Sage 9.2.beta5 released

Volker Braun

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Jul 12, 2020, 5:22:00 AM7/12/20

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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

467fbc70a0 (tag: 9.2.beta5, trac/develop) Updated SageMath version to 9.2.beta5

339b459959 Trac #25624: Latex code generated for the "cases" symbolic function does not get viewed.

3589ab188f Trac #30110: py3: remove doctests tagged py2 in graphs

0e2c306454 Trac #30102: Bug with trivial input in designs.difference_family

66094649c5 Trac #30101: Bug in Groebner basis for Tate algebras

fe021b3dcd Trac #30098: Remove remaining __div__ methods

f1cc526461 Trac #30089: some details about arm lengths and conjugate in partitions and Macdonald polynomials

02024327a3 Trac #30081: Cleaning and improving consistency in `distances` methods in graph module

feb50df138 Trac #30077: get rid of _cmp_ for list_clone

14ae83ba5f Trac #30072: fix some lgtm suggestions

452cdc5f19 Trac #30045: Bug in Reed-Solomon encoder and error-erasure decoder

c5474af424 Trac #30016: Combinatorial designs: add function to build biplanes

762e2753eb Trac #29895: move sage.misc.misc.*verbose* to new module sage.misc.verbose

62618754a7 Trac #29638: replace tuples by mpz vectors in free abelian monoids

ee5428363d Trac #29629: Ore polynomials

cd041d1849 Trac #30113: Fix error handling in sagelib setup.py

13cfd67048 Trac #30037: Added a construction for BIBDs from symmetric BIBDs

31ec7c350d Trac #30029: Implement another nonexistence check for symmetric BIBDs

3baa6aae05 Trac #30020: 1 internet doctest failing in combinat/species/library.py + combinat/tutorial.py

72a9b1c4f8 Trac #30011: Remove sage_setup/fpickle_setup.py

a212503167 Trac #30001: Update sphinx to 3.1

ed0fbf7078 Trac #29999: sage.rings.polynomial.evaluation: Split into ..._flint and ..._ntl

3117f5ac83 Trac #29958: Too many strong articulation points

a0d17af002 Trac #29942: More efficient rank and unrank for Permutations_mset

613162ede1 Trac #29923: Deprecate deprecated sage-cython script harder, remove use of it in the main sage script

16c2328fb8 Trac #29905: test basic properties of polyhedra

04219c9cd4 Trac #29898: vertex facet graph for trivial polyhedra fails

66a033851d Trac #29843: Set up linear transformation with precomputed data if injective

2429e944e4 Trac #29841: Improve obtaining combinatorial polyhedron

24c9b49aa6 Trac #29837: Improvement for incidence matrix of polyhedra

51a5d8f960 Trac #29688: Finite numbers in the signed InfinityRing ironically don't have a sign

2fb40d2b21 Trac #27171: Move file src/bin/sage-maxima.lisp, used by sage at import time, to live inside the package

ed49c85844 Trac #21559: Install src/bin scripts by sagelib's setup.py, not make

cc19847f77 Trac #29111: src/bin/sage: Delegate handling of options of sage-the-distribution, specifying a subset that is supported by sagelib proper

16e77bf806 Trac #4039: choose one name for partial fraction decompositions

9dec446d9e Trac #29422: DiFUB algorithm for diameter of real (unweighed) directed graphs

92a2618778 Trac #29280: expression parser should support unicode

eca054baeb Trac #29278: Callable symbolic expressions should be allowed to have unicode identifiers

1948ce39e4 Trac #27934: Implement efficient all eccentricity computation for undirected graphs

86f0ff5977 Trac #27874: Trace monoid support

a6d25fb8a5 Trac #30082: Make ./bootstrap less sensitive to stray files in build/pkgs (affects patchbot operation)

d1b661de65 Trac #30064: Fix tox-docker builds broken by #29884

249771280c Trac #22191: update ECL to 20.4.24

02b0be1ff8 (tag: 9.2.beta4) Updated SageMath version to 9.2.beta4

Thierry Dumont

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Jul 13, 2020, 4:13:41 AM7/13/20

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Upgrading from from 9.2 beta4 to beta 5 on my Ubuntu 20-04 with:

export MAKE="make -j4"
and:
export LANG=C.UTF-8 (french speaking machine)

No problem.

make ptestlong

All tests passed!

t.d.

tdumont.vcf

David Coudert

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Jul 13, 2020, 4:18:45 AM7/13/20

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incremental upgrade from 9.2.beta4 to beta5 on macOS with LANG set by default to fr_FR.UTF-8.
Everything is fine.
Best,
David.

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Kenji Iohara

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Jul 13, 2020, 8:39:26 AM7/13/20

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I am using Mac OS X.15.5. After uninstalling gcc (with Homebrew), I could compile Sage 9.2.beta5, but when I launch it, it crashed.

Sage_crash_report

Sébastien Labbé

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Jul 13, 2020, 8:58:59 AM7/13/20

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Running tests with few optional and external packages, I get

Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_numerical_backends_cplex,sage_numerical_backends_gurobi

----------------------------------------------------------------------
sage -t --long src/sage/combinat/designs/bibd.py # 2 doctests failed
sage -t --long src/sage/databases/findstat.py # 17 doctests failed
sage -t --long src/sage/databases/oeis.py # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py # Bad exit: 1
sage -t --long src/sage/graphs/generators/smallgraphs.py # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,imagemagick,internet,latex,pandoc

I get the same when rerunning failed tests.

The issue with oeis is new and is copied below.

Follow up at https://trac.sagemath.org/ticket/25536

sage -t --long src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 93, in sage.databases.oeis
Failed example:
    p.cross_references(fetch=True)                # optional -- internet
Expected:
    0: A000798: Number of different quasi-orders (or topologies, or transitive digraphs) with n labeled elements.
    1: A001035: Number of partially ordered sets ("posets") with n labeled elements (or labeled acyclic transitive digraphs).
    2: A001930: Number of topologies, or transitive digraphs with n unlabeled nodes.
    3: A006057: Number of topologies on n labeled points satisfying axioms T_0-T_4.
    4: A079263: Number of constrained mixed models with n factors.
    5: A079265: Number of antisymmetric transitive binary relations on n unlabeled points.
    6: A263859: Triangle read by rows: T(n,k) (n>=1, k>=0) is the number of posets with n elements and rank k (or depth k+1).
    7: A316978: Number of factorizations of n into factors > 1 with no equivalent primes.
    8: A319559: Number of non-isomorphic T_0 set systems of weight n.
    9: A326939: Number of T_0 sets of subsets of {1..n} that cover all n vertices.
    10: A326943: Number of T_0 sets of subsets of {1..n} that cover all n vertices and are closed under intersection.
    ...
Got:
     0: A000798: Number of different quasi-orders (or topologies, or transitive digraphs) with n labeled elements.
     1: A001035: Number of partially ordered sets ("posets") with n labeled elements (or labeled acyclic transitive digraphs).
     2: A001930: Number of topologies, or transitive digraphs with n unlabeled nodes.
     3: A006057: Number of topologies on n labeled points satisfying axioms T_0-T_4.
     4: A079263: Number of constrained mixed models with n factors.
     5: A079265: Number of antisymmetric transitive binary relations on n unlabeled points.
     6: A263859: Triangle read by rows: T(n,k) (n>=1, k>=0) is the number of posets with n elements and rank k (or depth k+1).
     7: A000608: Number of connected partially ordered sets with n unlabeled elements.
     8: A316978: Number of factorizations of n into factors > 1 with no equivalent primes.
     9: A319559: Number of non-isomorphic T_0 set systems of weight n.
    10: A326939: Number of T_0 sets of subsets of {1..n} that cover all n vertices.
    11: A326943: Number of T_0 sets of subsets of {1..n} that cover all n vertices and are closed under intersection.
    12: A326944: Number of T_0 sets of subsets of {1..n} that cover all n vertices, contain {}, and are closed under intersection.
    13: A326947: BII-numbers of T_0 set-systems.
**********************************************************************
1 item had failures:
   1 of 26 in sage.databases.oeis
    5 webbrowser tests not run
    0 tests not run because we ran out of time
    [287 tests, 1 failure, 42.09 s]

Emmanuel Charpentier

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Jul 14, 2020, 10:44:18 AM7/14/20

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On Debian testing running on ore i7 + 16 GB RAM, upgrading a rebuilt Sage 9.2.beta4 to 9.2.beta5 and running ptestlong~ gives one transient timeout and three permanent errors:

File	Result	P/T
src/sage/tests/parigp.py	Timed out	T
src/sage/rings/complex_arb.pyx	6 doctests failed	P
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/rings/real_arb.pyx	2 doctests failed	P

Those errors are identical to those already reported for beta2 and beta4.

Furthermore, the jupyter notebook, which worked until rebuilding 9.2.beta4, is now somehow broken:

harpent@zen-book-flip:~$ sage -n jupyter
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta5, Release Date: 2020-07-12               │
│ Using Python 3.7.3. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
Please wait while the Sage Jupyter Notebook server starts...
[I 15:55:11.828 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 15:55:12.097 NotebookApp] The port 8888 is already in use, trying another port.
[I 15:55:12.106 NotebookApp] Serving notebooks from local directory: /home/charpent
[I 15:55:12.106 NotebookApp] The Jupyter Notebook is running at:
[I 15:55:12.106 NotebookApp] http://localhost:8889/?token=8d1b867d9e40a773d742265910124cc9653e6dd28e35df52
[I 15:55:12.106 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 15:55:12.137 NotebookApp] 

    To access the notebook, open this file in a browser:
        file:///run/user/1000/jupyter/nbserver-734665-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/?token=8d1b867d9e40a773d742265910124cc9653e6dd28e35df52

Attempt to create a Python 3 sheet :

[I 15:55:21.557 NotebookApp] Creating new notebook in 
[W 15:55:22.259 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (::1) 26.95ms referer=http://localhost:8889/notebooks/Untitled.ipynb?kernel_name=python3

Attempt to create a Sage sheet :

[I 15:55:38.201 NotebookApp] Creating new notebook in 
[W 15:55:38.610 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (::1) 4.22ms referer=http://localhost:8889/notebooks/Untitled1.ipynb?kernel_name=sagemath

Attempt to create a Gap sheet :

[I 15:56:23.326 NotebookApp] Creating new notebook in 
[W 15:56:23.715 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (::1) 5.99ms referer=http://localhost:8889/notebooks/Untitled2.ipynb?kernel_name=gap

Attempt to create a Pari sheet :

[I 15:57:23.483 NotebookApp] Creating new notebook in 
[W 15:57:23.877 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (::1) 5.48ms referer=http://localhost:8889/notebooks/Untitled3.ipynb?kernel_name=pari_jupyter

Attempt to create an R sheet (IR kernel is a systemwide Jupyter kernel,
symlinked into Sage) :

[I 15:57:52.365 NotebookApp] Creating new notebook in 
[W 15:57:52.762 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (::1) 5.52ms referer=http://localhost:8889/notebooks/Untitled4.ipynb?kernel_name=ir
[W 15:58:50.787 NotebookApp] delete /Untitled.ipynb
[W 15:58:50.791 NotebookApp] delete /Untitled2.ipynb
[W 15:58:50.794 NotebookApp] delete /Untitled1.ipynb
[W 15:58:50.797 NotebookApp] delete /Untitled3.ipynb
[W 15:58:50.800 NotebookApp] delete /Untitled4.ipynb
[I 15:58:54.627 NotebookApp] Shutting down on /api/shutdown request.
[I 15:58:54.627 NotebookApp] Shutting down 0 kernels

In all these cases, the browser (Debian’s chromium) create a new tab, that remains blank and inactive until (manually) closed.

In contrast, the system Jupyter notebook, using symlinked kernels, can create and use active Sagemath and Gap sheets ; the Pari kernel fails to start its interpreter, however :

charpent@zen-book-flip:~$ jupyter notebook
[I 16:21:06.627 NotebookApp] The port 8888 is already in use, trying another port.
[I 16:21:06.632 NotebookApp] Serving notebooks from local directory: /home/charpent
[I 16:21:06.632 NotebookApp] The Jupyter Notebook is running at:
[I 16:21:06.632 NotebookApp] http://localhost:8889/?token=a6b03587590b0615808a11b8c65e98554a5896f701a3bf78
[I 16:21:06.632 NotebookApp]  or http://127.0.0.1:8889/?token=a6b03587590b0615808a11b8c65e98554a5896f701a3bf78
[I 16:21:06.632 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 16:21:06.650 NotebookApp] 

    To access the notebook, open this file in a browser:
        file:///home/charpent/.local/share/jupyter/runtime/nbserver-736070-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/?token=a6b03587590b0615808a11b8c65e98554a5896f701a3bf78
     or http://127.0.0.1:8889/?token=a6b03587590b0615808a11b8c65e98554a5896f701a3bf78
[I 16:21:22.870 NotebookApp] Creating new notebook in

Successful creation (modulo minor booboos) of a Sagemath sheet :

[I 16:21:23.866 NotebookApp] Kernel started: e462e630-07a7-418c-b3c9-be44595bae8f
[I 16:21:25.256 NotebookApp] Adapting from protocol version 5.1 (kernel e462e630-07a7-418c-b3c9-be44595bae8f) to 5.3 (client).
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.version
[IPKernelApp] ERROR | No such comm target registered: jupyter.widget.version

Successful creation (modulo minor booboos) of a Gap sheet :

[I 16:21:39.302 NotebookApp] Creating new notebook in 
[I 16:21:40.193 NotebookApp] Kernel started: 1f2c926b-0da9-42e5-b386-c4480ae3d5a3
[IPKernelApp] ERROR | ('starting GAP: gap',)
[I 16:21:41.794 NotebookApp] Adapting from protocol version 5.1 (kernel 1f2c926b-0da9-42e5-b386-c4480ae3d5a3) to 5.3 (client).
[IPKernelApp] WARNING | Unknown message type: 'comm_open'
[IPKernelApp] WARNING | Unknown message type: 'comm_open'
[IPKernelApp] ERROR | ('command JUPYTER_RunCommand("1+2; ;");',)
[IPKernelApp] ERROR | ('reply {"result" : {"name" : "stdout","text" : "3"},"status" : "ok"}',)
[IPKernelApp] ERROR | ('json part: {"result" : {"name" : "stdout","text" : "3"},"status" : "ok"}',)
[IPKernelApp] ERROR | ('rest part: ',)

Unsuccessful creation of a Pari sheet (the sheet is created and seems active, but the kernel doesn’t start) :

[I 16:22:55.964 NotebookApp] Creating new notebook in 
[I 16:22:56.903 NotebookApp] Kernel started: 5e902bf3-eb88-42f3-b830-ab3386b66372
/usr/bin/python3: No module named PARIKernel
[I 16:22:59.903 NotebookApp] KernelRestarter: restarting kernel (1/5), new random ports
/usr/bin/python3: No module named PARIKernel
[I 16:23:02.908 NotebookApp] KernelRestarter: restarting kernel (2/5), new random ports
/usr/bin/python3: No module named PARIKernel
[I 16:23:05.914 NotebookApp] KernelRestarter: restarting kernel (3/5), new random ports
/usr/bin/python3: No module named PARIKernel
[I 16:23:08.920 NotebookApp] KernelRestarter: restarting kernel (4/5), new random ports
/usr/bin/python3: No module named PARIKernel
[W 16:23:11.925 NotebookApp] KernelRestarter: restart failed
[W 16:23:11.926 NotebookApp] Kernel 5e902bf3-eb88-42f3-b830-ab3386b66372 died, removing from map.
[I 16:23:24.665 NotebookApp] Saving file at /Untitled.ipynb
[I 16:23:40.661 NotebookApp] Saving file at /Untitled1.ipynb
[W 16:23:56.964 NotebookApp] Timeout waiting for kernel_info reply from 5e902bf3-eb88-42f3-b830-ab3386b66372
[E 16:23:56.965 NotebookApp] Error opening stream: HTTP 404: Not Found (Kernel does not exist: 5e902bf3-eb88-42f3-b830-ab3386b66372)
[W 16:23:58.014 NotebookApp] 404 GET /api/kernels/5e902bf3-eb88-42f3-b830-ab3386b66372/channels?session_id=1834273a3dab45cdb9e19c7648034db2 (::1): Kernel does not exist: 5e902bf3-eb88-42f3-b830-ab3386b66372
[W 16:23:58.134 NotebookApp] 404 GET /api/kernels/5e902bf3-eb88-42f3-b830-ab3386b66372/channels?session_id=1834273a3dab45cdb9e19c7648034db2 (::1) 122.97ms referer=None
[W 16:24:00.152 NotebookApp] Replacing stale connection: 5e902bf3-eb88-42f3-b830-ab3386b66372:1834273a3dab45cdb9e19c7648034db2
[W 16:24:10.322 NotebookApp] 410 DELETE /api/sessions/f70aa579-9aaf-42e7-97a1-c6f34210d33c (::1): Kernel deleted before session
[W 16:24:10.323 NotebookApp] Kernel deleted before session
[W 16:24:10.323 NotebookApp] 410 DELETE /api/sessions/f70aa579-9aaf-42e7-97a1-c6f34210d33c (::1) 2.21ms referer=http://localhost:8889/notebooks/Untitled2.ipynb?kernel_name=pari_jupyter
[I 16:24:19.946 NotebookApp] Starting buffering for 1f2c926b-0da9-42e5-b386-c4480ae3d5a3:bc7e5478bf2d4ffc9356a9ceb165f180
[I 16:24:19.951 NotebookApp] Kernel shutdown: 1f2c926b-0da9-42e5-b386-c4480ae3d5a3
[I 16:24:25.634 NotebookApp] Starting buffering for e462e630-07a7-418c-b3c9-be44595bae8f:0fb85877a57b42debd5f4d4ca8f9aa9c
[I 16:24:25.640 NotebookApp] Kernel shutdown: e462e630-07a7-418c-b3c9-be44595bae8f
[W 16:24:55.592 NotebookApp] delete /Untitled.ipynb
[W 16:24:55.604 NotebookApp] delete /Untitled1.ipynb
[W 16:24:55.606 NotebookApp] delete /Untitled2.ipynb
[I 16:25:00.491 NotebookApp] Shutting down on /api/shutdown request.
[I 16:25:00.492 NotebookApp] Shutting down 0 kernels

FWIW :

charpent@zen-book-flip:~$ sage -jupyter kernelspec list
Available kernels:
gap /usr/local/sage-9/local/share/jupyter/kernels/gap
pari_jupyter /usr/local/sage-9/local/share/jupyter/kernels/pari_jupyter
python3 /usr/local/sage-9/local/share/jupyter/kernels/python3
sagemath /usr/local/sage-9/local/share/jupyter/kernels/sagemath
ir /usr/local/share/jupyter/kernels/ir
charpent@zen-book-flip:~$ jupyter kernelspec list
Available kernels:
ir /usr/local/share/jupyter/kernels/ir
gap /usr/share/jupyter/kernels/gap
pari_jupyter /usr/share/jupyter/kernels/pari_jupyter
python3 /usr/share/jupyter/kernels/python3

HTH,

sagemath /usr/share/jupyter/kernels/sagemath

Dima Pasechnik

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Jul 14, 2020, 10:47:04 AM7/14/20

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./sage -b

should make jupyter notebook work again

see https://trac.sagemath.org/ticket/30123

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Emmanuel Charpentier

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Jul 14, 2020, 11:23:32 AM7/14/20

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Le mardi 14 juillet 2020 16:47:04 UTC+2, Dima Pasechnik a écrit :

./sage -b

should make jupyter notebook work again

Indeed... This also allows to create a Sage or Gap sheet in the systemwide Jupyter. the Pari kernel still fails.

BTW : the singular kernel does not qwork in euther Sage's or systemide Jupyter , complaining of :

[I 17:03:33.105 NotebookApp] Creating new notebook in

[I 17:03:34.029 NotebookApp] Kernel started: 4e45ede1-0b60-4cd6-be87-e8cc02f05161