Sage 9.7.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

843eb03e7e (tag: 9.7.beta4, trac/develop) Updated SageMath version to 9.7.beta4
232d0434cf Trac #33866: Make jupyter_packaging standard; add hatchling, editables, pathspec, poetry_core, tomlkit, deprecation; update tomli, flit_core, setuptools, pip, wheel
9307820a88 Trac #33821: Remove use of SAGE_LIB in sage.misc
b23b788586 Trac #33409: Size of docker images has increased in 9.5
b5d2fcaeb0 Trac #33029: Feature and doctest tag for runtime cython
be2bda4921 Trac #29779: pkgconf: Update to 1.8.0, remove runtime dep on environment variable SAGE_LOCAL
c02edcb15b Trac #25374: Upgrade cryptominisat to 5.8.0, fix build on Cygwin
e22b33a0c1 Trac #34017: Fix tox-docker builds after #29941
c4236d0844 Trac #34008: pycodestyle cleanup in sage.graphs.generic_graph_pyx.pyx
6f961ffa38 Trac #34007: Allow start parameter in Python's sum
c59c86cfbd Trac #33996: ascii_art fail in jupyter notebook
c40983afcd Trac #33991: remove some unused imports
b02c408763 Trac #33978: various details about typing in combinat
6fb1e3f13a Trac #34037: Make doctest from #25626 more robust
4169d7d6c0 Trac #34035: Add __reversed__ method to FrozenBitsets
45c963e0c7 Trac #34030: move supercommutator to superalgebras
d4706f96f9 Trac #34019: minor code details in combinat
3d336f0435 Trac #34014: Clean src/sage/graphs/pq_trees.py
c9aa34b34c Trac #33957: Manifold.options.omit_function_arguments ineffective for arguments not in alphabetic order
0b2741d399 Trac #33619: clean up ell_curve_isogeny.py
c0e59251e2 Trac #34036: fix the linter
2b36879ae1 Trac #34025: Fix doctest in sage/modular/overconvergent/hecke_series.py
c0abe3f5ee Trac #33213: Replace SAGE_TMP by the system location in the sage library
7ab174a70d Trac #32340: document behavior of .is_prime() for number fields
c69f4af336 Trac #28263: Degree for Affine Morphism or Affine Dynamical System
e516392523 Trac #34001: Add flag to avoid OrePolynomialRing cast to PolynomialRing
01b8bcb85f Trac #33993: pep cleanup for words/morphism.py
716c5ce262 Trac #33992: remove class inheritance of object in remaining places
de375bce02 Trac #33990: Subset_s _an_element_
0593e83957 Trac #33987: modernize super() in structure, symbolic, doctest, databases
d9a45e29eb Trac #33985: modernize super() in monoids,modules,modular
7ed404657b Trac #33984: modernize super() in schemes,libs,sets,quivers
1df260e842 Trac #33979: .roots() does not always return elements of the base ring
c6c2b85405 Trac #33974: Documentation addition for symmetric functions - Cauchy identity
f92916e358 Trac #33840: bool(matrix) ignores exceptions raised while comparing entries
f8df80820d (tag: 9.7.beta3) Updated SageMath version to 9.7.beta3

[G. M.-S.]

This is on Apple Silicon Macs with Homebrew up to date (make and make pytest and  make ptestlong).

On macOS 12.4 (Monterey) with Xcode 13.4.1:  no problems.

On macOS 11.6.7 (Big Sur) with Xcode 13.2.1  make ptestlong gives the usual

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

sage -t --long --warn-long 49.7 --random-seed=82948061555362082515714844199946257016 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed

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

(see https://trac.sagemath.org/ticket/33212 and https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1).

Guillermo

[Kenji Iohara]

On Mac OS 12.4 with Intel Core i5 with Homebrew and Xcode 13.4.1, it compiled from the first build.

But, make ptestlong return me this one:

sage -t --long --random-seed=184626740109741532373427720110400467629 src/sage/doctest/test.py  # 1 doctest failed

sage -t --long --random-seed=184626740109741532373427720110400467629 src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 1 doctest failed

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

Total time for all tests: 9880.4 seconds

    cpu time: 19292.3 seconds

    cumulative wall time: 38972.9 seconds

Features detected for doctesting: dvipng,gfan,graphviz,imagemagick,nauty,palp,pandoc,pdf2svg,pdftocairo,polytopes_db,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.misc.cython,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

============================= test session starts ==============================

platform darwin -- Python 3.10.5, pytest-7.1.2, pluggy-1.0.0

rootdir: /Users/iohara/Desktop/sage-9.7.beta4/src, configfile: tox.ini

collected 26 items / 104 skipped                                               

src/sage/manifolds/differentiable/symplectic_form_test.py .............. [ 53%]

........                                                                 [ 84%]

src/sage/manifolds/differentiable/examples/symplectic_space_test.py .... [100%]

================== 26 passed, 104 skipped in 84.28s (0:01:24) ==================

09/07/2022 3:26、G. M.-S. <list...@gmail.com>のメール:

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[Marc Culler]

When I tried to build 9.7.beta4 on an M1 mac mini with macOS 12.4 using no external libraries except the Homebrew gfortran I got this error:

  error: Multiple top-level packages discovered in a flat-layout: ['cmake', 'symengine'].

  To avoid accidental inclusion of unwanted files or directories,
  setuptools will not proceed with this build.

  If you are trying to create a single distribution with multiple packages
  on purpose, you should not rely on automatic discovery.

Indeed, the symengine setup.py does not specify any packages, so pip tries to automatically discover the packages and it decides that the cmake directory is a package.

I don't seem to have the option of attaching the log file, but it does not have much more information than what is above.

- Marc

[Matthias Köppe]

Yes, we also see this in the CI for optional packages - https://github.com/sagemath/sage/actions/runs/2632874850

This is fallout from upgrading setuptools in https://trac.sagemath.org/ticket/33866

Looks like this is already fixed in upstream symengine.py. I've opened https://trac.sagemath.org/ticket/34141 

[david....@gmail.com]

on MacOS 12.3.1 with Xcode 13.4.1 and a recent brew upgrade, I did: bootstrap, source .homebrew-build-env, configure and make.

The compilation went well, but sage is not working at all.

- Sage looks for /usr/local/Cellar/flint/2.9.0/lib/libflint-16.dylib. but I have /usr/local/Cellar/flint/2.9.0/lib/libflint-17.dylib

- Also, the completion is not working anymore in the console.

What can I try to fix the issue ?

Thanks,

David.

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

sapristi:sage dcoudert$ ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.7.beta4, Release Date: 2022-07-07               │
│ Using Python 3.9.13. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┃ Warning: sage.all is not available; this is a limited REPL.        ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: import sage.all
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-d287b22e1156> in <module>
----> 1 import sage.all

~/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/all.py in <module>
    136 from sage.modules.all    import *
    137 from sage.monoids.all    import *
--> 138 from sage.algebras.all   import *
    139 from sage.modular.all    import *
    140 from sage.sat.all        import *

~/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/algebras/all.py in <module>
     19 from sage.misc.lazy_import import lazy_import
     20
---> 21 import sage.algebras.catalog as algebras
     22
     23 from .quantum_groups.all import *

~/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/algebras/catalog.py in <module>
     78
     79 from sage.algebras.free_algebra import FreeAlgebra as Free
---> 80 from sage.algebras.quatalg.quaternion_algebra import QuaternionAlgebra as Quaternion
     81 from sage.algebras.steenrod.steenrod_algebra import SteenrodAlgebra as Steenrod
     82 from sage.algebras.finite_dimensional_algebras.finite_dimensional_algebra import FiniteDimensionalAlgebra as FiniteDimensional

~/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/algebras/quatalg/quaternion_algebra.py in <module>
     66     QuaternionAlgebraElement_rational_field,
     67     QuaternionAlgebraElement_number_field)
---> 68 from . import quaternion_algebra_cython
     69
     70 from sage.modular.modsym.p1list import P1List

~/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/algebras/quatalg/quaternion_algebra_cython.pyx in init sage.algebras.quatalg.quaternion_algebra_cython (build/cythonized/sage/algebras/quatalg/quaternion_algebra_cython.cpp:6388)()
----> 1 # distutils: language = c++
      2 # distutils: libraries = gmp m NTL_LIBRARIES
      3 # distutils: extra_compile_args = NTL_CFLAGS
      4 # distutils: include_dirs = NTL_INCDIR
      5 # distutils: library_dirs = NTL_LIBDIR

ImportError: dlopen(/Users/dcoudert/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/flint/lib/libflint-16.dylib
  Referenced from: /Users/dcoudert/sage/local/lib/liblinbox.0.dylib
  Reason: tried: '/usr/local/opt/flint/lib/libflint-16.dylib' (no such file), '/usr/local/lib/libflint-16.dylib' (no such file), '/usr/lib/libflint-16.dylib' (no such file), '/usr/local/Cellar/flint/2.9.0/lib/libflint-16.dylib' (no such file), '/usr/local/lib/libflint-16.dylib' (no such file), '/usr/lib/libflint-16.dylib' (no such file)
sage:                                                                                                                                                                                                

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

[Dima Pasechnik]

On Sun, 10 Jul 2022, 09:43 david....@gmail.com, <david....@gmail.com> wrote:

on MacOS 12.3.1 with Xcode 13.4.1 and a recent brew upgrade, I did: bootstrap, source .homebrew-build-env, configure and make.

The compilation went well, but sage is not working at all.

- Sage looks for /usr/local/Cellar/flint/2.9.0/lib/libflint-16.dylib. but I have /usr/local/Cellar/flint/2.9.0/lib/libflint-17.dylib

- Also, the completion is not working anymore in the console.

you apparently have some bits not rebuilt, which were built against older Flint.

I'd do

   make sagelib-clean sagelib-uninstall

followed by

   make

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[David Coudert]

I tried, but I still get the same issue.

I will try with a make distclean.

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[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.7.beta3 to 9.7.beta4 aonr running ptestlong gets me four permanent failures :

sage -t --long --warn-long 194.8 --random-seed=306940939898170022951447712153853509405 src/sage/modular/overconvergent/hecke_series.py  # Timed out
sage -t --long --warn-long 194.8 --random-seed=306940939898170022951447712153853509405 src/sage/libs/eclib/mwrank.pyx  # 1 doctest failed
sage -t --long --warn-long 194.8 --random-seed=306940939898170022951447712153853509405 src/sage/libs/eclib/interface.py  # 7 doctests failed
sage -t --long --warn-long 194.8 --random-seed=306940939898170022951447712153853509405 src/sage/calculus/calculus.py  # 1 doctest failed
sage -t --long --warn-long 194.8 --random-seed=306940939898170022951447712153853509405 src/sage/groups/perm_gps/permgroup_named.py  # 2 doctests failed

i. e. the same results as in the previous beta.

HTH,

​

[David Coudert]

Working properly again after distclean. Sorry for the noise.