Sage 9.4.beta1 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 

30ee8d6505 (tag: 9.4.beta1, trac/develop) Updated SageMath version to 9.4.beta1

7690208434 Trac #31903: Build errors in padic_relaxed_element

605c100c46 Trac #31848: Random failure: sage.libs.gap.util.GAPError: Error, OnSets: <set> must be a set

24a34ee595 Trac #31825: Failure when testing sage_conf version

5067635403 Trac #31692: Refactor display behavior of mixed forms

08b5a55b44 Trac #31691: Turn mixed form algebra into de Rham complex

e30645c055 Trac #31686: Speed up factoring finite field multiplicative order

490c3ddfeb Trac #31684: Improve WordMorphism._language_naive

3e413ce3b4 Trac #31681: DiGraph.layout_acyclic_dummy assumes it can sort lists of vertices

5b23c1fac2 Trac #31677: Open subsets of arbitrary subsets of manifolds

a8ed75663a Trac #31676: Hash of mpmath complex numbers produces OverFlowError

24c78cf7f3 Trac #31674: Make open subsets of immersed/embedded submanifolds immersed/embedded submanifolds

2f2b1540f7 Trac #31658: Slight speed-up in copy method

fc7a3728c8 Trac #31654: copy_from for scalar fields

db698c31ed Trac #31653: Images of continuous maps and embedded submanifolds as manifold subsets

b573a54ba3 Trac #31650: improve LazyImport

8600573a7f Trac #31647: Update sympy to 1.8

b2aa0f6261 Trac #31633: Simplify VectorField.__call__

4200c96400 Trac #31619: Cholesky factorization and positive-definite testing over inexact rings

60380a3cf3 Trac #31618: Some documentation improvements in sage.modular.quatalg.brandt

ab0715d126 Trac #31615: faster order complex for posets

c95fe8492a Trac #31614: Remove dead _cholesky_decomposition_ from matrix2.pyx

749b0ad122 Trac #31613: ClusterAlgebra.greedy_element bug and further improvements

ad89df812b Trac #31609: Add method tangent_vector to differentiable manifolds

63c3d0fecb Trac #31594: Accept giac-1.7.x from the system

c58463cf86 Trac #31526: Drop support for optional packages with system gcc 4.x on ubuntu-trusty, debian-jessie, linuxmint-17, centos-7

8d55a3f756 Trac #31489: Galois subgroups

9c85a6c1cf Trac #30352: Interface to the KnotInfo and LinkInfo databases

9f031cdb05 Trac #29222: Improvements to padic polylog

9caac06757 Trac #28890: Install fewer static libraries

e94bd31252 Trac #26635: Major extensions to local components code

9f3988d9a5 Trac #21203: basic element and parent for k-regular sequences

3b414bea4b Trac #20331: A MIPVariable's repr should include some useful information

061d4b71df Trac #31860: Restore support for sage-bootstrap-python = python 3.6

6aa4ecee16 (tag: 9.4.beta0) Updated SageMath version to 9.4.beta0

[Justin C. Walker]

> On Jun 6, 2021, at 11:40 , 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

Built without problems from a fresh clone of the develop tree on macOS 10.13.6 (2017 iMac Pro, 18-core Xeon W).

Testing (‘ptestlong’) yielded two failures:

sage -t --long --warn-long 70.2 --random-seed=0 src/sage/geometry/polyhedron/base.py # 1 doctest failed
sage -t --long --warn-long 70.2 --random-seed=0 src/sage/graphs/bipartite_graph.py # 1 doctest failed

The first failure was reported for testing 9.4-B0 on this system. The second, as follows, is new:
File "src/sage/graphs/bipartite_graph.py", line 329, in sage.graphs.bipartite_graph.BipartiteGraph.__init__
Failed example:
print(round(get_memory_usage() - start_mem))
Expected:
0.0
Got:
3.0

Following a remark of Volker’s in an earlier thread, I ran each (separately) in a loop. The first consistently failed (“expected True, got False”).

The second mostly succeeded (70-80% of the time). The failures were similar, but with varying non-zero values. Maybe good garbage vs. bad garbage?

Justin

--
Justin C. Walker
Director, Institute for the Absorption of Federal Funds
--
Taxes, n.:
Of life's two certainties, the only one
for which you can get an extension.
--

[François Bissey]

I have trouble building the documentation in sage-on-gentoo because of #30352 which doesn’t seem to be
implementing features properly. That error wouldn’t happen on vanilla sage because the build is not done
in a sandbox and the build system wouldn’t try to write a system location.

* python3_9: running distutils-r1_run_phase python_compile_all
/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/rings/padics/padic_base_leaves.py:1104: DeprecationWarning: invalid escape sequence \Z
"""
/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/rings/padics/padic_base_leaves.py:1139: DeprecationWarning: invalid escape sequence \Q
"""
* ACCESS DENIED: unlinkat: /usr/share/sage/knotinfo
rm: cannot remove '/usr/share/sage/knotinfo': Permission denied
* ACCESS DENIED: mkdir: /usr/share/sage/knotinfo
Traceback (most recent call last):
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 420, in demo_version
self._num_knots = load(num_knots_file)
File "sage/misc/persist.pyx", line 187, in sage.misc.persist.load (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/persist.c:2807)
with open(filename, 'rb') as fobj:
FileNotFoundError: [Errno 2] No such file or directory: '/usr/share/sage/knotinfo/num_knots.sobj'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__main__.py", line 1, in <module>
from sage_docbuild import main
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 57, in <module>
import sage.all
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/all.py", line 215, in <module>
from sage.knots.all import *
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/knots/all.py", line 6, in <module>
if DatabaseKnotInfo().is_present():
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/features/__init__.py", line 162, in is_present
res = self._is_present()
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/features/__init__.py", line 823, in _is_present
importlib.import_module(self.name)
File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/knots/knotinfo.py", line 239, in <module>
from sage.databases.knotinfo_db import KnotInfoColumns, db
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 815, in <module>
dc = db.columns()
File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:12918)
self.cache = f(self._instance)
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 594, in columns
column_dict = self.read_column_dict()
File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:12918)
self.cache = f(self._instance)
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 617, in read_column_dict
if self.demo_version():
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 422, in demo_version
self.reset_filecache()
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/databases/knotinfo_db.py", line 391, in reset_filecache
sage_makedirs(sobj_path)
File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/misc/misc.py", line 93, in sage_makedirs
os.makedirs(dirname)
File "/usr/lib/python3.9/os.py", line 225, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/usr/share/sage/knotinfo’

Various bits of sage try to recreate share/knotinfo/num_knots.sobj which isn’t installed because I haven’t
packaged it yet. This shouldn’t be an issue since database_knotinfo is still optional.
The problem here is that it seems that _feature.is_present() is always true, including when it is called
at
https://github.com/sagemath/sage/blob/develop/src/sage/databases/knotinfo_db.py#L416

I cannot find where it could be found as being false in the current code.

François

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[François Bissey]

Checking how the feature works I think there was a mistake in the addition to sage/features/databases.py
for knotinfo. It checks for a sage python module presence, which will always be there since it is part of
sage, when it should have checked for a static file, like for the other databases.

[François Bissey]

This is now https://trac.sagemath.org/ticket/31921

[Thierry Dumont]

On Ubuntu 21-04, installation from a fresh git clone:

- Compilation : no problem.
- make ptestlong:

(Note that make ptestlong wanted ptest, which I iinstalled).

----------------------------------------------------------------------
Total time for all tests: 3492.9 seconds
cpu time: 10407.5 seconds
cumulative wall time: 13534.9 seconds
============================= test session starts
==============================
platform linux -- Python 3.9.5, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /usr/local/sages/dev/sage/src, configfile: tox.ini
collected 10 items / 1 error / 9 selected


==================================== ERRORS
====================================
_____________ ERROR collecting sage/structure/sage_object_test.py
______________
ImportError while importing test module
'/usr/local/sages/dev/sage/src/sage/structure/sage_object_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
src/sage/structure/sage_object_test.py:3: in <module>
from .sage_object import SageObject
E ImportError: attempted relative import with no known parent package
=========================== short test summary info
============================
ERROR src/sage/structure/sage_object_test.py
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection
!!!!!!!!!!!!!!!!!!!!
=============================== 1 error in 2.38s
===============================
make: *** [Makefile:201 : ptestlong] Erreur 1

[Emmanuel Charpentier]

On Debian testing, upgrading 9.4.beta0 to beta1 and running ptestlong leads to

• One timeout on parigp.py (already reported numerous times)

• one permanent failure on gap-packages.py, also reported numerous times but whose report has changed :

### This has been seen numerous times ####################
charpent@zen-book-flip:/usr/local/sage-9$ sage -t --long --warn-long 218.0 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
Running doctests with ID 2021-06-07-14-21-14-440d82f5.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,pip,pysingular,saclib,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 218.0 --random-seed=0 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:
      Status   Package   GAP Output
    +--------+---------+------------+
**********************************************************************
1 item had failures:
   1 of   5 in sage.tests.gap_packages
    [11 tests, 1 failure, 4.61 s]
----------------------------------------------------------------------
sage -t --long --warn-long 218.0 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 4.6 seconds
    cpu time: 4.2 seconds
    cumulative wall time: 4.6 seconds
### This is new :  ####################
============================= test session starts ==============================
platform linux -- Python 3.9.2, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /usr/local/sage-9/src, configfile: tox.ini
collected 1 item                                                               

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

==================================== ERRORS ====================================
_______________________ ERROR at setup of test_packages ________________________
file /usr/local/sage-9/src/sage/tests/gap_packages.py, line 25
  def test_packages(packages, only_failures=False):
E       fixture 'packages' 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/gap_packages.py:25
=========================== short test summary info ============================
ERROR src/sage/tests/gap_packages.py::test_packages
=============================== 1 error in 0.15s ===============================

I suppose that installing pytest may have changed failure reports.

HTH,

​

[Dima Pasechnik]

Please try https://trac.sagemath.org/ticket/31498 which should also
fix gap_packages.py error.

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[John H Palmieri]

It builds for me on OS X Big Sur and I see no new doctest failures, but the PDF documentation doesn't build. When building it/a_tour_of_sage, I see this error:

    ! Package inputenc Error: Unicode character リ (U+30EA)

Indeed, the file `local/share/doc/sage/latex/it/a_tour_of_sage/a_tour_of_sage.tex has the line

    \renewcommand{\releasename}{リリース}

Why does the Italian tour have these Japanese characters in it? A few lines earlier, I also see

    \date{2021年06月08日}

and at the bottom

    \renewcommand{\indexname}{索引}

These lines are the same as in ja/a_tour_of_sage/a_tour_of_sage.tex.

I've opened https://trac.sagemath.org/ticket/31936 for this.

[Samuel Lelièvre]

Thanks for the new release.

On Debian 10 buster
- `./bootstrap -q && ./configure -q` -- ok but lost a lot of quiet
- `make -s V=0` -- ok
- `make -s V=0 doc-pdf` -- ok
- `make -s V=0 testlong` -- all tests pass

On Ubuntu 20.04:
- `./bootstrap -q && ./configure -q` -- ok but lost a lot of quiet
- `make -s V=0` -- ok
- `make -s V=0 doc-pdf` -- ok
- `make -s V=0 testlong` -- many failures,
apparently related to pari/gp (rich?) output.
Logs at:
www.math.u-psud.fr/
~lelievre/t/slel-2021-06-07-s94b1-parigp.zip

[Samuel Lelièvre]

Le jeu. 10 juin 2021 à 18:30, Samuel Lelièvre:

>
> Thanks for the new release.
>
> On Debian 10 buster
> - `./bootstrap -q && ./configure -q` -- ok but lost a lot of quiet
> - `make -s V=0` -- ok
> - `make -s V=0 doc-pdf` -- ok
> - `make -s V=0 testlong` -- all tests pass
>
> On Ubuntu 20.04:
> - `./bootstrap -q && ./configure -q` -- ok but lost a lot of quiet
> - `make -s V=0` -- ok
> - `make -s V=0 doc-pdf` -- ok
> - `make -s V=0 testlong` -- many failures,
> apparently related to pari/gp (rich?) output.

The problem, after searching a bit more, might have more
to do with pexpect and/or readline and/or bracketed-paste,
than with PARI/GP.

[Samuel Lelièvre]

Le jeu. 10 juin 2021 à 21:35, Samuel Lelièvre:

Fixed by installing Sage's readline:
```
$ make -s V=0 readline && make -s V=0 testlong
```
All tests pass!

[Dima Pasechnik]

What exactly is wrong with Ubuntu system readline ?

Is it underlinked?

config.log please.

```
All tests pass!

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[Justin C. Walker]

> On Jun 6, 2021, at 11:40, 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

Built without problems from a fresh clone of the develop tree on macOS 10.15.7 (2019 MBP, 8-core Core i9).

Testing (‘ptestlong’) yielded one failures:

sage -t --long --warn-long 78.7 --random-seed=0 src/sage/graphs/bipartite_graph.py

The failure is the same as I reported earlier, for another system:

File "src/sage/graphs/bipartite_graph.py", line 329, in sage.graphs.bipartite_graph.BipartiteGraph.__init__
Failed example:
print(round(get_memory_usage() - start_mem))
Expected:
0.0
Got:
3.0

Again, the failures were more or less the same, with varying non-0.0 values appearing about 20-30% of the time, when I ran the test in a loop.

Justin

[Volker Braun]

I'm also getting random "memleak" errors that probably aren't. We are mostly interested in linear memory growth with multiple calls (i.e. malloc without free), not overall constants (like a new ring was used and the parent is now cached somewhere). The memory leak tests should probably do multiple tries and only fail if ram usage consistently grows.