Sage 9.8.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

84f02afa5c8 (trac/develop, tag: 9.8.beta4) Updated SageMath version to 9.8.beta4
03f68f4aa96 Trac #34737: less use of gap.eval in linear code
96c4ae9184a Trac #34735: some details in hyperelliptic_padic_field
f9cee4ddd29 Trac #34731: math display broken because of missing .
1b9ac4d11cd Trac #34727: .multiplication_by_m_isogeny() fails for negative m
bcabe95d75f Trac #34723: elliptic_curves/hom_velusqrt.py: random test failure
8e1b55bb21e Trac #34710: Keep object entries in TOC in short form
576ea23021f Trac #34746: Upgrade cmake to 3.24.3, increase minimum system cmake version to 3.11
6cc6cf548ee Trac #34739: get rid of some usage of "long" python2 type in pyx files
80c3f4658dc Trac #34736: cleanup for QQ-curves
e338c18b412 Trac #34733: polynomial quo_rem gives wrong answer for noncommutative rings
6fda98d9de9 Trac #34732: more opportunistic caching of elliptic-curve and point orders
d883104bb2e Trac #34692: Frobenius endomorphism creation fail for infinite ring extension
df312d1b178 Trac #30217: tox.ini: Add tests with Ubuntu + deadsnakes
b52855ecc64 Trac #34730: Rebase sage_autodoc to sphinx 5.3.0
1df550e3c3d Trac #34729: topcom now requires autotools
c4edf81bf10 Trac #34709: fix cython warning in blas_dict
a30f206758b Trac #34652: Import NN directly rather than lazily throughout the Sage library
4b9a50080bd Trac #34589: VectorFieldModule, TensorFieldModule, DiffFormModule: Add methods tensor_product, tensor_power, update category of TensorFieldModule
9e0f15669b9 Trac #33878: Upgrade cypari2 to 2.1.3
cf0b066c0d9 Trac #32570: tox.ini, GH Actions: Update macOS environments to macOS 11, 12
9574dd15131 Trac #26084: Detect default colorscheme (dark/light)
94bdf2f12f3 Trac #18917: Speed up NumberField.zeta()
b641e6f0166 Trac #34724: echelonize() on RR matrices should not use "classical" algorithm
5048fd4c544 Trac #34081: Upgrade scipy to 1.9.x, add meson toolchain
8443dc3d8a5 Trac #34719: move carmichael_lambda() from sage.crypto.util to sage.arith.misc
4edaafebeed Trac #34716: fix assertion failure in _discrete_log_pgroup() when group is trivial
50977491440 Trac #34705: fix and activate W605 and E306 in pyx files
127c01cd4a9 Trac #34704: clean whitespace W293 in py files
4f157b7bddc Trac #34703: remove traces of lgtm
30d86af37d2 Trac #34676: Upgrade pip 22.3 and various other Python packages
17cc8b3d400 Trac #34654: Pickling frobenius endomorphism is broken
642f1157431 Trac #24462: Add tests that discriminant() of number fields is Integer
69f026a80d4 Trac #34713: Update IPython to 8.6
a2850f84bd2 Trac #34712: partial pep8 cleanup for number_field.py
3478e6fa5d3 Trac #34707: Bug in Clifford algebra multiplication
dee975299c2 Trac #34702: fix deprecated use of PyEval_Call*
3b6033475ee Trac #34681: Error with multiplication of points on elliptic curves over Integers(n)
4b482ce49c9 Trac #34651: Add `multivariate_interpolation` for multivariate polynomial rings
139fe8eaa0b Trac #34611: fast implementation of exp
c709fa42921 Trac #34397: pycodestyle cleanup in src/sage/graphs/generic_graph.py (part 9)
58c9281ec67 Trac #32267: make hadamard_matrix() use all the Hadamard matrices Sage knows
edfa1f93738 Trac #30423: F-Matrix Factory
7aa226ced2f Trac #34699: some details about INPUT and INPUT in the doc
c4079b7488c Trac #34697: minor fixes in doc in pyx files
813072800d9 Trac #34691: companion matrix of constant polynomial has the wrong parent
6b70584ab66 Trac #34638: refresh the file categories/rings.py
f634f6b0195 Trac #34368: implement the F,H,M triangles
859c3516190 Trac #34689: make Compositions() an additive monoid
b5082885f9a Trac #34665: openssl spkg-configure.m4: Also require openssl if curl needs to be built
487f2f9bca8 Trac #34662: sage.combinat.permutation.from_cycles produces wrong result when 'cycles' is a generator
ab0944d9eaf Trac #34636: make sparsity a decision of the user
24d0a8a1219 Trac #34381: Add infinite q-Pochhammer symbol
ef1d3d23588 Trac #34260: Implement northwest diagrams
bff11ac3b18 Trac #33176: Fix a few cython "referenced before assignment" warnings
89af3469590 Trac #32267: make hadamard_matrix() use all the Hadamard matrices Sage knows
c3028e74d80 (tag: 9.8.beta3) Updated SageMath version to 9.8.beta3

[John H Palmieri]

scipy fails to build for me (OS X 13.0.1, Intel, with various homebrew packages, Sage built from a new tarball):

Successfully built scipy
WARNING: Skipping scipy as it is not installed.
Using pip 22.3 from /Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.8.beta4/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip (python 3.10)
Looking in links: /Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.8.beta4/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels
ERROR: scipy-1.9.2-cp310-cp310-macosx_13_x86_64.whl is not a supported wheel on this platform.
Warning: installing with "python3 -m pip install --verbose --no-index --find-links=/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.8.beta4/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels --disable-pip-version-check --isolated --no-cache-dir" failed. Retrying, adding "--no-deps --ignore-installed --ignore-requires-python"
Using pip 22.3 from /Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.8.beta4/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip (python 3.10)
Looking in links: /Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.8.beta4/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels
ERROR: scipy-1.9.2-cp310-cp310-macosx_13_x86_64.whl is not a supported wheel on this platform.

Error: installing with pip  failed

[Matthias Köppe]

I think this will be fixed by the meson-python upgrade in https://trac.sagemath.org/ticket/34658, please test

[John H Palmieri]

Yes, that works for me. (I see the same problem on OS X with Apple Silicon, and that ticket also fixes the problem there.)

[Kenji Iohara]

With my Mac OS 13.0.1, with Intel Core i5, and several packages with Homebrew, I have a problem with downloading 

* package:         numpy-1.23.5

  last build time: Nov 23 04:33

  log file:        /Users/iohara/Desktop/sage-9.8.beta4/logs/pkgs/numpy-1.23.5.log

* package:         meson_python-0.11.0

  last build time: Nov 23 04:33

  log file:        /Users/iohara/Desktop/sage-9.8.beta4/logs/pkgs/meson_python-0.11.0.log

. Something strange ?      Kenji

22/11/2022 22:13、John H Palmieri <jhpalm...@gmail.com>のメール:

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[Matthias Köppe]

If you're testing https://trac.sagemath.org/ticket/34658, you'll need "./configure --enable-download-from-upstream-url".

[Kenji Iohara]

Dear Matthias,

 

 Thanks for your indication. Even with this,It couldn’t download the tar.gz files and I had the following errors:

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

[meson_python-0.11.0] Traceback (most recent call last):

[meson_python-0.11.0]   File "/Users/iohara/Desktop/sage-9.8.beta4/build/bin/../sage_bootstrap/download/cmdline.py", line 126, in run_safe

[meson_python-0.11.0]     run()

[meson_python-0.11.0]   File "/Users/iohara/Desktop/sage-9.8.beta4/build/bin/../sage_bootstrap/download/cmdline.py", line 108, in run

[meson_python-0.11.0]     app.download_tarball(args.url_or_tarball, args.destination, args.allow_upstream)

[meson_python-0.11.0]   File "/Users/iohara/Desktop/sage-9.8.beta4/build/bin/../sage_bootstrap/download/app.py", line 41, in download_tarball

[meson_python-0.11.0]     tarball.download(allow_upstream=allow_upstream)

[meson_python-0.11.0]   File "/Users/iohara/Desktop/sage-9.8.beta4/build/bin/../sage_bootstrap/tarball.py", line 181, in download

[meson_python-0.11.0]     raise ChecksumError('checksum does not match')

[meson_python-0.11.0] sage_bootstrap.tarball.ChecksumError: checksum does not match

[meson_python-0.11.0] ************************************************************************

[meson_python-0.11.0] ************************************************************************

[meson_python-0.11.0] Error downloading meson_python-0.11.0.tar.gz

[meson_python-0.11.0] ************************************************************************

[meson_python-0.11.0] Please email sage-devel (http://groups.google.com/group/sage-devel)

[meson_python-0.11.0] explaining the problem and including the log files

[meson_python-0.11.0]   /Users/iohara/Desktop/sage-9.8.beta4/logs/pkgs/meson_python-0.11.0.log

[meson_python-0.11.0] and

[meson_python-0.11.0]   /Users/iohara/Desktop/sage-9.8.beta4/config.log

[meson_python-0.11.0] Describe your computer, operating system, etc.

[meson_python-0.11.0] ************************************************************************

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

make[3]: *** [/Users/iohara/Desktop/sage-9.8.beta4/local/var/lib/sage/venv-python3.9/var/lib/sage/installed/meson_python-0.11.0] Error 2

make[3]: Target `all-sage-docs' not remade because of errors.

make[3]: Target `all-sage' not remade because of errors.

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

real 0m46.199s

user 0m1.848s

sys 0m0.713s

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

Error building Sage.

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

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

* package:         numpy-1.23.5

  last build time: Nov 23 09:06

  log file:        /Users/iohara/Desktop/sage-9.8.beta4/logs/pkgs/numpy-1.23.5.log

* package:         meson_python-0.11.0

  last build time: Nov 23 09:06

  log file:        /Users/iohara/Desktop/sage-9.8.beta4/logs/pkgs/meson_python-0.11.0.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.

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

make: *** [all] Error 2

make: Target `default' not remade because of errors.

23/11/2022 5:57、Matthias Köppe <matthia...@gmail.com>のメール:

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[John H Palmieri]

Maybe you need to run `./bootstrap` and then `./configure --enable-download-from-upstream-url`?

[Kenji Iohara]

I have tried   “make distclean” and then “./bootstrap” and finally “./configure —enable-download-from-url” but they didn’t work. Instead, I have installed meson_python and numpy with pip install, and it worked. But it added a new problem on the compilation of

 scipy. I also installed the most updated version with pip install, and see whether I can compile sage9.8.b4 from the first built.

Kenji 

iPadから送信

23/11/2022 20:50、John H Palmieri <jhpalm...@gmail.com>のメール:



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[Kenji Iohara]

I still have a problem on downloading       scipy-1.9.3    Kenji

23/11/2022 20:50、John H Palmieri <jhpalm...@gmail.com>のメール:

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[Dima Pasechnik]

On Thu, Nov 24, 2022 at 2:59 AM Kenji Iohara <simplye...@gmail.com> wrote:
>
> I still have a problem on downloading scipy-1.9.3 Kenji

I've just checked that the checksums on
https://pypi.io/packages/source/s/scipy/scipy-1.9.3.tar.gz
match ones given in the branch of https://trac.sagemath.org/ticket/34658

I suppose your particular copy of scipy-1.9.3.tar.gz in upstream/ is
corrupt for one or another reason.
Remove it, and restart building.

HTH
Dima

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/32A38DF3-9953-41CF-BD1C-1D31CA09E608%40gmail.com.

[Kenji Iohara]

[Dima Pasechnik]

you need to run

./configure --enable-download-from-upstream-url

(this will hopefully be default, but not yet)

On Thu, 24 Nov 2022, 12:48 Kenji Iohara, <simplye...@gmail.com> wrote:

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The errors I had is this.. It indicates that it cannot download scipy-1.9.3.tar.gz owing to the wrong address…

Something strange.

24/11/2022 12:56、Dima Pasechnik <dim...@gmail.com>のメール:

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[Kenji Iohara]

Even with this, it didn’t work. 

24/11/2022 14:28、Dima Pasechnik <dim...@gmail.com>のメール:

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[Dima Pasechnik]

What exactly didn't work this time?

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/7931CAE9-A3E3-4B67-9F57-C06271F1F991%40gmail.com.

[Kenji Iohara]

In fact, I first did  ''make distclean’’  to redo these steps. And then, I did  '' ./bootstrap’’ and did

                           ''./configure --enable-download-from-upstream-url’’ . After this, I did <<make -k>>

                           After compilation, it gave me the message, which sais that <<scipy-1.9.3>> is not

                           Downloadable. 

By the way, I also saw some message which sais << Python 3.11>> is too new. Do you think this is related to the problem ?

24/11/2022 18:19、Dima Pasechnik <dim...@gmail.com>のメール:

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[Dima Pasechnik]

On Thu, Nov 24, 2022 at 5:25 PM Kenji Iohara <simplye...@gmail.com> wrote:
>
> In fact, I first did ''make distclean’’ to redo these steps. And then, I did '' ./bootstrap’’ and did
> ''./configure --enable-download-from-upstream-url’’ . After this, I did <<make -k>>
> After compilation, it gave me the message, which sais that <<scipy-1.9.3>> is not
> Downloadable.

I don't know what "not Downloadable" means.
You can try to download the needed file manually.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/79109A97-DE5D-4766-8EB8-C07BE64F1621%40gmail.com.

[Clemens Heuberger]

On one machine, I get

sage -t --long --warn-long 47.4
--random-seed=246094074504021516870962841122231333953
src/sage/graphs/generic_graph.py # Timed out

(log attached).

Using another random seed solves the problem:

sage -t --long --warn-long 47.2
--random-seed=58001952993324520911224750531791152113
src/sage/graphs/generic_graph.py



Am 22.11.22 um 00:16 schrieb Volker Braun:

[David Coudert]

This is again the MILP formulation of `edge_disjoint_spanning_trees`.

We now have a fast combinatorial algorithm (Roskind-Tarjan). We have not removed the MILP formulation to be able to check the validity of the result, but it frequently causes doctests errors. May be it’s time to remove it for undirected graphs.

For directed graphs, we have not finalized the implementation of Gabow’s algorithm yet. It is very complex. So we still rely on the MILP formulation.

David.

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> <generic_graph.log>

[Matthias Köppe]

https://trac.sagemath.org/ticket/21003 (PySCIPopt) adds a much better MILP solver, which has the potential for replacing GLPK as our standard solver.

[David Joyner]

Compiled fine on a brand new linux laptop running ubuntu 22,04 after
following the instructions at
https://doc.sagemath.org/html/en/installation/source.html
configure asked me to install
sudo apt-get install libec-dev eclib-tools fflas-ffpack libfplll-dev
libgivaro-dev liblinb
ox-dev liblrcalc-dev libprimesieve-dev libqhull-dev
and
sudo apt-get install 4ti2 gpgconf openssh-client git libigraph-dev
polymake libpolymake-de
v default-jdk libavdevice-dev

wdj@system76-pc:~$ uname -a
Linux system76-pc 6.0.6-76060006-generic
#202210290932~1667401208~22.04~d2df702~dev-Ubuntu SMP PREEMPT_DY x86_
64 x86_64 x86_64 GNU/Linux

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[Kenji Iohara]

Is Python3.11 on Mac OS too new too build Sage 9.8.beta4 ?
This seems to be related to some problem with scipy-1.9.3.
K.

> 28/11/2022 21:19、David Coudert <david....@gmail.com>のメール:

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/32D66B01-3BD3-48F4-813E-1A42313D32AB%40gmail.com.

[Matthias Köppe]

Yes, Python 3.11 is not yet supported. https://trac.sagemath.org/ticket/33842 adds support for it and is waiting for review.

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.8.beta3 to 9.8.beta4 and running ptestlong gives me 3 (permanent) failures :

----------------------------------------------------------------------
sage -t --long --warn-long 233.1 --random-seed=40705015305494208121726835907964991561 src/sage/graphs/generators/families.py  # 3 doctests failed
sage -t --long --warn-long 233.1 --random-seed=40705015305494208121726835907964991561 src/sage/graphs/graph_generators.py  # 1 doctest failed
sage -t --long --warn-long 233.1 --random-seed=40705015305494208121726835907964991561 src/sage/algebras/quantum_groups/quantum_group_gap.py  # 3 doctests failed
----------------------------------------------------------------------

The first one is real (difference in results). The second one may be a byproduct of a new nauty version (different “Uwage” error message). The third one may be cosmetic (obnoxious deprecation warning).

HTH,

​