775: Mostly fix slow down by #30022

1277457340 Trac #32774: Bug in continued fraction doctest

0ddec55ee2 Trac #32772: Fix two random test failures in graphs

99b5174789 Trac #32771: Fix incorrect doctest introduced in #29978

7e8ac9f7f8 Trac #32769: sage.categories.coxeter_groups: Remove module-level imports from sage.rings, sage.graphs

10eefaecf4 Trac #32767: Split initialization and basic access of polyhedra out as a separate module

1012c70fcc Trac #32766: fix E713 and E714 in matrix, modules, groups

f097900004 Trac #32762: fix E713 and E714 in algebras, categories, sets, etc

9d1f3131ee Trac #32760: Update database_knotinfo to 2021.10.1

caa4d1858a Trac #32750: sage.rings.abc: Add pAdicRing, pAdicField; deprecate is_pAdic...

37d880bc20 Trac #32748: clean the processing of networkx (Multi)(Di)Graph in the (Di)Graph constructor

89d2a53015 Trac #32742: Use sage.rings.abc.RealField, sage.rings.abc.ComplexField more

9c23f2a2c2 Trac #32734: Remove .all import of infinity

e6fb2820c2 Trac #32731: Avoid ceil, floor from sage.functions.other in non-symbolic uses

0986d36585 Trac #32730: Import Expression from sage.structure.element

6e741ff32c Trac #32725: Modularization changes in sage.modules, sage.matrix

154137a687 Trac #32701: sage.rings.{real,complex}_double: Remove compile time dependency on cypari2

71bf351939 Trac #32677: sage.rings.real_double: Move methods using GSL to a separate extension module

2b36f5d4cf Trac #32641: Decentralize sage.rings.numbers_abc

e3c14c2930 Trac #32625: Parent._is_numerical, _is_real_numerical - remove hard dependency on real_mpfr, complex_mpfr

c855f39449 Trac #32357: Implement derivative for modular forms and quasimodular forms

906387d5e4 Trac #31385: Improve interface of list_packages

e786d48c21 Trac #32746: fedora-{26,27,...,34}-minimal: scipy build fails - openblas not found

4267a3130b Trac #32745: slackware-14.2-standard: conway_polynomials, elliptic_curves: Installation fails

f716a0b366 (tag: 9.5.beta5,) Updated SageMath version to 9.5.beta5

[Matthias Köppe]

On Friday, November 12, 2021 at 2:58:48 PM UTC-8 Volker Braun 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 

 6ec717a56d (trac/develop, tag: 9.5.beta6) Updated SageMath version to 9.5.beta6

Thanks, Volker, for preparing the new beta.

A quick look at the portability status as tested on GH Actions at https://github.com/sagemath/sage/actions/runs/1455057668:

ubuntu-{trusty,xenial,bionic,focal}, debian-{jessie,stretch}: Clean

debian-buster-standard (https://github.com/sagemath/sage/runs/4195320940): A failure related to linbox

sage -t --random-seed=297515214631081454774021642286369805588 src/sage/matrix/matrix_integer_dense.pyx

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

File "src/sage/matrix/matrix_integer_dense.pyx", line 3706, in sage.matrix.matrix_integer_dense.Matrix_integer_dense.determinant

Failed example:

    A.determinant(algorithm='linbox',proof=False) == d

Expected:

    True

Got:

    False

ubuntu-groovy-standard, debian-bullseye-standard: Severe numerics problems (https://trac.sagemath.org/ticket/31621), also the same failure related to linbox.

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/geometry/polyhedron/base.py  # 1 doctest failed

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/geometry/polyhedron/library.py  # 1 doctest failed

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/matrix/matrix_double_dense.pyx  # 1 doctest failed

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/matrix/matrix_integer_dense.pyx  # 1 doctest failed

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/stats/time_series.pyx  # 8 doctests failed

sage -t --random-seed=181813248514244772040490537802294480955 src/sage/tests/books/computational-mathematics-with-sagemath/float_doctest.py  # 1 doctest failed

ubuntu-hirsute-standard (https://github.com/sagemath/sage/runs/4195320730): Abort in glp_free

sage -t --random-seed=239469024450973543529159161026976515160 src/sage/numerical/linear_tensor_element.pyx

glp_free: memory allocation error

Error detected in file env/alloc.c at line 70

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

/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0x8614)[0x7f6cb66aa614]

/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0x86c9)[0x7f6cb66aa6c9]

/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0xb763)[0x7f6cb66ad763]

/lib/x86_64-linux-gnu/libpthread.so.0(+0x141f0)[0x7f6cb767e1f0]

/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f6cb74bcfbb]

/lib/x86_64-linux-gnu/libc.so.6(abort+0x116)[0x7f6cb74a2864]

/lib/x86_64-linux-gnu/libglpk.so.40(+0x5b45)[0x7f6c5e6fcb45]

/lib/x86_64-linux-gnu/libglpk.so.40(+0x53a93)[0x7f6c5e74aa93]

/lib/x86_64-linux-gnu/libglpk.so.40(+0x63397)[0x7f6c5e75a397]

/lib/x86_64-linux-gnu/libglpk.so.40(+0x172bc)[0x7f6c5e70e2bc]

/lib/x86_64-linux-gnu/libglpk.so.40(glp_delete_prob+0x23)[0x7f6c5e7111e3]

/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/numerical/backends/glpk_backend.cpython-39-x86_64-linux-gnu.so(+0x124e5)[0x7f6c5e7e14e5]

/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/numerical/mip.cpython-39-x86_64-linux-gnu.so(+0xfc15)[0x7f6c62a93c15]

python3[0x505837]

python3[0x5f804e]

python3[0x52c3bc]

python3(_PyObject_GenericGetAttrWithDict+0x65d)[0x52b71d]

    Killed due to abort

ubuntu-impish (https://github.com/sagemath/sage/runs/4195320765): cysignals build failure (https://trac.sagemath.org/ticket/32576) and pyzmq build failure (https://trac.sagemath.org/ticket/32828 - needs review)

[Enrique Artal]

In Fedora 35 it builds  applying https://trac.sagemath.org/ticket/32828 and the proposed solution of https://trac.sagemath.org/ticket/32576

[Dima Pasechnik]

With the latest Python 3.9, I need to apply
https://trac.sagemath.org/ticket/32852

Dima

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[Eric Gourgoulhon]

On Ubuntu 20.04 running on Xeon E5-2623 + 16 GB RAM:
- incremental build (-j16) from 9.5.beta5, with system python (3.8.10): OK

- make ptestlong results in 1 failure:

**********************************************************************
File "src/sage/plot/plot.py", line 1782, in sage.plot.plot.plot
Failed example:
    plot(f, (x, -3.5, 3.5), detect_poles='show', exclude=[-3..3], ymin=-5, ymax=5)
Expected:
    Graphics object consisting of 12 graphics primitives
Got:
    Graphics object consisting of 13 graphics primitives
**********************************************************************

Strangely, the test is passed when run standalone:

./sage -t --long src/sage/plot/plot.py
Running doctests with ID 2021-11-16-11-30-56-31426e61.
Git branch: develop
Using --optional=build,debian,dochtml,pip,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 66.6 --random-seed=321008040313156700460941679315322569825 src/sage/plot/plot.py
    [461 tests, 61.81 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 61.9 seconds
    cpu time: 58.9 seconds
    cumulative wall time: 61.8 seconds

I am wondering how can one have 13 graphics primitives in ptestlong and 12 in standalone mode...

Eric.

[Sébastien Labbé]

On Ubuntu 18.04, testing with few optional and external packages gives:

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

sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/databases/findstat.py  # 9 doctests failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/finance/stock.py  # 1 doctest failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/interfaces/fricas.py  # 1 doctest failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/sat/solvers/dimacs.py  # 2 doctests failed
sage -t --long --random-seed=132752562576186471630888746423217429031 src/sage/tests/cmdline.py  # 10 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,internet,latex,lualatex,octave,pandoc,pdf2svg,pdflatex,xelatex

Rerunning failed tests gives the same list.

The failure with fricas is new (copied below).

The number of failures for cmdline.py increased from 2 to 10 (they are copied below).

Other failures are not new.

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




sage -t --long --random-seed=95793739889582718715876286644092626071 src/sage/interfaces/fricas.py
**********************************************************************
File "src/sage/interfaces/fricas.py", line 1193, in sage.interfaces.fricas.FriCASElement._latex_
Failed example:
    latex(fricas("integrate(sin(x+1/x),x)"))                      # optional - fricas
Expected:
    \int ^{\displaystyle x} {{\sin \left( {{{{{ \%O} ^{2}}+1} \over  \%O}} \right)} \  {d \%O}}
Got:
    \int ^{\displaystyle x} {{\sin \left( {{{{{ \%A} ^{2}}+1} \over  \%A}} \right)} \  {d \%A}}
**********************************************************************
1 item had failures:
   1 of   4 in sage.interfaces.fricas.FriCASElement._latex_
    2 0.1 tests not run
    1 test not run due to known bugs
    3 not tested tests not run
    2 tol tests not run
    0 tests not run because we ran out of time
    [277 tests, 1 failure, 45.74 s]





sage -t --long --random-seed=95793739889582718715876286644092626071 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 596, in sage.tests.cmdline.test_executable
Failed example:
    out.find("cython") >= 0  # optional - internet
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/tests/cmdline.py", line 598, in sage.tests.cmdline.test_executable
Failed example:
    err  # optional - internet
Expected:
    ''
Got:
    'Traceback (most recent call last):\n  File "/home/slabbe/GitBox/sage/src/bin/sage-list-packages", line 102, in <module>\n    pkg.installed_version = pkg.installed_version or \'not_installed\'\nAttributeError: can\'t set attribute\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 600, in sage.tests.cmdline.test_executable
Failed example:
    ret  # optional - internet
Expected:
    0
Got:
    1
**********************************************************************
File "src/sage/tests/cmdline.py", line 604, in sage.tests.cmdline.test_executable
Failed example:
    out.find("database_cremona_ellcurve") >= 0  # optional - internet
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/tests/cmdline.py", line 606, in sage.tests.cmdline.test_executable
Failed example:
    err  # optional - internet
Expected:
    ''
Got:
    '/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/sage/misc/package.py:117: UserWarning: failed to fetch the version of pkg=\'ore_algebra\' at https://pypi.org/pypi/ore_algebra/json\n  warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url))\nTraceback (most recent call last):\n  File "/home/slabbe/GitBox/sage/src/bin/sage-list-packages", line 102, in <module>\n    pkg.installed_version = pkg.installed_version or \'not_installed\'\nAttributeError: can\'t set attribute\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 608, in sage.tests.cmdline.test_executable
Failed example:
    ret  # optional - internet
Expected:
    0
Got:
    1
**********************************************************************
File "src/sage/tests/cmdline.py", line 612, in sage.tests.cmdline.test_executable
Failed example:
    out.find("valgrind") >= 0  # optional - internet
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/tests/cmdline.py", line 614, in sage.tests.cmdline.test_executable
Failed example:
    err  # optional - internet
Expected:
    ''
Got:
    'Traceback (most recent call last):\n  File "/home/slabbe/GitBox/sage/src/bin/sage-list-packages", line 102, in <module>\n    pkg.installed_version = pkg.installed_version or \'not_installed\'\nAttributeError: can\'t set attribute\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 616, in sage.tests.cmdline.test_executable
Failed example:
    ret  # optional - internet
Expected:
    0
Got:
    1
**********************************************************************
File "src/sage/tests/cmdline.py", line 732, in sage.tests.cmdline.test_executable
Failed example:
    print(open(output, 'r').read() == t)          # optional - pandoc
Expected:
    True
Got:
    False
**********************************************************************
1 item had failures:
  10 of 250 in sage.tests.cmdline.test_executable
    3 gdb tests not run
    4 r tests not run
    0 tests not run because we ran out of time
    [249 tests, 10 failures, 48.27 s]

[Sébastien Labbé]

The 9 failing doctests in cmdline.py are related to the fact that sage --standard, sage --optional and sage --experimental are currently broken. I created ticket https://trac.sagemath.org/ticket/32885

for it.

[Emmanuel Charpentier]

FWIW (and belatedly…), on Debian testing, upgrading a freshly-rebuilt 9.5.beta2 to 9.5.beta6leads to one (permanent)ptesttlong` failure:

sage -t --long --random-seed=74846359479693131545811923291043381414 src/sage/lfunctions/pari.py  # 1 doctest failed

Re-running this doctests shows :

charpent@p-202-021:/usr/local/sage-9$ sage -t --long --random-seed=74846359479693131545811923291043381414 src/sage/lfunctions/pari.py 
Running doctests with ID 2021-11-18-16-05-31-e48e9c5b.
Git branch: develop
Using --optional=build,debian,dochtml,pip,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 72.2 --random-seed=74846359479693131545811923291043381414 src/sage/lfunctions/pari.py
**********************************************************************
File "src/sage/lfunctions/pari.py", line 318, in sage.lfunctions.pari.lfun_number_field
Failed example:
    L(0)
Expected:
    0.000000000000000
Got:
      ***   Warning: normalizing a series with 0 leading term.
    0.000000000000000
**********************************************************************
1 item had failures:
   1 of   8 in sage.lfunctions.pari.lfun_number_field
    [166 tests, 1 failure, 0.82 s]
----------------------------------------------------------------------
sage -t --long --warn-long 72.2 --random-seed=74846359479693131545811923291043381414 src/sage/lfunctions/pari.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 5.9 seconds
    cpu time: 0.7 seconds
    cumulative wall time: 0.8 seconds
Pytest is not installed, skip checking tests that rely on it.

… that this is essentially a cosmetic bug.

Note that upgrading this system to 9.5.beta2 somehow led to a large number of ptestlong failures, leading me to rebuild from scratch (i. e. after make distclean).

HTH,

​

[Antonio Rojas]

See https://trac.sagemath.org/ticket/32797 (needs review)