Sage 8.9.beta7 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 

7d561d89cf (tag: 8.9.beta7, trac/develop) Updated SageMath version to 8.9.beta7

8c985712ae Trac #18267: libgap for PermutationGroup

5b698dd631 Trac #28354: pexpect GAP interface: Handle errors when subprocess isn't wait()-ed by ptyprocess

6fcbcf19be Trac #18312: Construction of a sparse matrix from sparse vectors does not exploit sparseness

d253db88ac Trac #28338: wrong AC_LINK_IFELSE call in spkg-configure

2ea8fa1d96 Trac #27724: GAP Bernoulli function crashes on Cygwin with system GMP

dcaab57016 Trac #28331: AttributeError when computing manifold chart after computing its vector field module

d43cf1e44a Trac #28352: Fix dependencies on png.h, m4ri.h, m4rie.h

ee85c4bea5 Trac #28020: configure check for zlib and libzma can leave bogus compiler flags

2654e1529d Trac #28341: Allow doc to build with SAGE_PARI_CFG undefined

7a41f585a8 Trac #27864: spkg-configure.m4 for isl

54be98be5d Trac #28328: Fix base ring conversion of non-associative unital algebras

b115ef9e63 Trac #28318: linbox for sparse integer matrix

b20a286c90 Trac #27081: Section for composite maps

459699b47f Trac #28327: ModulesWithBasis random_element() uses coercion from base ring that might not exist

d4db3bd999 Trac #28323: expose is_comparability and is_permutation in graph

b656376291 Trac #28333: spkg-configure.m4 for eclib

ea6f35b74c Trac #28320: Further fixes for sage-env-less installs

ecdd4043be Trac #28242: spkg-configure.m4 for pari

9a77264504 Trac #27859: Implementing the Yen's algorithm and its improved versions

213fe0ba4d (tag: 8.9.beta6) Updated SageMath version to 8.9.beta6

[Emmanuel Charpentier]

FWIW, on a Debian testing installation running on core I7 + 16 GB RAM, an upgrade to 8.9.beta7 from a freshly reinstalled 8.9.beta6 gives three failure that seem identical to those reported for 8.9.beta6:

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

sage -t --long --warn-long 157.5 src/sage/graphs/strongly_regular_db.pyx  # 4 doctests failed

sage -t --long --warn-long 157.5 src/sage/rings/polynomial/polynomial_rational_flint.pyx  # 1 doctest failed

sage -t --long --warn-long 157.5 src/sage/algebras/quantum_groups/quantum_group_gap.py  # Killed due to segmentation fault

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

HTH,

[Simon King]

Hi!

With 8.9.beta7 I get the following doctest failure with gap_packages:

$ ./sage -t --warn-long 51.5 src/sage/tests/gap_packages.py
Running doctests with ID 2019-08-21-21-10-47-72e22124.
Git branch: develop
Using --optional=build,ccache,dochtml,frobby,gap_packages,gdb,gfortran,libsemigroups,meataxe,memlimit,mpir,p_group_cohomology,python2,sage
Doctesting 1 file.
sage -t --warn-long 51.5 src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
test_packages(pkgs, only_failures=True) # optional - gap_packages
Expected:
Status Package GAP Output
+--------+---------+------------+
Got:
#I method installed for Matrix matches more than one declaration
Status Package GAP Output
+--------+---------+------------+
**********************************************************************
1 item had failures:
1 of 5 in sage.tests.gap_packages
[11 tests, 1 failure, 5.77 s]
----------------------------------------------------------------------
sage -t --warn-long 51.5 src/sage/tests/gap_packages.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 5.8 seconds
cpu time: 4.2 seconds
cumulative wall time: 5.8 seconds

I wonder if (in addition to gap_packages) the error depends on meataxe,
as the error mentions "Matrix", and meataxe does provide a matrix
implemenation.

See https://trac.sagemath.org/ticket/28378

Best regards,
Simon

[Dima Pasechnik]

On Mon, Aug 19, 2019 at 3:40 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> FWIW, on a Debian testing installation running on core I7 + 16 GB RAM, an upgrade to 8.9.beta7 from a freshly reinstalled 8.9.beta6 gives three failure that seem identical to those reported for 8.9.beta6:
>
> ----------------------------------------------------------------------
> sage -t --long --warn-long 157.5 src/sage/graphs/strongly_regular_db.pyx # 4 doctests failed

I cannot reproduce this one on Debian stable (buster), everything works for me.

$ ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 8.9.beta7, Release Date: 2019-08-18 │
│ Using Python 3.7.3. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage:
Exiting Sage (CPU time 0m0.05s, Wall time 4m23.57s).
dimpase@penguin:~/sage$ ./sage -tp --long
src/sage/graphs/strongly_regular_db.pyx
Running doctests with ID 2019-08-22-23-07-31-38aea923.
Git branch: p3
Using --optional=build,dochtml,gap_packages,libsemigroups,memlimit,python2,sage
Doctesting 1 file using 4 threads.
sage -t --long --warn-long 75.7 src/sage/graphs/strongly_regular_db.pyx
[334 tests, 42.41 s]
----------------------------------------------------------------------
All tests passed!

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[Sébastien Labbé]

Bonjour!

With the new version, I have problems fetching the internet:

sage: oeis([3,7,15,1], max_results=4)
Traceback (most recent call last)
...
IOError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:726)>
Error fetching https://oeis.org/search?q=3%2C+7%2C+15%2C+1&start=0&fmt=text&n=4.

I did my upgrade as usual, so I do not know where is the problem from. Am I alone to have this issue? Should I upgrade SSL or something?

Naturally, this leads to lots of failures while running optional and external packages:

Using --optional=4ti2,awali,bliss,cbc,ccache,cmake,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,mpir,ninja_build,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,python2,qhull,rst2ipynb,sage,topcom

----------------------------------------------------------------------
sage -t --long src/sage/combinat/words/paths.py  # 2 doctests failed
sage -t --long src/sage/tests/cmdline.py  # 1 doctest failed
sage -t --long src/sage/databases/oeis.py  # 147 doctests failed
sage -t --long src/sage/graphs/generators/families.py  # 1 doctest failed
sage -t --long src/sage/combinat/tutorial.py  # 2 doctests failed
sage -t --long src/sage/symbolic/integration/external.py  # 14 doctests failed
sage -t --long src/sage/matrix/matrix2.pyx  # 2 doctests failed
sage -t --long src/sage/combinat/root_system/integrable_representations.py  # 1 doctest failed
sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --long src/doc/en/thematic_tutorials/lie/integrable.rst  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/combinat/species/library.py  # 4 doctests failed
sage -t --long src/sage/combinat/quickref.py  # 2 doctests failed
sage -t --long src/sage/sat/solvers/dimacs.py  # 1 doctest failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/doc/en/developer/coding_basics.rst  # 1 doctest failed
sage -t --long src/sage/combinat/designs/design_catalog.py  # 3 doctests failed
sage -t --long src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/modular_forms_and_hecke_operators.rst  # 1 doctest failed
sage -t --long src/sage/combinat/integer_lists/invlex.pyx  # 1 doctest failed
sage -t --long src/sage/combinat/designs/covering_design.py  # 2 doctests failed
sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

[Dima Pasechnik]

On Fri, Aug 23, 2019 at 11:01 AM Sébastien Labbé <sla...@gmail.com> wrote:
>
> Bonjour!
>
> With the new version, I have problems fetching the internet:
>
> sage: oeis([3,7,15,1], max_results=4)
> Traceback (most recent call last)
> ...
> IOError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:726)>
> Error fetching https://oeis.org/search?q=3%2C+7%2C+15%2C+1&start=0&fmt=text&n=4.
>
> I did my upgrade as usual, so I do not know where is the problem from. Am I alone to have this issue? Should I upgrade SSL or something?

This works for me on Debian buster, what OS are you on? And, is it
python 2 or 3?

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[Sébastien Labbé]

> I did my upgrade as usual, so I do not know where is the problem from. Am I alone to have this issue? Should I upgrade SSL or something?

This works for me on Debian buster, what OS are you on? And, is it
python 2 or 3?

I am running Ubuntu 16.04 with this:

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 8.9.beta7, Release Date: 2019-08-18               │

│ Using Python 2.7.15. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘

[Eric Gourgoulhon]

Hello Sebastien,

This works for me on Ubuntu 18.04, with both Python 2 and 3 versions of Sage 8.9.beta7.

Maybe you should upgrade your SSL?

Best regards,

Eric.

[Sébastien Labbé]

On Friday, August 23, 2019 at 3:12:54 PM UTC+2, Eric Gourgoulhon wrote:

Hello Sebastien,

This works for me on Ubuntu 18.04, with both Python 2 and 3 versions of Sage 8.9.beta7.

Maybe you should upgrade your SSL?

Ok I will check this out next week!

Sébastien

 

[Justin C. Walker]

> On Aug 18, 2019, at 11:19 , Volker Braun <vbrau...@gmail.com> 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

Results from building fresh clone of develop branch are the same as for 8.9-b6, on three macOS systems: 10.11.6 (mid-2015 MBP, Quad-core i7), 10.13.6 (2017 iMac Pro, 18-core Xeon W), and 10.14.6 (2017 MBP, Quad-core Core i7).

All built w/o problems.

Testing (‘ptestlong’):
- all tests passed on 10.11.6 and 10.14.6
- test failures in one file on 10.13.6:
1 item had failures:
1 of 12 in sage.libs.singular.polynomial.singular_polynomial_call
[55 tests, 1 failure, 406.69 s]
----------------------------------------------------------------------
sage -t --long --warn-long 70.3 src/sage/libs/singular/polynomial.pyx # 1 doctest failed
———————————————————————————————————

Last time 8.9-b6), the test failed twice when run by itself.

This time, it passed twice when run by itself.

Go figure...

Justin

--
Justin C. Walker
Director
Institute for the Enhancement of the Director's Income
--
Fame is fleeting, but obscurity
just drags on and on. F&E

[Emmanuel Charpentier]

FWIW, on the same machine, I upgraded a 8.8 installation to 8.9.beta7 (I wanted to check sometong about the R interface). Ptestlong got three failures:

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

sage -t --long --warn-long 155.5 src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py  # 1 doctest failed

sage -t --long --warn-long 155.5 src/sage/tests/gap_packages.py  # 1 doctest failed

sage -t --long --warn-long 155.5 src/sage_setup/optional_extension.py  # 1 doctest failed

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

The first one (already multireported) is transient, the other two are permanent, but seemingly cosmetic. Details :

charpent@zen-book-flip:/usr/local/sage-8$ sage -t --long --warn-long 155.5 src/sage/tests/gap_packages.py 

Running doctests with ID 2019-08-25-15-41-16-ec0ea2a1.

Git branch: develop

Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,mpir,python2,sage

Doctesting 1 file.

sage -t --long --warn-long 155.5 src/sage/tests/gap_packages.py

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

File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages

Failed example:

    test_packages(pkgs, only_failures=True)    # optional - gap_packages

Expected:

      Status   Package   GAP Output

    +--------+---------+------------+

Got:

    #I  method installed for Matrix matches more than one declaration

      Status   Package   GAP Output

    +--------+---------+------------+

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

1 item had failures:

   1 of   5 in sage.tests.gap_packages

    [11 tests, 1 failure, 2.90 s]

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

sage -t --long --warn-long 155.5 src/sage/tests/gap_packages.py  # 1 doctest failed

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

Total time for all tests: 2.9 seconds

    cpu time: 2.5 seconds

    cumulative wall time: 2.9 seconds

charpent@zen-book-flip:/usr/local/sage-8$ sage -t --long --warn-long 155.5 src/sage_setup/optional_extension.py 

Running doctests with ID 2019-08-25-15-42-00-8f82ff2e.

Git branch: develop

Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,mpir,python2,sage

Doctesting 1 file.

sage -t --long --warn-long 155.5 src/sage_setup/optional_extension.py

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

File "src/sage_setup/optional_extension.py", line 72, in sage_setup.optional_extension.OptionalExtension

Failed example:

    print(ext.__class__.__name__)

Expected:

    Extension

Got:

    CythonizeExtension

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

1 item had failures:

   1 of  10 in sage_setup.optional_extension.OptionalExtension

    [12 tests, 1 failure, 0.25 s]

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

sage -t --long --warn-long 155.5 src/sage_setup/optional_extension.py  # 1 doctest failed

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

Total time for all tests: 0.3 seconds

    cpu time: 0.0 seconds

    cumulative wall time: 0.2 seconds

HTH,

[Sébastien Labbé]

I reinstalled my openssl which looks recent:

(sage-sh) $ openssl version
OpenSSL 1.1.1b  26 Feb 2019

But this does not fix the issue.

[Samuel Lelievre]

Le mardi 27 août 2019 22:04:42 UTC+2, Sébastien Labbé a écrit :

I reinstalled my openssl which looks recent:

(sage-sh) $ openssl version
OpenSSL 1.1.1b  26 Feb 2019

But this does not fix the issue.

After installing openssl, you need to force-reinstall python.

sage -f python2

sage -f python3

so that their ssl module gets compiled, taking into account

the (new) presence of OpenSSL.

[Sébastien Labbé]

It does not work. I will try rebuilding from scratch...

[Sébastien Labbé]

It does not work. I will try rebuilding from scratch...

After rebuilding from scratch from a git clone, the SSL problem disapeared:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 8.9.beta8, Release Date: 2019-08-25               │

│ Using Python 2.7.15. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘

sage:  oeis([3,7,15,1], max_results=4)

0: A001203: Simple continued fraction expansion of Pi.
1: A240698: Partial sums of divisors of n, cf. A027750.
2: A082495: a(n) = (2^n - 1) mod n.
3: A165416: Irregular array read by rows: The n-th row contains those distinct positive integers that each, when written in binary, occurs as a substring in binary n.