Sage 9.6.beta5 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

55a711e3d6 (tag: 9.6.beta5, trac/develop) Updated SageMath version to 9.6.beta5
4eea459401 Trac #33486: fix indentation (E111) in some pyx files
273836b6ab Trac #33485: maxima docs fail to build if SAGE_SPKG_INSTALL_DOCS=yes
80e28d3e51 Trac #32560: Add auto_scaling option to threejs plots
29feeeab2b Trac #33481: Remove upgrade option description from ./sage --help
11b44ec1b7 Trac #33465: sage.graphs: Use Executable.absolute_filename()
f9df4f8a45 Trac #33464: Deprecate _coerce_try
7ba1752e5e Trac #33436: Documentation addition for Gessel-Reutenauer symmetric function
ca4f346d20 Trac #33321: Implement GradedModulesWithBasis(R).Subobjects() and FilteredModulesWithBasis(R).Subobjects()
f4e532f7bf Trac #33164: fix & refactor caching in EllipticCurve_generic.division_polynomial()
66c1ceff43 Trac #33120: Update plantri to 5.2
93277349a3 Trac #33117: Restore the Condon-Shortley phase in spherical harmonics and fix their derivatives
045292b46e Trac #32609: Remove or tag uses of SR and symbolic functions in combinat, categories, etc.
4842b3b990 Trac #24536: find_local_maximum/minimum() fails with expressions containing complex numbers
ec79bea8cd Trac #33480: Adjust docstrings and doctest in `polyhedron/base6`
3e4d80faf3 Trac #33472: fix title in one species file
005fbbc14d Trac #33459: Make matrix_gfpn_dense.pyx compatible with randomly seeded doctests
4b99c49c24 Trac #25688: Inaccuracy in symbolic series result on 32bit Linux
64cca20548 Trac #33479: adjust error messages in plot/
71973678c2 Trac #33478: more doctests in modules/misc
6fa0bc3b7f Trac #33476: make "standard_coxeter_elements" work more generally
d73b4f4126 Trac #33470: provide size of findstat query result
fa0c93f11c Trac #33467: sage.geometry: Use PalpExecutable(...).absolute_filename()
b9155bf890 Trac #33463: Fix some corner and special cases concerning localization of integral domains
48a3b47536 Trac #33460: adjust error messages in groups/
769709207b Trac #33448: opensuse-tumbleweed: More fplll issues
1b9dbfe1d6 Trac #33347: Enforce MathJax for every page of Sage documentation
7149a31ea3 Trac #33305: cython: Update to 0.29.28
c0aa17e176 Trac #33251: polymake: Update to 4.6
d14aae14f4 Trac #33147: use PARI's ellmul() for elliptic curves over finite fields
0335d0761a Trac #33116: Update pillow to 9.0.1
82fba97b33 Trac #33075: Constant field extension of function fields
950ecf80b5 Trac #32893: Features for palp, polytopes_db, polytopes_db_4d
ed49c68b23 Trac #32736: LU permutation matrix has the wrong base ring
c6092dcc00 Trac #32645: sage.geometry.polyhedron.backend_cdd: Go through sage.features for _cdd_executable
78990d526e Trac #32069: Upgrade jupyterlab to 3.3.x, add "sage -n nbclassic" and "sage -n retrolab"
314d846a6d Trac #31590: Allow passing command to plantri
6376bce02f Trac #31296: sage.features.Executable: Prepend $SAGE_VENV/bin:$SAGE_LOCAL/bin to PATH
20577cc758 Trac #31292: sage.features.Executable: Add method absolute_filename
64f765c246 Trac #27637: Equivariant Ehrhart Theory
6e05da6810 Trac #33398: Upgrade SymPy to 1.10 and update doctests
f250edf043 Trac #30767: Update Python to 3.10.x
eb21746961 Trac #33473: numpy incompatibility when using system python and numpy 1.22 is installed in the system
b21ca55c56 (tag: 9.6.beta4) Updated SageMath version to 9.6.beta4

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.6.beta4 and running ptestlong results in ine new, permanent failure whose replay is :

charpent@zen-book-flip:/usr/local/sage-9$ sage -t --long --warn-long 196.7 --random-seed=324394855732554287454374140314955467178 src/sage/structure/coerce_actions.pyx  # 1 doctest failed
Running doctests with ID 2022-03-12-22-25-19-46f7f3f4.
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 196.7 --random-seed=324394855732554287454374140314955467178 src/sage/structure/coerce_actions.pyx
**********************************************************************
File "src/sage/structure/coerce_actions.pyx", line 773, in sage.structure.coerce_actions.IntegerMulAction._act_
Failed example:
    alarm(0.1); (2^(10^7)) * P
Expected:
    Traceback (most recent call last):
    ...
    AlarmInterrupt
Got:
    (0 : 1 : 0)
**********************************************************************
1 item had failures:
   1 of  15 in sage.structure.coerce_actions.IntegerMulAction._act_
    [150 tests, 1 failure, 0.28 s]
----------------------------------------------------------------------
sage -t --long --warn-long 196.7 --random-seed=324394855732554287454374140314955467178 src/sage/structure/coerce_actions.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.3 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 0.3 seconds
Features detected for doctesting: sage.groups
Pytest is not installed, skip checking tests that rely on it.

HTH,

​

[Volker Braun]

This is from https://trac.sagemath.org/ticket/33147

[Samuel Lelièvre]

2022-03-12 16:28 UTC, Volker Braun:
>
> 55a711e3d6 (tag: 9.6.beta5) Updated SageMath version to 9.6.beta5

Thanks Volker for this new release!

Congratulations on clearing the backlog of positively reviewed tickets:

https://trac.sagemath.org/query?milestone=sage-9.6&status=positive_review
&col=summary&col=dependencies&col=reporter&col=author&col=reviewer&col=cc
&col=component&col=keywords&col=time&col=changetime
&max=999&order=changetime&group=priority

On Debian 10 buster, after `git pull origin develop`
on an existing installation.

```
$ ./bootstrap -q && ./configure -q && make -s V=0
...
***********************************************
make --no-print-directory .../local/var/lib/sage/installed/.dummy
make --no-print-directory .../local/var/lib/sage/installed/.dummy
make --no-print-directory .../local/var/lib/sage/installed/.dummy
make --no-print-directory .../local/var/lib/sage/installed/.dummy
[sagelib-9.6.beta5] installing. Log file: .../logs/pkgs/sagelib-9.6.beta5.log
[sagelib-9.6.beta5] successfully installed.
[sagemath_doc_html-none] installing. Log file:
.../logs/pkgs/sagemath_doc_html-none.log
[sagemath_doc_html-none] error installing, exit status 2. End of log file:
[sagemath_doc_html-none] [reference] structure: 7 todos, 32
index, 0 citations, 31 modules
[sagemath_doc_html-none] [reference] tensor_free_modules: 2
todos, 19 index, 0 citations, 15 modules
[sagemath_doc_html-none] [reference] topology: 0 todos, 14
index, 0 citations, 13 modules
[sagemath_doc_html-none] [reference] valuations: 1 todos, 14
index, 0 citations, 13 modules
[sagemath_doc_html-none] [reference] ... done (509 todos, 2599
index, 1665 citations, 2189 modules)
[sagemath_doc_html-none] [reference] preparing documents...
skipping loading of indexes... done
[sagemath_doc_html-none] [reference] The inventory files are in
local/share/doc/sage/inventory/en/reference.
[sagemath_doc_html-none] Build finished. The built documents can
be found in .../local/share/doc/sage/inventory/en/reference
[sagemath_doc_html-none] [reference] WARNING: failed to reach any
of the inventories with the following issues:
[sagemath_doc_html-none] [reference] intersphinx inventory
'.../local/share/doc/pplpy/objects.inv' not fetchable due to <class
'FileNotFoundError'>: [Errno 2] No such file or directory:
'.../local/share/doc/pplpy/objects.inv'
[sagemath_doc_html-none] [reference] building [html]: targets for
1 source files that are out of date
[sagemath_doc_html-none] [reference] dumping search index in
English (code: en)... done
[sagemath_doc_html-none] [reference] The HTML pages are in
local/share/doc/sage/html/en/reference/references.
[sagemath_doc_html-none] [reference] Extension error
(matplotlib.sphinxext.plot_directive):
[sagemath_doc_html-none] [reference] Handler <function
_copy_css_file at 0x7fa10be9fae8> for event 'build-finished' threw an
exception (exception: [Errno 17] File exists:
'.../local/share/doc/sage/html/en/reference/references/_static')
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none] File "/usr/lib/python3.7/runpy.py",
line 193, in _run_module_as_main
[sagemath_doc_html-none] "__main__", mod_spec)
[sagemath_doc_html-none] File "/usr/lib/python3.7/runpy.py",
line 85, in _run_code
[sagemath_doc_html-none] exec(code, run_globals)
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/__main__.py",
line 2, in <module>
[sagemath_doc_html-none] main()
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/__init__.py",
line 1745, in main
[sagemath_doc_html-none] builder()
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/__init__.py",
line 785, in _wrapper
[sagemath_doc_html-none] getattr(DocBuilder, build_type)(self,
*args, **kwds)
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/__init__.py",
line 135, in f
[sagemath_doc_html-none] runsphinx()
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/sphinxbuild.py",
line 326, in runsphinx
[sagemath_doc_html-none] sys.stderr.raise_errors()
[sagemath_doc_html-none] File
".../local/var/lib/sage/venv-python3.7/lib/python3.7/site-packages/sage_docbuild/sphinxbuild.py",
line 262, in raise_errors
[sagemath_doc_html-none] raise OSError(self._error)
[sagemath_doc_html-none] OSError: WARNING: failed to reach any of
the inventories with the following issues:
[sagemath_doc_html-none]
[sagemath_doc_html-none] Note: incremental documentation
builds sometimes cause spurious
[sagemath_doc_html-none] error messages. To be certain that
these are real errors, run
[sagemath_doc_html-none] "make doc-clean doc-uninstall" first
and try again.
[sagemath_doc_html-none] make[6]: *** [Makefile:24:
doc-html--reference-references] Error 1
[sagemath_doc_html-none] make[5]: *** [Makefile:47:
doc-html-reference] Error 2
[sagemath_doc_html-none] Full log file:
.../logs/pkgs/sagemath_doc_html-none.log
make[4]: *** [Makefile:2905: sagemath_doc_html-SAGE_DOCS-no-deps] Error 2
make[3]: *** [Makefile:2905:
.../local/var/lib/sage/installed/sagemath_doc_html-none] Error 2
make[2]: *** [Makefile:2466: all-start] Error 2

real 27m23,384s
user 35m47,840s
sys 1m40,702s
***************************************************************
Error building Sage.

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

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [Makefile:39: all-start] Error 1
make: *** [Makefile:13: all] Error 2
```

[Eric Gourgoulhon]

On Ubuntu 20.04 running on Xeon E5-2623 + 16 GB RAM:

- incremental build (-j16) from Sage 9.6.beta4 with system python (3.8.10):

  first attempt failed in building Sage doc;

  running  "make doc-clean doc-uninstall" and make again lead to a successful build.

- make ptestlong --> "All tests passed!"

Eric.

[G. M.-S.]

Thanks, Volker.

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

SageMath 9.6.beta5 together with #32207 #33492 #33512 #33522 gives:

macOS 11.6.5 (Big Sur) with Xcode 13.2.1:  make succeeds and make ptestlong gives 3 errors:

----------------------------------------------------------------------
sage -t --long --warn-long 49.3 --random-seed=6666668585394009336185461470756360233 src/sage/interfaces/expect.py  # 2 doctests failed
sage -t --long --warn-long 49.3 --random-seed=6666668585394009336185461470756360233 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed
----------------------------------------------------------------------

The first two

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

disappear when run alone.

The third 

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

is due to the fact that M4RIE fails on this configuration (see https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1). This could be a bug in Xcode 13.2.1.

macOS 12.2.1 (Monterey) with Xcode 13.2.1:  make succeeds and make ptestlong gives only 1 error:

----------------------------------------------------------------------
sage -t --long --warn-long 49.3 --random-seed=6666668585394009336185461470756360233 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://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1). This could be a bug in Xcode 13.2.1.

macOS 12.2.1 (Monterey) with Xcode 13.3:  make succeeds and make ptestlong gives no errors:

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

All tests passed!

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

macOS 12.3 (Monterey) with Xcode 13.3:  make succeeds and make ptestlong gives no errors:

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

All tests passed!

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

On Monterey there were as usual 5 alerts "Pyhton quit unexpectedly", which were ignored.

Guillermo