Sage 9.3.beta3 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 

ca088c9c93 (tag: 9.3.beta3, trac/develop) Updated SageMath version to 9.3.beta3

3290413be6 Trac #30747: Deprecate sage.misc.package functions standard_packages, optional_packages, experimental_packages

d312143740 Trac #30580: sage_setup: Remove import-time dependency (`setup_requires`) on `pkgconfig`, `numpy`

52b91c88ce Trac #31012: Modify RandomChordalGraph according a deprecation warning introduced in Python 3.9

660cac43a2 Trac #30990: flake8 details in parent.pyx

09971a9476 Trac #30986: add module tree_decomposition.pyx

a540625234 Trac #30976: incidence_structures.py tries to import 'warn' from the wrong module

14e3c694a0 Trac #30975: Silence packaging 20.5 deprecation warnings

5fadc42c3b Trac #30963: remove CombinatorialClass in graph_path.py

3fb2f3eab9 Trac #30961: Fix valid input types for NumberField element constructor

e97b79ea1c Trac #30951: tox.ini, build/bin/write-dockerfile.sh: Simplify by using new options of "sage -package list"

9502bb0cc1 Trac #30921: Fix verbose "epsilon" output in polynomial small roots

313d0b7c47 Trac #30346: Exception for the unknot in Homfly-PT polynomial

0229ac6fd5 Trac #27921: Script package for checking presence of system libxml2 (polymake and igraph prerequisite)

e3e45a122f Trac #30995: Repair setting of SAGE_NUM_THREADS during build

de62cc35da Trac #30903: Fix broken symlink to documentation in the Sage jupyter kernelspec

4722b13a2b Trac #30891: Normaliz cone from precomputed data has lattice messed up

d40e7902c5 Trac #30579: Clean up sage_setup.library_order

c3d9bf77a6 Trac #30965: fix precision in Padé method of power series

768bd5117a Trac #30960: Update/fix top-level makefile target fast-rebuild-clean (used in Docker build)

169d6aeb7a Trac #30959: almost get rid of "_multiply_basis"

409d545873 Trac #30954: Implement a proper equality check for polyhedron representation objects

42a76a6037 Trac #30935: Fix IP is none error in doctests

97edd4674e Trac #30929: GH Actions: Update macos test environments

130d7d1199 Trac #30925: Multizeta does not copy its argument

f4909e1cb9 Trac #30915: Three.js: Upgrade to r122

66c1a87a12 Trac #30895: Developers' guide: Update "Packaging Third-Party Code" regarding upstream_url

d7b71743c2 Trac #30850: No Future

b4c0f6d0c3 Trac #30624: Improve wording and formatting of configure's recommendation message

e7369840f0 Trac #22731: Replace "$SAGE_LOCAL/bin" by more specific variables to make Sage easier to package, use in venvs

17132a6832 Trac #9407: fixed fields for dirichlet characters and conductors and dirichlet characters for abelian fields

2e4c869c9f Trac #30958: Remove C99 syntax in data_structures/bitset_intrinsics.h

f844baa06b Trac #30928: Backslash line continuation broken when defining a callable symbolic expression

755a789d99 Trac #30752: switch the default mp library to gmp

9a9dea3ab4 Trac #30529: Use reference instead of pointer to simplify code

b0aafbd101 Trac #28745: Add SAGE_ROOT/environment.yml for "conda env create -f".

57a72ba9b4 Trac #30946: Add "minimal=True" option to affine_hull_projection

d5221469dc Trac #30941: let monoid algebras be bialgebras

98e615fae3 Trac #30939: is_primitive and is_grouplike for bialgebra elements

02df5b9a74 Trac #30931: refresh yang baxter graph file

d47fefd2bc Trac #30865: sage_bootstrap: Update/extend "sage -package", fix "make download"

e846153d99 Trac #30859: Add more debian system package information, including packages without spkg-configure.m4

809db9f6ad Trac #30842: Genus representatives

d85bedb6d5 Trac #30432: Slice Doesn't Work For Unramified or 2-Step Padic Extensions

2ed5a13e21 Trac #30015: Schlegel projection breaks convexity

164b7ea000 Trac #29286: sage -package create: Fix argument handling

0372dd9633 Trac #30910: GH Actions: Fixes for WSL workflow

720fac06c4 Trac #30777: Improve deleting of edges of graphs

2458f594bf Trac #30745: Allow using arb, flint and ntl from Homebrew

97c6b930bd Trac #30559: Refine python3's SAGE_SPKG_DEPCHECK: Remove sqlite

020bd59ec2 (tag: 9.3.beta2) Updated SageMath version to 9.3.beta2

[Sébastien Labbé]

On Ubuntu 18.04, testing various optional and external packages, and using

--optional=4ti2,cbc,ccache,cryptominisat,database_jones_numfield,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,libnauty,lidia,lrslib,memlimit,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg

I get:

----------------------------------------------------------------------
sage -t --long --warn-long 73.3 --random-seed=0 src/sage/interfaces/singular.py  # Killed due to segmentation fault
sage -t --long --warn-long 73.3 --random-seed=0 src/sage/sat/boolean_polynomials.py  # 1 doctest failed
sage -t --long --warn-long 73.3 --random-seed=0 src/sage/databases/findstat.py  # 1 doctest failed
sage -t --long --warn-long 73.3 --random-seed=0 src/sage/databases/oeis.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

Rerunning failed tests, I obtain:

----------------------------------------------------------------------
sage -t --long --warn-long 71.7 --random-seed=0 src/sage/databases/findstat.py  # 1 doctest failed
sage -t --long --warn-long 71.7 --random-seed=0 src/sage/databases/oeis.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: internet

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

Failures are copied below.

sage -t --long --warn-long 71.7 --random-seed=0 src/sage/databases/findstat.py
**********************************************************************
File "src/sage/databases/findstat.py", line 1247, in sage.databases.findstat.findmap
Failed example:
    findmap("Dyck paths", "Set partitions", lambda D: [(a+1, b) for a,b in D.tunnels()]) # optional -- internet
Expected:
    0: Mp00092oMp00146 (quality [50])
Got:
    0: Mp00092oMp00146 (quality [68])
**********************************************************************
1 item had failures:
   1 of  12 in sage.databases.findstat.findmap
    11 webbrowser tests not run
    0 tests not run because we ran out of time
    [392 tests, 1 failure, 34.88 s]


sage -t --long --warn-long 71.7 --random-seed=0 src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 989, in sage.databases.oeis.OEISSequence.keywords
Failed example:
    f.keywords()                          # optional -- internet
Expected:
    ('nonn', 'fini', 'full')
Got:
    ('nonn', 'fini', 'full', 'changed')
**********************************************************************
1 item had failures:
   1 of   7 in sage.databases.oeis.OEISSequence.keywords
    5 webbrowser tests not run
    0 tests not run because we ran out of time
    [290 tests, 1 failure, 39.62 s]

[Clemens Heuberger]

I get (Linux Mint 19.3 Tricia):

$ LANG=C ./sage -t --long --random-seed=0 src/sage/tests/cmdline.py
Running doctests with ID 2020-12-07-09-45-22-291831e7.
Using --optional=build,ccache,debian,dochtml,memlimit,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 44.1 --random-seed=0 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 592, in sage.tests.cmdline.test_executable
Failed example:
out.startswith("3.")
Expected:
True
Got:
False
**********************************************************************
File "src/sage/tests/cmdline.py", line 594, in sage.tests.cmdline.test_executable
Failed example:
err
Expected:
''
Got:
'/local/cheuberg/local/sage-9.3.beta3/src/bin/sage: line 571: exec:
sqlite3: not found\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 596, in sage.tests.cmdline.test_executable
Failed example:
ret
Expected:
0
Got:
127

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

3 of 231 in sage.tests.cmdline.test_executable
[230 tests, 3 failures, 26.02 s]
----------------------------------------------------------------------
sage -t --long --warn-long 44.1 --random-seed=0 src/sage/tests/cmdline.py # 3
doctests failed
----------------------------------------------------------------------
Total time for all tests: 26.1 seconds
cpu time: 0.3 seconds
cumulative wall time: 26.0 seconds




Am 07.12.20 um 00:37 schrieb Volker Braun:

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[Kenji Iohara]

On Mac OS 11.0.1, the first built worked without problem. 

2020年12月7日(月) 9:50 Clemens Heuberger <clemens....@aau.at>:

To unsubscribe from this group and stop receiving emails from it, send an email to sage-release...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/d6f55bf1-28a3-fdf1-30b7-31b0d4b2799a%40aau.at.

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, rebuilding 9.3.beta3 (due to a change of system’s python version) configured to use all available system packages leads to :

• ./configure insists on installing texlive-generic-extra, texlive-xetex, latexmk, pandoc, dvipng, default-jdk, ffmpeg, libavdevice-dev and pari-gp2c, notwithstanding the fact that all of them are already installed

• ptestlong results in one transient and three permanent failures, on of them (trace.py)seen in previous versions :

File	Results	P/T
src/sage/functions/other.py	1 doctest failed	P
src/sage/interfaces/sagespawn.pyx	1 doctest failed	T
src/sage/misc/trace.py	1 doctest failed	P
src/sage/groups/abelian_gps/abelian_group_gap.py	1 doctest failed	P

The permanent failures are as follows :

Running doctests with ID 2020-12-07-16-41-18-dd0455c6.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/functions/other.py
**********************************************************************
File "src/sage/functions/other.py", line 1628, in sage.functions.other.Function_factorial._eval_
Failed example:
    factorial(float(3.2))        # abs tol 1e-14
Expected:
    7.7566895357931776
Got:
    doctest:warning
      File "/usr/local/sage-9/src/bin/sage-runtests", line 182, in <module>
        err = DC.run()
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/control.py", line 1236, in run
        self.run_doctests()
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/control.py", line 937, in run_doctests
        self.dispatcher.dispatch()
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 2040, in dispatch
        self.parallel_dispatch()
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 1935, in parallel_dispatch
        w.start()  # This might take some time
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 2207, in start
        super(DocTestWorker, self).start()
      File "/usr/lib/python3.9/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/lib/python3.9/multiprocessing/context.py", line 277, in _Popen
        return Popen(process_obj)
      File "/usr/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/lib/python3.9/multiprocessing/popen_fork.py", line 71, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
        self.run()
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 2179, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 2508, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 2555, in _run
        result = runner.run(test)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 906, in run
        return self._run(test, compileflags, out)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 1133, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.functions.other.Function_factorial._eval_[8]>", line 1, in <module>
        factorial(float(RealNumber('3.2')))        # abs tol 1e-14
      File "/usr/lib/python3.9/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    DeprecationWarning: Using factorial() with floats is deprecated
    7.756689535793181
**********************************************************************
1 item had failures:
   1 of  11 in sage.functions.other.Function_factorial._eval_
    [485 tests, 1 failure, 12.62 s]
----------------------------------------------------------------------
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/functions/other.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 12.7 seconds
    cpu time: 17.8 seconds
    cumulative wall time: 12.6 seconds

Running doctests with ID 2020-12-07-16-41-50-6b956c8f.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/misc/trace.py
**********************************************************************
File "src/sage/misc/trace.py", line 66, in sage.misc.trace.trace
Failed example:
    print(s.before[s.before.find(b'--'):].decode())
Expected:
    --...
    ipdb> c
    2 * 5
Got:
    --Call--
    > <CSI-0;32m>/usr/local/sage-9/local/lib/python3.9/site-packages/sage/arith/misc.py<CSI-0m>(2422)<CSI-0;36m>factor<CSI-0;34m>()<CSI-0m>
    <CSI-0;32m>   2420 <CSI-0;31m><CSI-0;34m><CSI-0m><CSI-0m>
    <CSI-0m><CSI-0;32m>   2421 <CSI-0;31m><CSI-0;34m><CSI-0m><CSI-0m>
    <CSI-0m><CSI-0;32m>-> 2422 <CSI-0;31m><CSI-0;32m>def<CSI-0m> <CSI-0m>factor<CSI-0m><CSI-0;34m>(<CSI-0m><CSI-0m>n<CSI-0m><CSI-0;34m>,<CSI-0m> <CSI-0m>proof<CSI-0m><CSI-0;34m>=<CSI-0m><CSI-0;32m>None<CSI-0m><CSI-0;34m>,<CSI-0m> <CSI-0m>int_<CSI-0m><CSI-0;34m>=<CSI-0m><CSI-0;32m>False<CSI-0m><CSI-0;34m>,<CSI-0m> <CSI-0m>algorithm<CSI-0m><CSI-0;34m>=<CSI-0m><CSI-0;34m>'pari'<CSI-0m><CSI-0;34m>,<CSI-0m> <CSI-0m>verbose<CSI-0m><CSI-0;34m>=<CSI-0m><CSI-0;36m>0<CSI-0m><CSI-0;34m>,<CSI-0m> <CSI-0;34m>**<CSI-0m><CSI-0m>kwds<CSI-0m><CSI-0;34m>)<CSI-0m><CSI-0;34m>:<CSI-0m><CSI-0;34m><CSI-0m><CSI-0;34m><CSI-0m><CSI-0m>
    <CSI-0m><CSI-0;32m>   2423 <CSI-0;31m>    """
    <CSI-0m><CSI-0;32m>   2424 <CSI-0;31m>    <CSI-0m>Return<CSI-0m> <CSI-0m>the<CSI-0m> <CSI-0m>factorization<CSI-0m> <CSI-0m>of<CSI-0m><CSI-0;31m> <CSI-0m><CSI-0;31m>`<CSI-0m><CSI-0;31m>`<CSI-0m><CSI-0m>n<CSI-0m><CSI-0;31m>`<CSI-0m><CSI-0;31m>`<CSI-0m><CSI-0;34m>.<CSI-0m>  <CSI-0m>The<CSI-0m> <CSI-0m>result<CSI-0m> <CSI-0m>depends<CSI-0m> <CSI-0m>on<CSI-0m> <CSI-0m>the<CSI-0m><CSI-0;34m><CSI-0m><CSI-0;34m><CSI-0m><CSI-0m>
    <CSI-0m>
    <CSI-?2004h>ipdb> c
    <CSI-?2004l>2 * 5
    <BLANKLINE>
**********************************************************************
1 item had failures:
   1 of  11 in sage.misc.trace.trace
    [10 tests, 1 failure, 2.44 s]
----------------------------------------------------------------------
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/misc/trace.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 2.5 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 2.4 seconds

Running doctests with ID 2020-12-07-16-41-55-9adf414f.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,memlimit,pip,pysingular,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/groups/abelian_gps/abelian_group_gap.py
**********************************************************************
File "src/sage/groups/abelian_gps/abelian_group_gap.py", line 201, in sage.groups.abelian_gps.abelian_group_gap.AbelianGroupElement_polycyclic
Failed example:
    TestSuite(G.an_element()).run()       # optional - gap_packages
Expected nothing
Got:
    Failure in _test_pickling:
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/misc/sage_unittest.py", line 297, in run
        test_method(tester=tester)
      File "sage/structure/sage_object.pyx", line 647, in sage.structure.sage_object.SageObject._test_pickling (build/cythonized/sage/structure/sage_object.c:5023)
        tester.assertEqual(loads(dumps(self)), self)
      File "sage/misc/persist.pyx", line 936, in sage.misc.persist.loads (build/cythonized/sage/misc/persist.c:7536)
        return unpickler.load()
      File "sage/structure/parent.pyx", line 898, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9335)
        return mor._call_(x)
      File "sage/structure/coerce_maps.pyx", line 161, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4622)
        raise
      File "sage/structure/coerce_maps.pyx", line 156, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4514)
        return C._element_constructor(x)
      File "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/groups/abelian_gps/abelian_group_gap.py", line 360, in _element_constructor_
        x *= gens_gap[i]**(exp[i] % orders[i])
      File "sage/rings/integer.pyx", line 3413, in sage.rings.integer.Integer.__mod__ (build/cythonized/sage/rings/integer.c:22615)
        raise ZeroDivisionError("Integer modulo by zero")
    ZeroDivisionError: Integer modulo by zero
    ------------------------------------------------------------
    The following tests failed: _test_pickling
**********************************************************************
1 item had failures:
   1 of   4 in sage.groups.abelian_gps.abelian_group_gap.AbelianGroupElement_polycyclic
    [245 tests, 1 failure, 0.50 s]
----------------------------------------------------------------------
sage -t --long --warn-long 174.6 --random-seed=0 src/sage/groups/abelian_gps/abelian_group_gap.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.6 seconds
    cpu time: 0.5 seconds
    cumulative wall time: 0.5 seconds

The first one seems the result of the oversight of the consequence of a deprecation of a function on its doctest ; the second one has already been reported on previous version ; the third one is new to me, but may appear nly no because this is the first time I have been able to install gap_packages.

HTH,

​

[François Bissey]

It looks like you are missing sqlite3, not on the system or in sage.
You probably have the library but not the executable.

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[jonatha...@googlemail.com]

Yes.

Long time ago, I created a list of known failures when using some system packages (most of them are taken care of by now and new ones came up, however this one is old):

https://trac.sagemath.org/ticket/27122#comment:40

From this you see that this is ticket 29092: https://trac.sagemath.org/ticket/29092

[Clemens Heuberger]

Am 07.12.20 um 21:00 schrieb 'jonatha...@googlemail.com' via sage-release:

> Yes.
>
> Long time ago, I created a list of known failures when using some system
> packages (most of them are taken care of by now and new ones came up, however
> this one is old):
>
> https://trac.sagemath.org/ticket/27122#comment:40
>
> From this you see that this is ticket 29092: https://trac.sagemath.org/ticket/29092

I confirm that installing sqlite3 resolves the issue.

However, I'd like to point out that until 9.3.beta2, there was no such failure
on the same machine (Before installing sqlite3 now, I just recompiled 9.3.beta2
to be sure). So for me this is a regression in 9.3.beta3.