Sage 10.4.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

744939e037a (github/develop, tag: 10.4.beta5) Updated SageMath version to 10.4.beta5
e77b3df44ad gh-37915: Replace doctests from jacobian_khuri_makdisi.py taking too long time
422c59e95ce gh-37911: Fix overflow in hypergeometric trace
67f26757bcb gh-37904: Change `SetSystem` representation
a1354a74b91 gh-37883: gap: don't use deprecated LaTeX() and LaTeXObj()
53566be0ca2 gh-37882: eclib: fix doctests after 20240408 update
31cf6d3b0fa gh-37872: sage.{topology,homology}: Remove deprecated chomp interface
75c86c8f28c gh-37870: `sage.ext`: Remove deprecated code
c46302c3a6d gh-37868: `sage.misc.misc`: Remove deprecated code
b14d3ec8dc3 gh-37856: `sage.misc.dist`: Remove; deprecated in #30207 (2022)
6753fbdecdc gh-37855: `sage.misc.package`: Remove deprecated code
9ce51d09089 gh-37853: Work around inconsistent iteration in `multi_polynomial_sequence.py`
969b687c5f6 gh-37851: Fix issue 37587 regarding the Link class plot method
620babd49fb gh-37841: `.ci/write-dockerfile.sh`: Move here from build/bin/
af6c2085804 gh-37836: fricas/do not get inputform twice
ac9c1b07203 gh-37835: Optimize `DisjointSet`
6e58d87dcc1 gh-37833: `build/pkgs/{python3,setuptools}`: Update fedora distro info
5ab5dc3c3fe gh-37829: src/sage/manifolds/differentiable: Docstring/doctest edits
db630cdf2d9 gh-37827: `sage.tensor`: Tiny doc fixes
7d0a347f99b gh-37826: FreeModuleAutomorphism: Add more invariants
698774f5289 gh-37825: `FiniteRankFreeModuleMorphism.display`: Show matrix decorated with basis element names
3041aac4a21 gh-37823: Fix LaTeX output of FreeModuleTensor.display_comp
8296cec240f gh-37822: Fix bug in TensorField.apply_map
71d2a96e0d7 gh-37810: build/pkgs/gambit: Remove
f87f3e3581e gh-37808: Removed non-working and utterly old @rename_keyword in farey_symbol.pyx
d64f1a8accb gh-37807: Added some documentation in the developer's guide regarding deprecation
68e657c09c3 gh-37802: Add the downward monotonic cone to the cone catalogue
abad24ff15f gh-37800: some cython-lint suggestions fixed in real rings
106c0d76be6 gh-37799: little details in quadratic_forms (pep8, ruff, etc)
2406c159c81 gh-37798: some ruff C4 fixes in combinat
ac8792fc3d2 gh-37797: fix the category of quasi-modular form rings
1b5a3450555 gh-37793: add links to standard errors in various places
ca3d59a8f09 gh-37792: remove a stray leftover in in sa2si_ZZmod()
e9e3a3db928 gh-37750: CI Build&Test: Fix "test modularized distributions" after #37022
9097fa25d4b gh-37738: CI Build&Test: Show segfaults using GitHub annotations
46b7ec223c3 gh-37722: Remove `CombinatorialClass`
19b06ac7387 gh-37715: `sage.{calculus,functions,numerical,symbolic}`: Docstring/doctest cosmetics, `# needs`
e4e33257ab6 gh-37693: Implement the hypercenter and upper central series for finite dimensional Lie algebras
f0a28504d47 gh-37692: `matrix`, `Graph.incidence_matrix`, `LinearMatroid.representation`: Support constructing `Hom(CombinatorialFreeModule)` elements
9783f965806 gh-37681: Quaternion Ideal Pushforwards and Pullbacks
0a75254c9ea gh-37650: src/sage/features/sagemath.py: Add feature SAGE_SRC
721fc792a23 gh-37492: make sagelib work with singular>=4.3.2.p15 (future 4.4)
2d77ac5ea3c gh-37277: pip 24, setuptools 69.5.1, hatchling 1.22.5, hatch_fancy_pypi_readme 24.1.0, platformdirs 4.2.0, packaging 24.0, trove_classifiers 2024.4.10, wheel 0.43.0
248fde327ef gh-37099: GH Actions: Build platform-independent wheels of sagemath-environment, sage-setup, sage-sws2rst for PyPI
90e08c88c60 gh-37057: deprecated functions is_Cone, is_Polyhedron, is_LatticePolytope
ca1b5e6ea0d gh-37041: update FriCAS to 1.3.10, allow building with sbcl
f19f431d095 gh-36982: Make pyproject.toml the source for build dependencies
23ba3d8f174 gh-36768: Retrieve more information of fundamental groups of plane curves
f633de0146a gh-36498: CI build, doc-build: Run containers explicitly, separate jobs for pyright, build, modularized tests, long tests
f3847837395 gh-35618: Use `pypa/build` instead of `pip wheel`
c4363fc97eb (tag: 10.4.beta4) Updated SageMath version to 10.4.beta4

[david....@gmail.com]

Thank you for this new release.

With Fedora 39, I have the following issue that I don't observe on macOS 

maserati:/some/path/sage> ./sage -t src/sage/graphs/generators/smallgraphs.py

too few successful tests, not using stored timings

Running doctests with ID 2024-05-03-12-10-24-1c65d6ef.

Git branch: develop

Git ref: 10.4.beta5

Running with SAGE_LOCAL='/home/dcoudert/sage/local' and SAGE_VENV='/home/dcoudert/sage/local/var/lib/sage/venv-python3.12'

Using --optional=benzene,bliss,buckygen,csdp,dot2tex,fedora,gap_packages,glucose,igraph,libsemigroups,mcqd,pip,plantri,python_igraph,sage,sage_spkg,tdlib,texttable

Features to be detected: 4ti2,SAGE_SRC,benzene,bliss,buckygen,conway_polynomials,csdp,cvxopt,cvxopt,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_cubic_hecke,database_ellcurves,database_graphs,database_jones_numfield,database_knotinfo,dvipng,ecm,fpylll,fricas,gap_package_atlasrep,gap_package_design,gap_package_grape,gap_package_guava,gap_package_hap,gap_package_polycyclic,gap_package_qpa,gap_package_quagroup,gfan,graphviz,imagemagick,ipython,jmol,jupymake,kenzo,latte_int,lrcalc_python,lrslib,matroid_database,mcqd,meataxe,mpmath,msolve,nauty,networkx,numpy,palp,pandoc,pdf2svg,pdftocairo,pexpect,phitigra,pillow,plantri,polytopes_db,polytopes_db_4d,pplpy,primecountpy,ptyprocess,pynormaliz,pyparsing,python_igraph,requests,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.sat,sage.schemes,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,scipy,singular,sphinx,symengine_py,sympy,tdlib,threejs

Doctesting 1 file.

sage -t --random-seed=97244284769564606085961768045450911646 src/sage/graphs/generators/smallgraphs.py

    Timed out (and interrupt failed)

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

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

sage -t --random-seed=97244284769564606085961768045450911646 src/sage/graphs/generators/smallgraphs.py  # Timed out (and interrupt failed)

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

Total time for all tests: 660.1 seconds

    cpu time: 0.0 seconds

    cumulative wall time: 0.0 seconds

Features detected for doctesting: networkx,sage.geometry.polyhedron,sage.groups,sage.libs.pari,sage.modules,sage.numerical.mip,sage.plot,sage.rings.finite_rings,sage.rings.number_field,sage.symbolic

pytest is not installed in the venv, skip checking tests that rely on it

Same issue with

sage -t --random-seed=76417292471192601569274824800602906818 src/sage/graphs/strongly_regular_db.pyx  # Timed out (and interrupt failed)

sage -t --random-seed=76417292471192601569274824800602906818 src/sage/graphs/generators/classical_geometries.py  # Timed out (and interrupt failed)

sage -t --random-seed=76417292471192601569274824800602906818 src/sage/graphs/generators/distance_regular.pyx  # Timed out (and interrupt failed)

sage -t --random-seed=76417292471192601569274824800602906818 src/sage/graphs/generators/smallgraphs.py  # Timed out (and interrupt failed)

I don't know what's going on.

David.

[dim...@gmail.com]

Do we officially support Python 3.12 ?

Anyway, it would be useful to see where exactly these tests time out.

Dima

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[david....@gmail.com]

on macOS, I'm also running Python 3.12 and it's working well (see below).

How can I extract data to see where the tests time out ?

Thanks,

David.

MAC-04017247:sage dcoudert$ ./sage -t src/sage/graphs/generators/

Running doctests with ID 2024-05-03-11-03-11-89a06eef.

Git branch: develop

Git ref: 10.4.beta3-802-g744939e037

Running with SAGE_LOCAL='/Users/dcoudert/sage/local' and SAGE_VENV='/Users/dcoudert/sage/local/var/lib/sage/venv-python3.12'

Using --optional=benzene,bliss,buckygen,csdp,dot2tex,gap_packages,glucose,homebrew,igraph,libsemigroups,mcqd,pip,plantri,python_igraph,sage,sage_spkg,tdlib,texttable

Features to be detected: 4ti2,SAGE_SRC,benzene,bliss,buckygen,conway_polynomials,csdp,cvxopt,cvxopt,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_cubic_hecke,database_ellcurves,database_graphs,database_jones_numfield,database_knotinfo,dvipng,ecm,fpylll,fricas,gap_package_atlasrep,gap_package_design,gap_package_grape,gap_package_guava,gap_package_hap,gap_package_polycyclic,gap_package_qpa,gap_package_quagroup,gfan,graphviz,imagemagick,ipython,jmol,jupymake,kenzo,latte_int,lrcalc_python,lrslib,matroid_database,mcqd,meataxe,mpmath,msolve,nauty,networkx,numpy,palp,pandoc,pdf2svg,pdftocairo,pexpect,phitigra,pillow,plantri,polytopes_db,polytopes_db_4d,pplpy,primecountpy,ptyprocess,pynormaliz,pyparsing,python_igraph,requests,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.sat,sage.schemes,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,scipy,singular,sphinx,symengine_py,sympy,tdlib,threejs

Doctesting 12 files.

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/degree_sequence.py

    [17 tests, 3.72 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/distance_regular.pyx

    [181 tests, 14.73 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/smallgraphs.py

    [510 tests, 12.77 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/families.py

    [449 tests, 9.25 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/all.py

    [0 tests, 0.00 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/random.py

    [217 tests, 7.83 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/chessboard.py

    [42 tests, 0.30 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/basic.py

    [171 tests, 4.28 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/platonic_solids.py

    [34 tests, 3.40 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/intersection.py

    [72 tests, 1.27 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/classical_geometries.py

    [144 tests, 3.83 s]

sage -t --warn-long 22.9 --random-seed=239687165614427705433447704824745784831 src/sage/graphs/generators/world_map.py

    [20 tests, 0.08 s]

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

All tests passed!

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

Total time for all tests: 79.3 seconds

    cpu time: 24.5 seconds

    cumulative wall time: 61.5 seconds

Features detected for doctesting: gap_package_atlasrep,gap_package_design,gap_package_grape,networkx,numpy,sage.combinat,sage.geometry.polyhedron,sage.groups,sage.libs.flint,sage.libs.gap,sage.libs.pari,sage.modules,sage.numerical.mip,sage.plot,sage.rings.finite_rings,sage.rings.number_field,sage.schemes,sage.symbolic,scipy

pytest is not installed in the venv, skip checking tests that rely on it

[John H Palmieri]

After running `make configure`, the git repository is not clean:

% git status
On branch develop
Your branch is up to date with 'upstream/develop'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)
pkgs/sagemath-categories/requirements-editable.txt
pkgs/sagemath-environment/requirements-editable.txt
pkgs/sagemath-objects/requirements-editable.txt
pkgs/sagemath-repl/requirements-editable.txt

[Matthias Köppe]

Hi John, thanks for the report; fixed in https://github.com/sagemath/sage/pull/37929

[Jaap Spies]

On Fedora 40 building fails with

* package:         ppl-1.2.p1
 last build time: mei 3 22:09
 log file:        /home/jaap/sagemath/sage-10.4.beta5/logs/pkgs/ppl-1.2.p1.log
From the log file:

[spkg-install] config.lt: creating libtool
[spkg-install] checking for the GMP library version 4.1.3 or above... no
[spkg-install] configure: error: Cannot find GMP version 4.1.3 or higher.

But Fedora 40 comes with gmp version 6.2.1

Jaap

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[Enrique Artal]

In a test installation of Fedora 40, I have the same issue, solved installing gmp package, but then doc has a problem with libharfbuzz. On the other side trying to install it with gcc 14 fails with sagelib

[Dima Pasechnik]

You probably have an incomplete install of system GMP packages, or/and, perhaps, a spurious install of GMP in /usr/local ...


Please post top-level config.log

[Jaap Spies]

Last metadata expiration check: 3:24:12 ago on za 04 mei 2024 08:57:46 CEST.
Package gmp-1:6.2.1-8.fc40.x86_64 is already installed.
Package gmp-devel-1:6.2.1-8.fc40.x86_64 is already installed.
Package gmp-ecm-7.0.5-5.fc40.x86_64 is already installed.
Package gmp-ecm-devel-7.0.5-5.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!

The config.log attached.

Jaap

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[Jaap Spies]

Sorry wrong attachment!

[Dima Pasechnik]

hmm, no, your system GMP looks fine,  it was duly detected by the top level configure.

It is however rejected by ppl.
Can you post the appropriate logs/pkgs/ppl... log file?

[Jaap Spies]

Here it is.

Jaap

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[Dima Pasechnik]

I guess you might be missing gmp-c++ system package.
Please install it and try again. It seems we need to look at what ppl does in its gmp detection code and do the same in our configure.

<https://packages.fedoraproject.org/pkgs/gmp/gmp-c++/fedora-40.html>

[Enrique Artal]

In my config.log it says that it tries to install ppl since gcc is built. No ppl package in fedora 39

[Jaap Spies]

jaap@peace:~$ gcc --version
gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

jaap@peace:~$ cd sagemath/sage-10.4.beta5/
jaap@peace:~/sagemath/sage-10.4.beta5$ sudo dnf install gmp-c++
[sudo] password for jaap:  
Last metadata expiration check: 0:58:43 ago on za 04 mei 2024 12:34:46 CEST.
Package gmp-c++-1:6.2.1-8.fc40.x86_64 is already installed.

Dependencies resolved.
Nothing to do.
Complete!

jaap@peace:~/sagemath/sage-10.4.beta5$  

gmp-c++ was already installed.

I see more errors to come related to the gcc version.

Jaap

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[Jaap Spies]

[spkg-install] checking pkg-config is at least version 0.9.0... yes
[spkg-install] checking for GIVARO... yes
[spkg-install] checking for GIVARO usability... no
[spkg-install] configure: error: The Givaro library could not be used with the compiler and the flags se
t up by the configure script
[spkg-install] ********************************************************************************
[spkg-install] Error configuring fflas_ffpack-2.4.3.p0
[spkg-install] See the file
[spkg-install]     /home/jaap/sagemath/sage-10.4.beta5/local/var/tmp/sage/build/fflas_ffpack-2.4.3.p0/sr
c/config.log
[spkg-install] for details.
[spkg-install] ********************************************************************************
************************************************************************
Error installing package fflas_ffpack-2.4.3.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log files
 /home/jaap/sagemath/sage-10.4.beta5/logs/pkgs/fflas_ffpack-2.4.3.p0.log
and
 /home/jaap/sagemath/sage-10.4.beta5/config.log

[Emmanuel Charpentier]

On Debian testing running on core i7n + 16 GB RAM, upgrading 10.4.beta4 to 10.4.beta5 and running ptestlong gives one permanent failure :

---------------------------------------------------------------------- sage -t --long --warn-long 237.3 --random-seed=209914381797624961646623654578067480099 src/sage/misc/cython.py # 3 doctests failed ----------------------------------------------------------------------

Thi has already been reported for 10.4.beta4.

HTH,

​

[Kazuyoshi Furutaka]

Fedora 40 (x86_64), same as the previous beta (I've posted the result, but it seems to be missing...).

Logs attached.

Kazuyoshi

2024年4月28日(日) 8:35 Kazuyoshi Furutaka <furutaka....@gmail.com>:

On a linux box (Fedora-40 x86_64)...

Need to `configure --without-system-gcc`. (gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0))

Then, the build of fflas_ffpack-2.4.3.p0 and ppl-1.2.p1 failed.

(Logs attached)

Kazuyoshi

2024年5月3日(金) 8:08 Volker Braun <vbrau...@gmail.com>:

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[Volker Braun]

I get the same, there is an issue at https://github.com/sagemath/sage/issues/37698

[Enrique Artal]

There are some pacthes to be applied (explained in the issue) and then it is built with system gcc