Sage 10.5.beta4 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

a880b3f2d99 (tag: 10.5.beta4, github/develop) Updated SageMath version to 10.5.beta4
27fce1faa78 gh-38646: add typing annotation in temporary_file
c82c5099a7e gh-38644: pathlib in simplicial sets examples
94741f9cb9e gh-38638: interface to new nauty generator for Hasse diagrams
c0e0c378de8 gh-38636: fix something in quadratic forms
34d32dd03c8 gh-38635: fixing most ruff PERF4 warnings in combinat
4a9c985b769 gh-38628: Fix hypellfrob.pyx calling Python inside sig_on
c6463204b83 gh-38627: Require weaker Sphinx dependency for sagelib
caa5174974d gh-38625: Remove outdated setting of `sphinx_source_suffix`
72f2e28765f gh-38624: Fix issue report formatting
7ba90e10e8f gh-38622: pep8 fixes in schemes/toric
2015ab21b5c gh-38621: switch from `genbg` to `genbgL` in `nauty_genbg` to generate larger bipartite graphs.
1e57fe2cb97 gh-38620: cleaning the deprecation and removal of NoetherianRing class
bcedc6aa1e5 gh-38619: Re-add py3.9 support to sage_autodoc.py
011111cde42 gh-38616: `structure/sage_object.pyx`: remove excess `%s`s
05db5cdeb65 gh-38615:  `permgroup_element.pyx`: add some `const`s
884dded847d gh-38614: some pep8 fixes in combinat/designs
e9f546b2d36 gh-38613: `categories/morphism.pyx`: remove some `noexcept`s
de3035af74a gh-38612: pep8 cleanup in algebras
21b99b27cbe gh-38611: pep and ruff cleanup in semirings and tropicals
488b258cbd6 gh-38610: fix and activate E303 check in pyx files
6e6e84d5df1 gh-38609: fix the linter
abcf4a6011f gh-38608: Add warning filter for DeprecationWarning while doc build
ae77953f729 gh-38602: Allow for python sets to be counted as sets
92725c7c4f4 gh-38598: Add reflection_index_set() and reflection() methods for permutations
06495417f3c gh-38592: Add is_integral method to algebraic numbers
189a4a1122b gh-38585: adding a warning about iteration over words
05788941c3f gh-38581: README.md, src/doc/en/installation: Replace release tours links
ab35cb8eb56 gh-38577: Add various project URLs for PyPI
800c2279d7b gh-38576: `crypto/sbox.pyx`: remove unreachable code
483591122e8 gh-38575: Fix `is_homogeneous` weight bug
b3266925efa gh-38572: `build/pkgs/nauty`: Update to 2.8.9
558157ecda5 gh-38571: `build/pkgs/primecount` 7.14, `primesieve`: 12.4
468d3ee1f3b gh-38568: Right align sage/python tabs and alter vertical spacing
8f82c5279b3 gh-38558: `build/pkgs/python3`: Update to 3.12.5
1876c2cda09 gh-38548: `build/pkgs/pip` 24.2, `setuptools` 73.0.1 etc.
10bb5148d24 gh-38542: Fixes in pyx files
c7bbcb463b1 gh-38539: some details in strassen.pyx
1aad5fb6097 gh-38532: `build/pkgs/jupyter_jsmol`: Change to optional
9a30984ed16 gh-38504: Demote `jmol` to optional
280d51140c7 gh-38501: `build/pkgs/cython`: Update to 3.0.11
473a5712f69 gh-38435: add method `is_edge_cut` to graphs
76fbb6cc8a5 gh-38341: Implement EllipticCurve_with_prime_order() constructor
2270e23a8d9 gh-38299: graphs: add implementation of slice decomposition via an extended LexBFS algorithm
2a4f6e127a7 gh-37821: Fix category of ModularFormsRing and documentation cleanup
d1fe4120a99 gh-37569: Repair `sage -t --valgrind`
24698e7e7ec (tag: 10.5.beta3) Updated SageMath version to 10.5.beta3

[David Coudert]

I have the following issue at the end of an incremental update on macOS 14.6.1 (M1).

I observe the same error on Fedora 39.

I don’t know what to do with it.

I can start sage (10.5.beta4) in a shell and it seems ok.

Best,

David.

==================================================================

….

[sagelib-10.5.beta4] [spkg-install]     Installing sage-python script to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/bin

[sagelib-10.5.beta4] [spkg-install]     Installing sage-run script to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/bin

[sagelib-10.5.beta4] [spkg-install]     Installing sage-run-cython script to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/bin

[sagelib-10.5.beta4] [spkg-install]     Installing sage-startuptime.py script to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/bin

[sagelib-10.5.beta4] [spkg-install]     Installing sage-update-version script to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/bin

[sagelib-10.5.beta4] [spkg-install] 

[sagelib-10.5.beta4] [spkg-install]     Installed /Users/dcoudert/sage/src

[sagelib-10.5.beta4] [spkg-install] Successfully installed sagemath-standard

[sagelib-10.5.beta4] Moving package files from temporary location /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sagelib-10.5.beta4/inst to /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9

[sagelib-10.5.beta4] Deleting build directory /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sagelib-10.5.beta4

[sagelib-10.5.beta4] Finished installing sagelib-10.5.beta4

[sagelib-10.5.beta4] real 0m21.017s user 0m8.042s sys 0m3.618s

make --no-print-directory sagemath_environment-SAGE_VENV-no-deps

[sagemath_environment-10.5.beta4] Setting up build directory /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sagemath_environment-10.5.beta4

[sagemath_environment-10.5.beta4] Host system: Darwin MAC-04017247 23.6.0 Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:30 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6000 arm64

[sagemath_environment-10.5.beta4] C compiler: gcc, Apple clang version 15.0.0 (clang-1500.3.9.4), Target: arm64-apple-darwin23.6.0, Thread model: posix, InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

[sagemath_environment-10.5.beta4] No stamp file for package 'sagemath_environment' in /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/installed

[sagemath_environment-10.5.beta4] No spkg-legacy-uninstall script; nothing to do

[sagemath_environment-10.5.beta4] [spkg-install] * Creating isolated environment: venv+pip...

[sagemath_environment-10.5.beta4] [spkg-install] ERROR Failed to parse ./pyproject.toml: Invalid initial character for a key part (at line 32, column 79) 

[sagemath_environment-10.5.beta4] [spkg-install] Warning: building with "python3 -m build  --outdir=dist   ." failed.

[sagemath_environment-10.5.beta4] [spkg-install] Retrying with "python3 -m build  --outdir=dist --no-isolation --skip-dependency-check  .".

[sagemath_environment-10.5.beta4] [spkg-install] ERROR Failed to parse ./pyproject.toml: Invalid initial character for a key part (at line 32, column 79) 

[sagemath_environment-10.5.beta4] [spkg-install] ********************************************************************************

[sagemath_environment-10.5.beta4] [spkg-install] Error building a wheel for sagemath_environment-10.5.beta4

[sagemath_environment-10.5.beta4] [spkg-install] ********************************************************************************

[sagemath_environment-10.5.beta4] ************************************************************************

[sagemath_environment-10.5.beta4] Error installing package sagemath_environment-10.5.beta4

[sagemath_environment-10.5.beta4] ************************************************************************

[sagemath_environment-10.5.beta4] Please email sage-devel (http://groups.google.com/group/sage-devel)

[sagemath_environment-10.5.beta4] explaining the problem and including the log files

[sagemath_environment-10.5.beta4]   /Users/dcoudert/sage/logs/pkgs/sagemath_environment-10.5.beta4.log

[sagemath_environment-10.5.beta4] and

[sagemath_environment-10.5.beta4]   /Users/dcoudert/sage/config.log

[sagemath_environment-10.5.beta4] Describe your computer, operating system, etc.

[sagemath_environment-10.5.beta4] If you want to try to fix the problem yourself, *don't* just cd to

[sagemath_environment-10.5.beta4] /Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sagemath_environment-10.5.beta4 and type 'make' or whatever is appropriate.

[sagemath_environment-10.5.beta4] Instead, the following commands setup all environment variables

[sagemath_environment-10.5.beta4] correctly and load a subshell for you to debug the error:

[sagemath_environment-10.5.beta4]   (cd '/Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sagemath_environment-10.5.beta4' && '/Users/dcoudert/sage/sage' --buildsh)

[sagemath_environment-10.5.beta4] When you are done debugging, you can type "exit" to leave the subshell.

[sagemath_environment-10.5.beta4] ************************************************************************

make[4]: *** [sagemath_environment-SAGE_VENV-no-deps] Error 1

make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/installed/sagemath_environment-10.5.beta4] Error 2

make[2]: *** [all-build] Error 2

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

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all-build'):

* package:         sagemath_environment-10.5.beta4

  last build time: 16 sep 10:48

  log file:        /Users/dcoudert/sage/logs/pkgs/sagemath_environment-10.5.beta4.log

It is safe to delete any log files and build directories, but they

contain information that is helpful for debugging build problems.

WARNING: If you now run 'make' again, the build directory of the

same version of the package will, by default, be deleted. Set the

environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

real 0m41.584s user 0m9.791s sys 0m5.603s

make[1]: *** [all-build] Error 1

make: *** [build] Error 2

==================================================================

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[Antonio Rojas]

This is caused by malformed toml code introduced in https://github.com/sagemath/sage/pull/38577

[Volker Braun]

I've created https://github.com/sagemath/sage/pull/38667

[Emmanuel Charpentier]

On Ubuntu 24.04running under WSL2/Windows11 on core i7 = 32 GB rAM; upgrading 10.5.beta3 to 10.5.beta4 and running ptestlong gives two transient failures :

sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/plot/animate.py # 1 doctest failed sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/rings/real_mpfr.pyx # 1 doctest failed

(both are timeouts) and two permanent failures :

sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/plot/animate.py # 1 doctest failed sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/rings/real_mpfr.pyx # 1 doctest failed

The second one has been reported a few times. The first one is new, and seems genuine ; re-running it gives :

charpent@SAP5342949:/usr/local/sage-10$ sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/combinat/tiling.py # 1 doctest failed Running doctests with ID 2024-09-18-12-14-14-5faac000. Git branch: develop Git ref: a880b3f2d99 Running with SAGE_LOCAL='/usr/local/sage-10/local' and SAGE_VENV='/usr/local/sage-10/local/var/lib/sage/venv-python3.12' Using --optional=debian,dot2tex,fricas,gap_jupyter,gap_packages,jmol,jupyter_jsmol,libsemigroups,msolve,pip,pysingular,sage,sage_spkg,singular_jupyter Features to be detected: 4ti2,SAGE_SRC,benzene,bliss,buckygen,conway_polynomials,coxeter3,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,glucose,graphviz,imagemagick,ipython,jmol,jupymake,jupyter_sphinx,kenzo,kissat,latte_int,lrcalc_python,lrslib,mathics,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,pycosat,pycryptosat,pynormaliz,pyparsing,python_igraph,requests,rpy2,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.homfly,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,sirocco,sphinx,symengine_py,sympy,tdlib,threejs,topcom Doctesting 1 file. sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/combinat/tiling.py ********************************************************************** File "src/sage/combinat/tiling.py", line 2393, in sage.combinat.tiling.TilingSolver.animate Failed example: a # long time (2s), optional - imagemagick, needs sage.plot Expected: Animation with 123 frames Got: Command "['convert', '-dispose', 'Background', '-delay', '20', '-loop', '0', '*.png', '/tmp/tmpoei9tb2p/tmp_el93p2rx.gif']" returned nonzero exit status "1" (with stderr "convert-im6.q16: time limit exceeded `/tmp/tmpoei9tb2p/tmp_el93p2rx.gif' @ fatal/cache.c/GetImagePixelCache/1867." and stdout ""). doctest:warning File "<doctest sage.combinat.tiling.TilingSolver.animate[8]>", line 1, in <module> a # long time (2s), optional - imagemagick, needs sage.plot File "/usr/local/sage-10/src/sage/repl/rich_output/display_manager.py", line 799, in displayhook plain_text, rich_output = self._rich_output_formatter(obj, dict()) File "/usr/local/sage-10/src/sage/repl/rich_output/display_manager.py", line 621, in _rich_output_formatter rich_output = self._call_rich_repr(obj, rich_repr_kwds) File "/usr/local/sage-10/src/sage/repl/rich_output/display_manager.py", line 586, in _call_rich_repr warnings.warn( File "/usr/lib/python3.12/warnings.py", line 110, in _showwarnmsg sw(msg.message, msg.category, msg.filename, msg.lineno, : sage.repl.rich_output.display_manager.RichReprWarning: Exception in _rich_repr_ while displaying object: Error: Cannot generate GIF animation. The magick/convert command (ImageMagick) is present but does not seem to be functional. Verify that the objects passed to the animate command can be saved in PNG image format. See www.imagemagick.org more information. Animation with 123 frames ********************************************************************** 1 item had failures: 1 of 12 in sage.combinat.tiling.TilingSolver.animate [492 tests, 1 failure, 98.50 s] ---------------------------------------------------------------------- sage -t --long --warn-long 92.0 --random-seed=215891992822319941402876332559304583711 src/sage/combinat/tiling.py # 1 doctest failed ---------------------------------------------------------------------- Total time for all tests: 98.6 seconds cpu time: 85.8 seconds cumulative wall time: 98.5 seconds Features detected for doctesting: imagemagick,sage.combinat,sage.modules,sage.plot

HTH,

​

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, the same upgrade and test leads to the single permanent failure :

sage -t --long --warn-long 226.4 --random-seed=46422283117155399456693174241434601637 src/sage/rings/real_mpfr.pyx # 1 doctest failed

HTH,

​