Sage 9.7.beta7 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

cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated SageMath version to 9.7.beta7
c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and sage/rings
c29832b57c Trac #34165: Fix docstring markup in sage/tests/book_stein_modform.py
a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
83ba832260 Trac #34159: Fix docstring markup in sage/modular
e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
252d1327ec Trac #34153: pycodestyle cleanup in sage/geometry/hyperplane_arrangement/hyperplane.py
f75cc20505 Trac #34146: Modernize super in coding/
59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
c7817820c0 Trac #34101: cutwidth_dyn use after free
9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx - part 1
a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
3cd360b4f5 Trac #34078: pycodestyle cleanup in src/sage/graphs/graph_plot.py
fac74d59ab Trac #34077: pycodestyle cleanup in src/sage/graphs/graph_input.py
4c67a04450 Trac #34073: pycodestyle cleanup in src/sage/graphs/graph_coloring.pyx
ead25a50eb Trac #34068: pycodestyle cleanup in src/sage/graphs/connectivity.pyx
288834efb2 Trac #33971: Height of a dynamical system is wrong
c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive' makes Sage crash
c89955d2e5 Trac #34227: Compute the similarity class type of a given matrix; compute invariant subspace generating function from similarity class type
8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
b0107b91e9 Trac #34216: configure: Use --with-system-{gfortran,openssl,python3}=force on Cygwin
d9568109f7 Trac #34214: Faster version of longest_increasing_subsequence_length
1b0314ac79 Trac #34208: Remove package sip
79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in sage.rings
aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
0e5ef88d17 Trac #34176: update curl to version 7.84
9b6a99a720 Trac #33817: GH Actions: Add test of the modularized distributions
fd93be8851 Trac #32406: Make "./configure --enable-editable" the default
dcd778b1a9 Trac #31568: Add commands "sage --lldb", "sage -t --lldb"
7f0a555ccb Trac #31451: Faster version of longest_increasing_subsequences
b5baa7d3f9 Trac #34115: tox.yml: Refactor using reusable workflows, update Linux platforms
be272221fa Trac #33627: Remove sage-gdb-commands from src/bin
c19c47fd63 Trac #34174: insufficient precision in scaling elliptic curves over number fields by units
aa8a4647f9 Trac #34172: Fix docstring markup in sage/groups and sage/misc
4142099591 Trac #34168: Fix docstring markup in sage/categories
e9be1728bb Trac #34166: Fix docstring markup in sage/tests except sage/tests/book_stein_modform.py
6e41b53b09 Trac #34164: Fix docstring markup in sage/plot and sage/graphs
b03229e112 Trac #34163: Fix docstring markup in sage/interfaces
46849b8d41 Trac #34160: Fix docstring markup in sage/schemes
984137bbb8 Trac #34155: OpenSSL 3.0.5 security update
ced8f29e11 Trac #34151: get rid of Oops messages in quadratic forms
b0456638af Trac #34149: make documentation building compatible with sphinx 5
07d4b909f0 Trac #34105: ZeroDivisionError while reducing a polynomial w.r.t. the zero ideal
db21903ace Trac #33798: Implement the Links-Gould polynomial invariant for links
04ad7f9577 Trac #33705: "make doc-clean" should remove inventory, doctrees
977e691dc1 Trac #33636: replace loadable_module_extension() by importlib.machinery.EXTENSION_SUFFIXES
c744d7c09c Trac #29097: build/make/Makefile.in: Rename make targets SPKG-clean to SPKG-uninstall
8312ee1e90 Trac #33530: Upgrade ipython to 8.x
067a66c7e9 Trac #33428: prompt_toolkit 3.0.25+ breaks Ctrl-C
79ed9e5ddb Trac #33160: update Singular to 4.3.1
4cc4817aeb Trac #32088: gfan testsuite hangs on 32bit
10247d5f2a Trac #31049: "setup.py develop" rewrites the installed sage-version.sh as if it is a Python script
7f7149489c (tag: 9.7.beta6) Updated SageMath version to 9.7.beta6

[G. M.-S.]

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

Nothing new:

On macOS 12.5 (Monterey) with Xcode 13.4.1:  no problems.

On macOS 11.6.8 (Big Sur) with Xcode 13.2.1:  make ptestlong gives the usual matrix_gf2e_dense.pyx error (see https://trac.sagemath.org/ticket/33212).

Remarks for interested people:

1) As usual, the following

----------------------------------------------------------------------
sage -t --long --warn-long 52.1 --random-seed=324722062500301071147824685967887717794 src/sage/interfaces/expect.py  # 2 doctests failed
----------------------------------------------------------------------

eventually succeeds when tried alone enough times.

2)

The following

% brew uninstall --ignore-dependencies jpeg-xl
% brew install jpeg-xl

seemed necessary on one machine because of a persistent error when installing sagemath_doc_html-none (details on request).

Guillermo

[Thierry Dumont]

On Debian TESTING (Amd 64):

-installation ok.

- make ptestlong:
2 tests failed:

67134 src/sage/combinat/nu_dyck_word.py
[179 tests, 1.17 s]
sage -t --long --warn-long 34.1
--random-seed=3139455004425827870060396354068704
67134 src/sage/libs/gap/test_long.py
[6 tests, 34.43 s]
----------------------------------------------------------------------
sage -t --long --warn-long 34.1
--random-seed=313945500442582787006039635406870467134
src/sage/tests/cmdline.py # 1 doctest failed
----------------------------------------------------------------------


and:

7134 src/sage/libs/gap/test_long.py
[6 tests, 34.43 s]
----------------------------------------------------------------------
sage -t --long --warn-long 34.1
--random-seed=313945500442582787006039635406870467134
src/sage/tests/cmdline.py # 1 doctest failed
----------------------------------------------------------------------

[David Coudert]

With this new beta, I see that the source code and the compiled code are mixed.

For instance

sapristi:sage dcoudert$ ll src/sage/graphs/

total 76264

drwxr-xr-x  123 dcoudert  coati     3936  2 aoû 16:10 .

drwxr-xr-x   69 dcoudert  coati     2208  1 aoû 23:18 ..

drwxr-xr-x   19 dcoudert  coati      608  2 aoû 11:06 __pycache__

-rw-r--r--    1 dcoudert  coati     1275 11 jan  2022 all.py

-rw-r--r--    1 dcoudert  coati   644443  1 aoû 23:58 asteroidal_triples.c

-rwxr-xr-x    1 dcoudert  coati    90616  2 aoû 00:13 asteroidal_triples.cpython-39-darwin.so

-rw-r--r--    1 dcoudert  coati    10385 25 jul 08:35 asteroidal_triples.pyx

drwxr-xr-x   38 dcoudert  coati     1216  2 aoû 16:10 base

-rw-r--r--    1 dcoudert  coati    91222 31 jul 08:47 bipartite_graph.py

-rw-r--r--    1 dcoudert  coati   568709  1 aoû 23:58 bliss.cpp

-rwxr-xr-x    1 dcoudert  coati   142952  2 aoû 00:14 bliss.cpython-39-darwin.so

-rw-r--r--    1 dcoudert  coati    34879 25 jul 08:35 bliss.pyx

-rw-r--r--    1 dcoudert  coati  1067208  1 aoû 23:58 centrality.c

-rwxr-xr-x    1 dcoudert  coati   184776  2 aoû 00:14 centrality.cpython-39-darwin.so

-rwxr-xr-x    1 dcoudert  coati    34829 25 jul 08:35 centrality.pyx

-rw-r--r--    1 dcoudert  coati   765584  1 aoû 23:58 chrompoly.c

-rwxr-xr-x    1 dcoudert  coati   234744  2 aoû 00:14 chrompoly.cpython-39-darwin.so

-rw-r--r--    1 dcoudert  coati    20227 25 jul 08:35 chrompoly.pyx

...

Is this an expected behavior or is it an error ?

My source tree is now completely polluted. It makes it harder to find source files :(

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[Matthias Köppe]

On Tuesday, August 2, 2022 at 10:13:05 AM UTC-7 david....@gmail.com wrote:

With this new beta, I see that the source code and the compiled code are mixed.

For instance

sapristi:sage dcoudert$ ll src/sage/graphs/

total 76264

drwxr-xr-x  123 dcoudert  coati     3936  2 aoû 16:10 .

drwxr-xr-x   69 dcoudert  coati     2208  1 aoû 23:18 ..

drwxr-xr-x   19 dcoudert  coati      608  2 aoû 11:06 __pycache__

-rw-r--r--    1 dcoudert  coati     1275 11 jan  2022 all.py

-rw-r--r--    1 dcoudert  coati   644443  1 aoû 23:58 asteroidal_triples.c

-rwxr-xr-x    1 dcoudert  coati    90616  2 aoû 00:13 asteroidal_triples.cpython-39-darwin.so

-rw-r--r--    1 dcoudert  coati    10385 25 jul 08:35 asteroidal_triples.pyx

...

Is this an expected behavior or is it an error ?

My source tree is now completely polluted. It makes it harder to find source files :(

It's the new default

https://trac.sagemath.org/wiki/ReleaseTours/sage-9.7#Editableinstallationisnowthedefault

 

[Dima Pasechnik]

it's the -- enable-editable option which is now the default. 

One advantage is that after changing a .py file, one does not need ./sage -b

One can turn it off by running ./configure 

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/206D4F25-53D2-4D03-85F5-B6BE47DF1F9B%40gmail.com.

[David Coudert]

I see. Thank you for the answers.

So I will have to live with it.

Best.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq1c-oWEKsiRjwYfDw%3Dxy1DhRO-FSkZ%3D_%2B%2BXdNCeEg8juw%40mail.gmail.com.

[Dima Pasechnik]

there is a bit of vagueness there:

Support for system GCC older than 6.3 dropped ¶

Building Sage from source now requires a system installation of GCC >= 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode CLT installation should be used). #33316

---------

One can build Sage with clang on Linux (and on freebsd). As well, I think, one can build Sage with non-Xcode clang on macOS.

 

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[Matthias Köppe]

On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:

there is a bit of vagueness there:

Support for system GCC older than 6.3 dropped ¶

Building Sage from source now requires a system installation of GCC >= 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode CLT installation should be used). #33316

---------

One can build Sage with clang on Linux (and on freebsd). As well, I think, one can build Sage with non-Xcode clang on macOS.

We do not test such configurations. When did you last test this, and on what platform?

[Dima Pasechnik]

My point is that we do not *require* gcc on Linux.

I tested Homebrew clang on macOS in some 9.6 betas, it worked after minor tweaks. There was ea ticket about it:

https://trac.sagemath.org/ticket/32207

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[Matthias Köppe]

Do you know which versions of clang work if the user is using clang? 

Our compiler requirements are currently coming from https://docs.scipy.org/doc/scipy/dev/toolchain.html#c-language-standards, which unfortunately does not talk about clang.

[Isuru Fernando]

We build conda packages regularly with non-Xcode clang on macOS.

Isuru

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[Matthias Köppe]

I've added the sentence "An alternative is to use a sufficiently recent version of clang (LLVM)."

But having more details would be better.

[Matthias Köppe]

On Tuesday, August 2, 2022 at 10:51:04 AM UTC-7 isu...@gmail.com wrote:

We build conda packages regularly with non-Xcode clang on macOS.

Yes, we do also test the Sage distribution build on conda-forge-macos, which uses clang.

conda-forge-macos-standard succeeds, using lots of conda packages (https://github.com/mkoeppe/sage/runs/7592834217?check_suite_focus=true)

but conda-forge-macos-minimal fails (https://github.com/mkoeppe/sage/runs/7592834169?check_suite_focus=true)

while building R.

[Isuru Fernando]

Is there an issue for the R build failure? This seems like an upstream R issue and maybe updating to a newer R version will help. (R-3.6 is 3 years old)

```

In file included from gdi.c:26:
/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/include/omp.h:492:39: error: expected 'match' clause on 'omp declare variant' directive
    #pragma omp begin declare variant match(device={kind(host)})
                                      ^
/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/local/var/tmp/sage/build/r-3.6.3/src/include/Rinternals.h:1492:17: note: expanded from macro 'match'
#define match                   Rf_match
```

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[Matthias Köppe]

Yes, our R package is wildly outdated, which is problematic given that it is a standard package.

[Kwankyu Lee]

It would make a sense to release sage beta8 quickly that just contains

https://trac.sagemath.org/ticket/34252

so that developers can make use of the revived Build Documentation badge in trac.

[David Coudert]

And also https://trac.sagemath.org/ticket/22349 Deprecate sorting of Graph vertices and edges by default

This ticket touches many files and so can lead to conflicts.

Best,

David.

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[Matthias Köppe]

I've opened https://trac.sagemath.org/ticket/34268 (Reduce R to a dummy package, upgrade rpy2 to 3.4.5)