Sage 10.0.beta6 released

Volker Braun

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Mar 26, 2023, 8:54:16 AM3/26/23

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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

Also, in case you see a big scary man in the middle attack warning when you connect to github: Yes, github did rotate their ssh host key ;-)

82e02a10e90 (tag: 10.0.beta6, github/develop) Updated SageMath version to 10.0.beta6
4452928a1a4 gh-35206: fixing some E502 (unnecessary backslash) in pyx files
77a0c34f71e gh-35205: remove deprecated slicing semantics of polynomials
4676d932f42 gh-35204: Remove directories leftover from improper shutdown so sage-cleaner won't kill random processes
e70da89c8cb gh-35203: sagemath-standard: Add dependencies `typing_extensions`, `importlib_resources`, `importlib_metadata`
2540fe8f1f6 gh-35197: Fix bug with Set equality/inequality
e1cb236907a gh-35195: Workaround for an ecl race in maxima init
bd8ede6eb4d gh-35193: symbolics: add derivative operator
c140569c4e5 gh-35189: Add typing to tangent vectors
88a9ab82d35 gh-35186: Various improvements to Weyl character rings
249f67b60ea gh-35185: Bump actions/cache from 2 to 3
110a3ccca4d gh-35184: Bump actions/github-script from 3.1.0 to 6.4.0
a3e8d990255 gh-35183: Bump codecov/codecov-action from 2 to 3
b2965a270b4 gh-35180: fix(docs): use double backquotes for a command
002b464c35b gh-35177: Matplotlib 3.7.0 support
1e777978d91 gh-35174: cleaning and enhancement to PolyDict
85b1e026a2b gh-35173: Speedup of Poset characteristic polynomial
81bacf5e853 gh-35170: Fix bug in is_eulerian
883b99331ca gh-35169: CI: Add PDF doc building
25a085387e4 gh-35165: activate W293 and E714 in pyx files
dc4930a5342 gh-35164: compute the matrix of an isogeny on a given n-torsion subgroup
e5cc348b117 gh-35163: Fix the documentation for the so matrix Lie algebra
af27c833462 gh-35162: Fix a slow doctest in matrix_integer_dense_hnf.py
366d0cf3591 gh-35160: Move `filterwarnings` calls from `sage.all` to `sage.all__sagemath_repl`
6d1467955bd gh-35159: update msolve to 0.4.9
f8e7176e3d7 gh-35156: Fix index out of range exception (#35031)
525b34d3e76 gh-35155: Update the logo at README.md
a9624338824 gh-35153: `sage.matrix.operation_table`: Modularization and code style fixes
670710771fe gh-35151: fix all pycodestyle E303 warnings in all folders c*
e97e5874d57 gh-35146: Equal hashes for non-isomorphic bipartite graphs with edge labels
7bd91aab402 gh-35142: Fix broken link in README
a40b4883710 gh-35141: Revise the PR template
a21293e8801 gh-35140: Update normaliz to 3.10.0, update e_antic, pynormaliz
4018a78fbe6 gh-35138: Allow skew tableaux to be hashed
b6b5c2cce14 gh-35136: `sage.{geometry,rings}`: More `# optional` tags in doctests
9e9842541bc gh-35135: `sage.geometry.integral_points`: Use generic impl if no `matrix_integer_dense`
63ab60df4a4 gh-35132: fix pep8 E303 in various folders (plot, quadratic forms, etc)
e6bc06f274f gh-35131: PR for issue 32136: Add parameter 'induced' to `connected_subgraphs_iterator`
b80d04e4591 gh-35128: Fix French notation for Tableau plots
53362d1e69a gh-35127: Fix a very slow doctest in `sage/data_structures/stream.py`
9955e921ee7 gh-35123: fixing most of pycodestyle E271
b2e6ba78074 gh-35120: Add optional package cvxpy, update cylp, add CVXPY MIP backend
e6be37bbe59 gh-35118: `sage.env.sage_include_directories`: Don't use `distutils` and `SAGE_LIB`
8c79facb5c8 gh-35117: fix pep E303 in modular/ and algebras/
06db831d50f gh-35115: Make the key polynomials know their degree
0d01c38713d gh-35114: libgap: Remove some GC hazards
f18723da821 gh-35113: added check for invalid range in contour_plot and derivatives
90f14dc52ba gh-35111: Partly fix conda ci and update python versions tested
80511e167b8 gh-35110: Meta-PR: Replace imports from sage.*.all for namespace packages
eaf63933d94 gh-35080: Use the Docker images published on ghcr.io without 'docker' in the name
ce41bee6d97 gh-35056: Make automatic codecov report less noisy
c00e6c204b2 (tag: 10.0.beta5) Updated SageMath version to 10.0.beta5

Kenji Iohara

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Mar 26, 2023, 5:49:42 PM3/26/23

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Hello,

On my Mac Book Pro with Intel Core i5, OS 13.2.1 and updated homebrew,

It didn’t compile from the first built owing to the error :

package: scipy-1.10.1

last build time: Mar 26 23:41

log file: /Users/iohara/Desktop/sage-10.0.beta6/logs/pkgs/scipy-1.10.1.log

scipy-1.10.1.log

Matthias Köppe

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Mar 26, 2023, 6:07:16 PM3/26/23

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Please post config.log

Kenji Iohara

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Mar 26, 2023, 7:26:55 PM3/26/23

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config.log

Matthias Köppe

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Mar 26, 2023, 8:34:15 PM3/26/23

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Could you provide the output of "ls -l /usr/local/opt/openblas/lib/pkgconfig/openblas.pc local/lib/pkgconfig/*.pc" please, and also the file /Users/iohara/Desktop/sage-10.0.beta6/local/var/lib/sage/venv-python3.11/var/tmp/sage/build/scipy-1.10.1/src/.mesonpy-cu4n01zf/build/meson-logs/meson-log.txt (if it still exists)?

On Sunday, March 26, 2023 at 4:26:55 PM UTC-7 Kenji Iohara wrote:

Kenji Iohara

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Mar 27, 2023, 6:08:37 AM3/27/23

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The first one:

ls -l/usr/local/opt/openblas/lib/pkgconfig/openblas.pc gives

ls: invalid option -- /

usage: ls [-@ABCFGHILOPRSTUWabcdefghiklmnopqrstuvwxy1%,] [--color=when] [-D format] [file ...]

And the second one:

ls -l /usr/local/opt/openblas/lib/pkgconfig/openblas.pc local/lib/pkgconfig/*.pc gives

-r--r--r-- 1 iohara admin 556 Mar 26 20:26 /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

lrwxr-xr-x 1 iohara staff 49 Mar 26 20:38 local/lib/pkgconfig/blas.pc -> /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

lrwxr-xr-x 1 iohara staff 49 Mar 26 20:38 local/lib/pkgconfig/cblas.pc -> /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

-rw-r--r-- 1 iohara staff 353 Mar 26 20:52 local/lib/pkgconfig/eclib.pc

-rw-r--r-- 1 iohara staff 630 Mar 26 21:17 local/lib/pkgconfig/fflas-ffpack.pc

-rw-r--r-- 1 iohara staff 340 Mar 26 22:58 local/lib/pkgconfig/gf2x.pc

-rw-r--r-- 1 iohara staff 503 Mar 26 21:09 local/lib/pkgconfig/givaro.pc

-rw-r--r-- 1 iohara staff 338 Mar 26 20:38 local/lib/pkgconfig/gsl.pc

lrwxr-xr-x 1 iohara staff 49 Mar 26 20:38 local/lib/pkgconfig/lapack.pc -> /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

-rw-r--r-- 1 iohara staff 313 Mar 26 21:11 local/lib/pkgconfig/lcalc.pc

-rw-r--r-- 1 iohara staff 636 Mar 26 21:18 local/lib/pkgconfig/linbox.pc

-rw-r--r-- 1 iohara staff 332 Mar 26 20:45 local/lib/pkgconfig/m4ri.pc

-rw-r--r-- 1 iohara staff 326 Mar 26 21:19 local/lib/pkgconfig/m4rie.pc

And the last one

.mesonpy-cu4n01zf/

does not exist.

27/03/2023 2:34、Matthias Köppe <matthia...@gmail.com>のメール:

ls -l /usr/local/opt/openblas/lib/pkgconfig/openblas.pc local/lib/pkgconfig/*.pc

Dima Pasechnik

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Mar 27, 2023, 6:11:33 AM3/27/23

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On Mon, Mar 27, 2023 at 11:08 AM Kenji Iohara <simplye...@gmail.com> wrote:
>
> The first one:
>
>
> ls -l/usr/local/opt/openblas/lib/pkgconfig/openblas.pc gives
>
>
> ls: invalid option -- /

There must be a space between '-l' and the path, i.e

ls -l /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

> --
> You received this message because you are subscribed to the Google Groups "sage-release" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-release...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/F37757D1-3756-405A-9625-DF5AA5DAD113%40gmail.com.

Kenji Iohara

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Mar 27, 2023, 6:14:46 AM3/27/23

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It gives me

-r--r--r-- 1 iohara admin 556 Mar 26 20:26 /usr/local/opt/openblas/lib/pkgconfig/openblas.pc

.

27/03/2023 12:11、Dima Pasechnik <dim...@gmail.com>のメール:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq1%3Dx1qaMCb%3DWLnWtP1UAfwdBmZSXH-9oRjyWusuYXthZw%40mail.gmail.com.

Emmanuel Charpentier

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Mar 27, 2023, 10:55:19 AM3/27/23

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On Debian testing running on core i7 + 16 GB RAM, make fails. From install.log :

[sagemath_doc_html-none] Build finished. The built documents can be found in /usr/local/sage-10/local/share/doc/sage/inventory/en/reference/functions [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.are_satisfied: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.satisfied_as_equalities: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.loop_over_parallelotope_points: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.parallelotope_points: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.ray_matrix_normal_form: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.simplex_points: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] sage --docbuild --no-pdf-links reference/history_and_license inventory --no-prune-empty-dirs [sagemath_doc_html-none] [discrete_] The inventory files are in ../../local/share/doc/sage/inventory/en/reference/discrete_geometry. [sagemath_doc_html-none] Error building the documentation. [sagemath_doc_html-none] Traceback (most recent call last): [sagemath_doc_html-none] File "<frozen runpy>", line 198, in _run_module_as_main [sagemath_doc_html-none] File "<frozen runpy>", line 88, in _run_code [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 498, in <module> [sagemath_doc_html-none] sys.exit(main()) [sagemath_doc_html-none] ^^^^^^ [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 495, in main [sagemath_doc_html-none] builder() [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/builders.py", line 819, in _wrapper [sagemath_doc_html-none] getattr(DocBuilder, build_type)(self, *args, **kwds) [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/builders.py", line 163, in f [sagemath_doc_html-none] runsphinx() [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/sphinxbuild.py", line 327, in runsphinx [sagemath_doc_html-none] sys.stderr.raise_errors() [sagemath_doc_html-none] File "/usr/local/sage-10/pkgs/sage-docbuild/sage_docbuild/sphinxbuild.py", line 263, in raise_errors [sagemath_doc_html-none] raise OSError(self._error) [sagemath_doc_html-none] OSError: WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.are_satisfied: 'NoneType' object has no attribute 'find' [sagemath_doc_html-none] [sagemath_doc_html-none] Note: incremental documentation builds sometimes cause spurious [sagemath_doc_html-none] error messages. To be certain that these are real errors, run [sagemath_doc_html-none] "make doc-clean doc-uninstall" first and try again.

Same result after make doc-clean doc-uninstall.

I’m stuck…

Eric Gourgoulhon

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Mar 27, 2023, 11:00:12 AM3/27/23

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Hi,

On Ubuntu 22.04 running on Intel Core i7-8665U @1.9 GHz + 32 GB RAM, incremental parallel (-j8) build from Sage 10.0.beta4 failed while building the documentation.

Running

make doc-clean doc-uninstall

and then make again did not help.

The issue seems to be in sage.geometry.integral_points; the full error message is

[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.are_satisfied: 'NoneType' object has no attribute 'find'

[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.satisfied_as_equalities: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.loop_over_parallelotope_points: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.parallelotope_points: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.ray_matrix_normal_form: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none] [discrete_] WARNING: error while formatting arguments for sage.geometry.integral_points.simplex_points: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none] sage --docbuild --no-pdf-links reference/history_and_license inventory --no-prune-empty-dirs
[sagemath_doc_html-none] [discrete_] The inventory files are in ../../local/share/doc/sage/inventory/en/reference/discrete_geometry.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):

[sagemath_doc_html-none] File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
[sagemath_doc_html-none] return _run_code(code, main_globals, None,
[sagemath_doc_html-none] File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
[sagemath_doc_html-none] exec(code, run_globals)
[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 498, in <module>
[sagemath_doc_html-none] sys.exit(main())
[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/__main__.py", line 495, in main
[sagemath_doc_html-none] builder()
[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/builders.py", line 819, in _wrapper

[sagemath_doc_html-none] getattr(DocBuilder, build_type)(self, *args, **kwds)

[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/builders.py", line 163, in f
[sagemath_doc_html-none] runsphinx()
[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/sphinxbuild.py", line 327, in runsphinx
[sagemath_doc_html-none] sys.stderr.raise_errors()
[sagemath_doc_html-none] File "/home/eric/sage/10.0/pkgs/sage-docbuild/sage_docbuild/sphinxbuild.py", line 263, in raise_errors

[sagemath_doc_html-none] raise OSError(self._error)
[sagemath_doc_html-none] OSError: WARNING: error while formatting arguments for sage.geometry.integral_points.InequalityCollection.are_satisfied: 'NoneType' object has no attribute 'find'
[sagemath_doc_html-none]
[sagemath_doc_html-none] Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none] error messages. To be certain that these are real errors, run
[sagemath_doc_html-none] "make doc-clean doc-uninstall" first and try again.

Eric.

Eric Gourgoulhon

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Mar 27, 2023, 11:03:02 AM3/27/23

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Le lundi 27 mars 2023 à 17:00:12 UTC+2, Eric Gourgoulhon a écrit :

Hi,

On Ubuntu 22.04 running on Intel Core i7-8665U @1.9 GHz + 32 GB RAM, incremental parallel (-j8) build from Sage 10.0.beta4 failed while building the documentation.
Running
make doc-clean doc-uninstall
and then make again did not help.
The issue seems to be in sage.geometry.integral_points;

This is the same error as reported by Emanuel, our messages being posted at almost the same time.

Dima Pasechnik

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Mar 27, 2023, 11:06:35 AM3/27/23

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make sagelib-clean sagelib-uninstall

make

?

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Eric Gourgoulhon

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Mar 27, 2023, 3:25:31 PM3/27/23

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Le lundi 27 mars 2023 à 17:06:35 UTC+2, Dima Pasechnik a écrit :

make sagelib-clean sagelib-uninstall
make

This solved the issue.

Thank you Dima!

Eric.

Emmanuel Charpentier

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Mar 28, 2023, 2:36:13 PM3/28/23

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Ditto here.

Thanks again !

Emmanuel Charpentier

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Mar 28, 2023, 2:38:58 PM3/28/23

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On Debian testing running on core i7 + 16 GB RAM, upgrading 10.0.beta4 to beta6 (with rebuilding sagelib, see above...), ptestlong gives the foursae permanent errors alreadu reported for the previous beta.

HTH,

Le dimanche 26 mars 2023 à 14:54:16 UTC+2, Volker Braun a écrit :

G. M.-S.

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Mar 28, 2023, 8:52:45 PM3/28/23

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FWIW, this is on Apple Silicon Macs ("M" series) with Homebrew up to date (make and make pytest and make ptestlong), on macOS 11.7.5, macOS 12.6.4 and macOS 13.3.

(Sorry for my hasty previous comment.)

To make make work, make -j1 is usually needed.

make ptestlong gives

sage -t --long --warn-long … --random-seed=… src/sage/calculus/interpolators.pyx # 20 doctests failed
sage -t --long --warn-long … --random-seed=… src/sage/calculus/riemann.pyx # 81 doctests failed

sage -t --long --warn-long … --random-seed=… src/sage/matrix/matrix_double_dense.pyx # 11 doctests failed
sage -t --long --warn-long … --random-seed=… src/sage/matrix/matrix_space.py # 2 doctests failed
sage -t --long --warn-long … --random-seed=… src/sage/matrix/matrix2.pyx # 4 doctests failed

(see https://github.com/scipy/scipy/issues/18208)

sage -t --long --warn-long … --random-seed=… src/sage/graphs/generators/families.py # 2 doctests failed
sage -t --long --warn-long … --random-seed=… src/sage/graphs/graph_generators.py # 1 doctest failed

(see https://github.com/sagemath/sage/issues/35157)

sage -t --long --warn-long … --random-seed=… src/sage/modular/modform_hecketriangle/abstract_space.py # 3 doctests failed
sage -t --long --warn-long … --random-seed=… src/sage/modular/modform_hecketriangle/readme.py # 1 doctest failed
sage -t --long --warn-long … --random-seed=… src/sage/modular/modform_hecketriangle/space.py # 2 doctests failed

(see https://github.com/sagemath/sage/issues/35273)

Additionally:

On macOS 11.7.5:

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

(see https://github.com/sagemath/sage/issues/33212)

On macOS 13.3:

sage -t --long --warn-long … --random-seed=… src/sage/structure/coerce_actions.pyx # 3 doctests failed

(perhaps due to the processor being too fast?)

Guillermo

Matthias Köppe

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Mar 28, 2023, 9:50:56 PM3/28/23

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The matrix failures come from the homebrew openblas update. See https://github.com/sagemath/sage/pull/35377

Emmanuel Charpentier

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Mar 29, 2023, 5:59:59 AM3/29/23

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Identical result on another, slightly smaller machine.

HTH,

Kenji Iohara

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Mar 30, 2023, 4:57:17 PM3/30/23

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On Mac OS 13.2.1, with Intel Core i5 and updated homebrew, after make -j1, it compiled from the first built.

As for make ptestlong, I had:

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

sage -t --long --warn-long 263.7 --random-seed=17277742380544758668600774580300429123 src/sage/graphs/graph_generators.py # 1 doctest failed

sage -t --long --warn-long 263.7 --random-seed=17277742380544758668600774580300429123 src/sage/graphs/generators/families.py # 2 doctests failed

sage -t --long --warn-long 263.7 --random-seed=17277742380544758668600774580300429123 src/sage/modular/modform_hecketriangle/space.py # 2 doctests failed

sage -t --long --warn-long 263.7 --random-seed=17277742380544758668600774580300429123 src/sage/modular/modform_hecketriangle/readme.py # 1 doctest failed

sage -t --long --warn-long 263.7 --random-seed=17277742380544758668600774580300429123 src/sage/modular/modform_hecketriangle/abstract_space.py # 3 doctests failed

29/03/2023 11:59、Emmanuel Charpentier <emanuel.c...@gmail.com>のメール:

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