Sage 10.3.beta8 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

We should soon start with a release candidate, so if you have any ticket that you really want to get merged then now is the time to get it in!

30b3d78fac8 (origin/develop, tag: 10.3.beta8) Updated SageMath version to 10.3.beta8
81a374dc4da gh-37290: sagemath-standard: don't require Cython to create sdist
f71381c36f1 gh-37279: Fix some doctest warnings
36bf4afd280 gh-37272: enable the generation of acyclic orientations with `nauty_directg`
75afadb1669 gh-37270: Allow python 3.12 and scipy 1.12
d3deb285e50 gh-37269: sage_docbuild: add needs sphinx tags
5f9ac40378b gh-37258: add type annotations to gens methods
df5e77e5bf5 gh-37256: general cleanup of words/paths.py
2fd33b964b0 gh-37252: CI: Fix for failure in maximize-build-space
1cd7585c3c2 gh-37246: minor details in modular
1ac73d8adca gh-37245: a few details in combinat folder
46ef3fd7ac4 gh-37240: add one method to integer-valued polynomials
b33cb7515ae gh-37234: make a category of Dedekind domains, remove code from ring.pyx
4f78a5f3012 gh-37233: fix small mistake in BQFClassGroupQuotientMorphism documentation
cd61411b653 gh-37232: Still less use of isinstance of old-parents
3d38254edba gh-37230: some cython-lint fixes in ecl lib
1b02deb7f03 gh-37229: some pep8 fixes in coding, in particular E275
6b3e7642126 gh-37228: some pep8 fixes in rings, and activate E221
705cab1188f gh-37226: unit group of number field: do not expand product when S is empty
76b1a92acd3 gh-37225: splitting_field: polred -> polredbest
cdd42d4af9a gh-37223: Remove invariants commands in global namespace
9e9acfea423 gh-37222: CI Linux Incremental: Do not require label "c: packages: ..." to be set
81a23e1d96d gh-37218: Fix to ncsym.ncsym.nesting
23586cf4085 gh-37215: Remove unnecessary bullet point
15abc09a456 gh-37210: unify alias substitute for subs
d548c0023f7 gh-37209: Added rational Tamari lattices
bf1c793ecd6 gh-37207: allow algorithm=pari in LLL
f396146fe81 gh-37199: make FreeAlgebra graded and provide is_unit and __invert__
d1bbb83ef3f gh-37195: general LU: gather several calls to field inversion into a single call
adee77d9f49 gh-37193: Some fixes & improvements to autogenerated flint .pxd
0319fbba80f gh-37185: Fix `sage_setup.clean` doctest
43686380ed7 gh-37182: Implement Auslander-Reiten quivers
7c0a5ecd0cb gh-37170: Total refactor of `any_root()` to solve issue in characteristic two and clean up the code
49505110153 gh-37148: Add class CircuitsMatroid
dd9abe40439 gh-37143: special subs for fractions
53c3468f59a gh-37113: Define behaviour of < and > for fractional ideals in a quaternion algebra
138b265e5ad gh-37096: Fix `.multiplication_by_m` when m is not coprime to characteristic (#6413)
ed119f6d025 gh-37073: `build/pkgs/free_fonts`: Fix fedora system package information
60ffcefe9ac gh-37065: Installation guide: Use `.. envvar::` to define environment variables
96cb4849aa9 gh-37014: Upgrade database_knotinfo to version 2024.2.1
fe375288d78 gh-37007: normalize projective points over (quotients of) Euclidean domains
d4b28e18831 gh-36997: `build/pkgs/{givaro,fflas_ffpack,linbox}`: Accept matching set of new versions
647ec811c57 gh-36983: Prepare python3 `spkg-configure.m4` for Python 3.12 (setuptools instead of distutils)
20a6fde8fa0 gh-36927: src/sage/combinat/designs/subhypergraph_search.pyx: constness fix for clang 16
3942b62a2f0 gh-36915: `configure.ac`: Remove tests for outdated platforms
6ad8584b4d6 gh-36881: Fix cardinality of special linear group
bbe70e7a14e gh-36805: fast path for Vélu isogenies with a single kernel generator
5a3f8eb0af3 gh-36171: Implement Chevalley-Eilenberg complexes with module coefficients
2369ddb7f34 gh-35503: add order_from_multiple() to sage.groups.all
9d24006e703 gh-34976: compute isomorphisms between quaternion orders
0c390a06f72 (tag: 10.3.beta7) Updated SageMath version to 10.3.beta7

[axio...@yahoo.de]

Thank you so much!  sage-release ist ein Fels in der Brandung :-)

[Emmanuel Charpentier]

On Deblan testing running on core i7 + 16 GB RAM, the 7 tests relative to polybori still fail the same way : chash, with gdb indicating !

[Inferior 1 (process 120886) detached] 30 ../sysdeps/unix/sysv/linux/wait4.c: Aucun fichier ou dossier de ce type.

The 8th test fails indicating :

FileNotFoundError: [Errno 2] No such file or directory: 'src/sage/tests/gap_packages.py'

I’ll try a fresh rebuild (i. e. make distclean, etc.) before attempting ptestlong.

HTH,

​

[Kazuyoshi Furutaka]

Hi,

I've tried to build 10.3-beta8 on two Fedora-39 machines, one at home (AMD Ryzen 7 Cezanne) and the other at work (Intel Sandy Bridge(Core i7)).

The build on the former was successful w/o any problem,  but failed on the latter (and it was also the case for 10.3-beta7).

1. Failure in building scipy-1.11.4: needed to set "MKL_ENABLE_INSTRUCTIONS=SSE4_2" (the log was attached).

c.f. https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/CPU-Deprecation-Warning/m-p/1550243?profile.language=ja

2. Failure in building sagemath_doc_html-none: needed to do `./sage -i graphs` (the log when building 10.3-beta7 was attached).

After issuing the command to avoid the problem for 10.3-beta7, I have to do it again for 10.3-beta8.

Kazuyoshi

 

2024年2月14日(水) 8:40 Volker Braun <vbrau...@gmail.com>:

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Kazuyoshi Furutaka

[Dima Pasechnik]

On 15 February 2024 09:17:00 GMT, Kazuyoshi Furutaka <furutaka....@gmail.com> wrote:
>Hi,
>
>I've tried to build 10.3-beta8 on two Fedora-39 machines, one at home (AMD
>Ryzen 7 Cezanne) and the other at work (Intel Sandy Bridge(Core i7)).
>The build on the former was successful w/o any problem, but failed on
>the latter (and it was also the case for 10.3-beta7).
>
>1. Failure in building scipy-1.11.4: needed to set "MKL_ENABLE_INSTRUCTIONS=
>SSE4_2" (the log was attached).
>c.f.
>https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/CPU-Deprecation-Warning/m-p/1550243?profile.language=ja
>
>2. Failure in building sagemath_doc_html-none: needed to do `./sage -i
>graphs` (the log when building 10.3-beta7 was attached).
>After issuing the command to avoid the problem for 10.3-beta7, I have to do
>it again for 10.3-beta8.

Are you using Intel MKL is this build, rather than OpeBLAS?

Or it's only scipy that uses MKL ?

>> <https://groups.google.com/d/msgid/sage-release/2cb4e40e-4c79-4940-872d-cd4598585f26n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
>

[Emmanuel Charpentier]

After make distclean, rebuilding from scratch and reinstalling the same packages :

charpent@zen-book-flip:/usr/local/sage-10$ sage -optional | grep -v ot_instal /usr/local/sage-10/src/sage/misc/package.py:118: UserWarning: failed to fetch the version of pkg='auditwheel_or_delocate' at https://pypi.org/pypi/auditwheel_or_delocate/json warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url)) /usr/local/sage-10/src/sage/misc/package.py:118: UserWarning: failed to fetch the version of pkg='ore_algebra' at https://pypi.org/pypi/ore_algebra/json warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url)) [package]...............................[latest version] ([version]) antlr4_python3_runtime..................? (4.7.2) cmdstanpy...............................? (1.2.1) cypari2.................................? (2.1.4) dot2tex.................................2.11.3.p0 (2.11.3.p0) fricas..................................1.3.8.p1 (1.3.8.p1) gap_jupyter.............................0.9 (0.9) gap_packages............................4.12.2 (4.12.2) iniconfig...............................? (2.0.0) jupyter_contrib_core....................? (0.4.2) jupyter_contrib_nbextensions............? (0.7.0) jupyter_highlight_selected_word.........? (0.2.0) jupyter_kernel_gap......................? (0.9) jupyter_kernel_singular.................? (0.9.7) jupyter_nbextensions_configurator.......? (0.6.3) latex2sympy2............................? (1.9.1) libsemigroups...........................2.3.2 (2.3.2) lxml....................................? (5.1.0) metakernel..............................? (0.30.1) msolve..................................0.5.0 (0.5.0) nbclassic...............................? (1.0.0) octave_kernel...........................? (0.35.1) pandas..................................? (2.2.0) pysingular..............................0.9.7 (0.9.7) pytest..................................8.0.0rc2 (8.0.0) python3_venv............................? (3.11--usr-bin-python3) python_dateutil.........................? (2.8.2) qepcad..................................1.74 (1.74) qtconsole...............................? (5.5.1) qtpy....................................? (2.4.1) saclib..................................2.2.8 (2.2.8) sagemath_standard.......................? (10.3b8) singular_jupyter........................0.9.7 (0.9.7) stanio..................................? (0.3.0) tqdm....................................? (4.66.2)

ptestlong still fails the seven polybori tests already reported.
I”m stuck…

HTH,

​

[Antonio Rojas]

El jueves, 15 de febrero de 2024 a las 17:36:35 UTC+1, emanuel.c...@gmail.com escribió:

After make distclean, rebuilding from scratch and reinstalling the same packages :

ptestlong still fails the seven polybori tests already reported.

I”m stuck…

Have you recently upgraded gcc? In my experience, polybori/brial frequently needs a rebuild when libstdc++ is upgraded.

 

[Kazuyoshi Furutaka]

OneAPI compilers are installed on both PCs but not configured to use (not on the PATH, intentionally, to seek the cause of failure) on the PC on which the build failed.

On it, just done `./configure` and `make reconfigure`, and then `make`. 

The config.log is attached.

Kazuyoshi

2024年2月15日(木) 23:19 Dima Pasechnik <dim...@gmail.com>:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/21660A7F-6C7B-47A5-AB71-AA9E1980CADB%40gmail.com.

[Jaap Spies]

Operating System: Fedora Linux 39

Kernel Version: 6.7.3-200.fc39.x86_64 (64-bit)

Processors: 24 × 13th Gen Intel® Core™ i7-13700KF
Memory: 31,2 GiB of RAM

export MAKE="make -j24"

finishes in 24 m with no failures.

make ptestlong has one persistent failure:

 

Saved trace to /home/jaap/.sage/crash_logs/crash_qg25wumu.log
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------

**********************************************************************
----------------------------------------------------------------------
sage -t --long --warn-long 29.7 --random-seed=236714195655321939587235021745857565297 src/sage/libs/gap/elemen
t.pyx  # Killed due to segmentation fault
----------------------------------------------------------------------
Total time for all tests: 5.7 seconds
   cpu time: 0.0 seconds
   cumulative wall time: 0.0 seconds

Jaap

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[Kazuyoshi Furutaka]

Hi,

A build roughly along the procedure described in "Using conda to provide system packages for the Sage distribution" (`conda env update` instead of `cocnda env create` because the conda environment has been already installed), failed because of the lack of 'markupsafe':

[sagelib-10.3.beta8] Installing collected packages: sagemath-standard
[sagelib-10.3.beta8]   Running setup.py develop for sagemath-standard
[sagelib-10.3.beta8]     Running command python setup.py develop
[sagelib-10.3.beta8]     ************************************************************************
[sagelib-10.3.beta8]     Traceback (most recent call last):
[sagelib-10.3.beta8]       File "<string>", line 2, in <module>
[sagelib-10.3.beta8]       File "<pip-setuptools-caller>", line 34, in <module>
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/setup.py", line 85, in <module>
[sagelib-10.3.beta8]         from sage_setup.autogen import autogen_all
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_setup/autogen/__init__.py", line 3, in <module>
[sagelib-10.3.beta8]         from . import interpreters
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_setup/autogen/interpreters/__init__.py", line 118, in <module>
[sagelib-10.3.beta8]         from .generator import InterpreterGenerator, AUTOGEN_WARN
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_setup/autogen/interpreters/generator.py", line 19, in <module>
[sagelib-10.3.beta8]         from .memory import string_of_addr
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_setup/autogen/interpreters/memory.py", line 16, in <module>
[sagelib-10.3.beta8]         from .utils import je, reindent_lines as ri
[sagelib-10.3.beta8]       File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_setup/autogen/interpreters/utils.py", line 19, in <module>
[sagelib-10.3.beta8]         from jinja2 import Environment
[sagelib-10.3.beta8]       File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/jinja2/__init__.py", line 8, in <module>
[sagelib-10.3.beta8]         from .environment import Environment as Environment
[sagelib-10.3.beta8]       File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/jinja2/environment.py", line 14, in <module>
[sagelib-10.3.beta8]         from markupsafe import Markup
[sagelib-10.3.beta8]     ModuleNotFoundError: No module named 'markupsafe'
[sagelib-10.3.beta8]     ************************************************************************
[sagelib-10.3.beta8]     Error building the Sage library
[sagelib-10.3.beta8]     ************************************************************************
[sagelib-10.3.beta8]     Please email sage-devel (http://groups.google.com/group/sage-devel)
[sagelib-10.3.beta8]     explaining the problem and including the relevant part of the log file
[sagelib-10.3.beta8]       /home/furutaka/work/sage/sage-10.3.beta8-condaSys/logs/pkgs/sagelib-10.3.beta8.log
[sagelib-10.3.beta8]     Describe your computer, operating system, etc.
[sagelib-10.3.beta8]     ************************************************************************
[sagelib-10.3.beta8]     error: subprocess-exited-with-error
[sagelib-10.3.beta8]    
[sagelib-10.3.beta8]     × python setup.py develop did not run successfully.
[sagelib-10.3.beta8]     │ exit code: 1
[sagelib-10.3.beta8]     ╰─> See above for output.

Another `make` after doing `conda install conda-forge::markupsafe --name sage-build` then failed in building "sagemath-doc_html-none":

[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/localtime/_helpers.py", line 16, in _get_tzinfo
[sagemath_doc_html-none]     return pytz.timezone(tzenv)
[sagemath_doc_html-none]            ^^^^^^^^^^^^^
[sagemath_doc_html-none] AttributeError: module 'pytz' has no attribute 'timezone'
[sagemath_doc_html-none]
[sagemath_doc_html-none] During handling of the above exception, another exception occurred:
[sagemath_doc_html-none]
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none]   File "<frozen runpy>", line 198, in _run_module_as_main
[sagemath_doc_html-none]   File "<frozen runpy>", line 88, in _run_code
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-10.3.beta8-condaSys/src/sage_docbuild/__main__.py", line 65, in <module>
[sagemath_doc_html-none]     import sphinx.ext.intersphinx
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/sphinx/ext/intersphinx.py", line 36, in <module>
[sagemath_doc_html-none]     from sphinx.builders.html import INVENTORY_FILENAME
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 14, in <module>
[sagemath_doc_html-none]     from sphinx.environment import CONFIG_CHANGED_REASON, CONFIG_OK, BuildEnvironment
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/sphinx/environment/__init__.py", line 18, in <module>
[sagemath_doc_html-none]     from sphinx.transforms import SphinxTransformer
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/sphinx/transforms/__init__.py", line 20, in <module>
[sagemath_doc_html-none]     from sphinx.util.i18n import format_date
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/sphinx/util/i18n.py", line 11, in <module>
[sagemath_doc_html-none]     import babel.dates
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/dates.py", line 34, in <module>
[sagemath_doc_html-none]     from babel import localtime
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/localtime/__init__.py", line 41, in <module>
[sagemath_doc_html-none]     LOCALTZ = get_localzone()
[sagemath_doc_html-none]               ^^^^^^^^^^^^^^^
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/localtime/__init__.py", line 37, in get_localzone
[sagemath_doc_html-none]     return _get_localzone()
[sagemath_doc_html-none]            ^^^^^^^^^^^^^^^^
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/localtime/_unix.py", line 49, in _get_localzone
[sagemath_doc_html-none]     tzinfo = _get_tzinfo(zone_name)
[sagemath_doc_html-none]              ^^^^^^^^^^^^^^^^^^^^^^
[sagemath_doc_html-none]   File "/home/furutaka/mambaforge/envs/sage-build/lib/python3.11/site-packages/babel/localtime/_helpers.py", line 17, in _get_tzinfo
[sagemath_doc_html-none]     except pytz.UnknownTimeZoneError:
[sagemath_doc_html-none]            ^^^^^^^^^^^^^^^^^^^^^^^^^
[sagemath_doc_html-none] AttributeError: module 'pytz' has no attribute 'UnknownTimeZoneError'
[sagemath_doc_html-none] Error: 'sage --docbuild --all-documents' failed
[sagemath_doc_html-none] make[5]: *** [Makefile:41: doc-inventory-reference] Error 1
[sagemath_doc_html-none]
[sagemath_doc_html-none] real 0m0.485s
[sagemath_doc_html-none] user 0m0.339s
[sagemath_doc_html-none] sys 0m0.154s
[sagemath_doc_html-none] ************************************************************************
[sagemath_doc_html-none] Error installing package sagemath_doc_html-none
[sagemath_doc_html-none] ************************************************************************

The log is attached.

Kazuyoshi

2024年2月14日(水) 8:40 Volker Braun <vbrau...@gmail.com>:

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

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Kazuyoshi Furutaka

[Matthias Köppe]

Try the updated instructions from the 10.3.beta7 installation guide: https://deploy-livedoc--sagemath.netlify.app/html/en/installation/conda#using-conda-to-provide-system-packages-for-the-sage-distribution, which uses lock files

[Kazuyoshi Furutaka]

2024年2月18日(日) 3:40 Matthias Köppe <matthia...@gmail.com>:

Try the updated instructions from the 10.3.beta7 installation guide: https://deploy-livedoc--sagemath.netlify.app/html/en/installation/conda#using-conda-to-provide-system-packages-for-the-sage-distribution, which uses lock files

As I'm using the files from git, at first I did `./bootstrap-conda` (needless?).

Then I did `mamba env update --file environment-3.11-linux.yml --name sage-build` instead of using conda because the command with conda didn't seem to finish forever.

The `make` in the conda environment after `./bootstrap && ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX` stopped  at the same point as before in "building sagemath_doc_html-none".

[sagemath_doc_html-none] AttributeError: module 'pytz' has no attribute 'UnknownTimeZoneError'
[sagemath_doc_html-none] Error: 'sage --docbuild --all-documents' failed

On Fedora 39 (x86_64).

Kazuyoshi

 

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/ab7ed11d-5dc7-4145-a235-41cbfc28314cn%40googlegroups.com.

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Kazuyoshi Furutaka

[Emmanuel Charpentier]

Your suggestion was efficient : forcing Sage’s brial installation by sage -i brial (thus avoiding Debian’s brial) allowed these tests to pass.

Thanks a lot !

​