Sage 9.2.beta14 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 

Again, if there is anything that should be merged in this beta cycle then a positively-reviewed patch has to materialize real soon ;-)

1da6df404d (tag: 9.2.beta14) Updated SageMath version to 9.2.beta14

be1a62b3bc Trac #30671: Random failure in src/sage/interfaces/psage.py

ed7c4a3ee0 Trac #30605: improve cone containment tests

ad0f8e0a1f Trac #30601: Move bitset.pxi to bitset_base.pxd

89bf834ab3 Trac #30597: Define a sparse bitset structure

c539c2870a Trac #30663: tox.ini: Docker on Mac now needs $HOME too

112d9daff1 Trac #30658: conda-forge-ubuntu-standard: Pillow fails to install (follow up)

0ef7e3ece8 Trac #30631: fix R on macOS xcode 12

6576814c37 Trac #30603: Upgrade readline to 8.0

aa0a6d7b5f Trac #30546: python3 spkg-configure: Only search for "python3", implement "configure --with-python=/PATH/TO/PYTHON"

6969c604ad Trac #30664: Fixup for "Add quiet mode for bootstrap"

ebf4d9cf63 Trac #30662: Update conda package information, and fix building Sage on conda

cbd8e5db72 Trac #29061: Upgrade to symmetrica-3.0.1

99ab61da02 Trac #30596: Outsource functions in bitset.pxi that can be optimized by intrinsics

97802f668d Trac #30595: Remove deprecated sage.libs.ppl

9ed2f32d19 Trac #30585: Typo ticket: homogenous -> homogeneous

9c205e9694 Trac #30577: remove test file for python3 syntax

0b841a75e6 Trac #30575: add maple conversion for hypergeometric functions

de8e68e534 Trac #30572: Remove indirect typecasts when calling bitset.pxi

dbd108c10b Trac #30567: remove deprecated things in words

b4715d1b68 Trac #30563: Use configuration variable MAXIMA instead of hardcoding "maxima"

865f3ca815 Trac #30562: Gap downloads from wrong upstream directory

cd88566df0 Trac #30548: mention that sometimes it is wolfram, not math for Mathematica script

7169ec9867 Trac #30547: full flake8 for skew_tableau.py, as an experiment

95712fc6ad Trac #30544: spkg-configure, system package info for tox

2413f7b665 Trac #30523: polynomial_element.pyx: roots: SR: Fix if determinant is not real

28b594bb6e Trac #30486: Prepare doctests for Arb 2.18

43089d428d Trac #30337: Graphs: obtain distance-regular graphs from generalised quadrangles

82a9e2d091 Trac #29500: Install all Python packages via pip wheel (or setup.py bdist_wheel), store wheels in $SAGE_LOCAL/var/lib/sage/wheels

85906ba097 Trac #25119: Fail to integrate sqrt(x^2)/x

5bf821488c Trac #15223: Let the `TestSuite` test that the construction of a parent returns the parent

501019f5b5 Trac #30610: Fix openblas to build with Xcode 12

19be84362c Trac #30576: Python 3.6: Fix locale/encoding issues in docbuild, then re-enable Python 3.6

af71febd64 Trac #30008: After #30053, sphinx 3.1.2 does not build on ubuntu-{trusty,xenial,bionic}, debian-jessie, centos-7 (again)

82534f5b92 Trac #30538: some flake8 cleanup in manifolds

3d4a8d2e75 Trac #30533: Add quiet mode for bootstrap

8700f751cf Trac #30532: sage.rings.ideal: Do not import sage.interfaces.singular at load time

0957fb642a Trac #30526: Irrelevant Example for _polynomial_list at FP_template.pxi

3d4760ce77 Trac #30522: polynomial_element.pyx: roots: SR: Return value for vanishing determinant broken

2fd8ef799e Trac #30516: Infinite WeightedIntegerVectors does not coerce properly

e3de8ecdfb Trac #30515: implement string formatting for elements in RR and CC

6844bbe72a Trac #30514: fix pycodestyle E701/E702 in combinat

6b4b28b893 Trac #30513: fix pycodestyle E401

7314b0db62 Trac #30510: Speed up method subgraph

16b1089743 Trac #30509: Graphs: Faster implementation for HalfCube

15cebad2f0 Trac #30503: src/tox.ini: Add environment codespell

12c246ff72 Trac #30502: typo ticket 09/2020

8543b383c8 Trac #30497: more lgtm-suggested fixed

55568686a8 Trac #30493: bug in border case in highest weight vectors of tensor product of crystals

12aa127d55 Trac #30492: Provide conversion methods to remove cythonizing from doctests

49f3450dab Trac #29975: Make numerical and probability doctests ready for random seeds

055c07e8c6 Trac #28394: comparison of sage rationals with gmpy2 mpq broken

e1a7af2252 Trac #26060: Wrong limit(x / (x + 2^x + cos(x)), x=-oo)

cd50ac9ea4 Trac #5178: Make LLL_gram also work with Gram matrices with non-integer entries

69c51603dd Trac #30583: Upgrade: gmpy2 2.1.0.b5

6aa190cdee Trac #30531: Polyhedron_normaliz._triangulate_normaliz should not use NmzResult directly

ff880f9919 Trac #29164: Computing log(0, 2) takes a long time

d55e6c9835 Trac #30604: fix scipy for XCode 12

468f23815a (tag: 9.2.beta13) Updated SageMath version to 9.2.beta13

[John H Palmieri]

Builds for me on OS X 10.15.7 (Catalina) with Xcode 12, both with a full homebrew installation, and then also using only some homebrew packages:

  ./configure --with-system-readline=no --with-system-openblas=no --with-system-r=no --with-system-gsl-no --with-system-suitesparse=no

[Eric Gourgoulhon]

On Ubuntu 20.04 running on Intel Core i7-8665U + 32 GB RAM:

- incremental build (-j8) from 9.2.beta13 with system Python (=3.8.2): OK

- all tests from ptestlong passed

Although make ptestlong reports "All tests passed!", two Ubuntu crash reports have been generated during the ptestlong run:

1/ Title: nauty-gentourng crashed with SIGSEGV in __libc_start_main()

     nauty-gentourng is from the Ubuntu package nauty 2.6r10+ds-1ubuntu1

2/ Title: mwrank crashed with SIGABRT in std::terminate()

     mwrank is from the Ubuntu package eclib-tools 20190909-2build2

Eric.

[François Bissey]

This has been around for ages. In fact for as long as nauty has been in sage.
I remember spotting it for the first time in dmesg several years ago.
Because it is mostly silent very little effort has put into fixing that so far,
at least that I know of.

> On 1/10/2020, at 9:20 PM, Eric Gourgoulhon <egourg...@gmail.com> wrote:
>
> 1/ Title: nauty-gentourng crashed with SIGSEGV in __libc_start_main()
> nauty-gentourng is from the Ubuntu package nauty 2.6r10+ds-1ubuntu1
>

François

[Emmanuel Charpentier]

Upgrading from 9.2.beta13 failed : I had successfully installed the optional jupyterlab, and now make insists on installing jupyterlab_widgets 2.0.0, which fails as follows :

cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
[dochtml] Traceback (most recent call last):
[dochtml]   File "/usr/lib/python3.8/runpy.py", line 185, in _run_module_as_main
[dochtml]     mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
[dochtml]   File "/usr/lib/python3.8/runpy.py", line 144, in _get_module_details
[dochtml]     return _get_module_details(pkg_main_name, error)
[dochtml]   File "/usr/lib/python3.8/runpy.py", line 111, in _get_module_details
[dochtml]     __import__(pkg_name)
[dochtml]   File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage_setup/docbuild/__init__.py", line 58, in <module>
[dochtml]     import sage.all
[dochtml]   File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/all.py", line 129, in <module>
[dochtml]     from sage.data_structures.all import *
[dochtml]   File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/all.py", line 3, in <module>
[dochtml]     from .bitset import Bitset, FrozenBitset
[dochtml] ImportError: /usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/bitset.cpython-38-x86_64-linux-gnu.so: undefined symbol: _bitset_issubset
make[3]: *** [Makefile:1887 : doc-html] Erreur 1

Attempts to uninstall jupyterlab_widgets and jupyterlab, both via sage-spkg-uninstall and sage -pip uninstall... failed : make reinstalls them.

Being stuck, I’m trying to rebuild from scratch (i. e. aftrer mace distclean. Stay tuned…

HTH,

​

[Dima Pasechnik]

On Thu, Oct 1, 2020 at 10:13 AM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> Upgrading from 9.2.beta13 failed : I had successfully installed the optional jupyterlab, and now make insists on installing jupyterlab_widgets 2.0.0, which fails as follows :
>
> cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
> [dochtml] Traceback (most recent call last):
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 185, in _run_module_as_main
> [dochtml] mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 144, in _get_module_details
> [dochtml] return _get_module_details(pkg_main_name, error)
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 111, in _get_module_details
> [dochtml] __import__(pkg_name)
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage_setup/docbuild/__init__.py", line 58, in <module>
> [dochtml] import sage.all
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/all.py", line 129, in <module>
> [dochtml] from sage.data_structures.all import *
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/all.py", line 3, in <module>
> [dochtml] from .bitset import Bitset, FrozenBitset
> [dochtml] ImportError: /usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/bitset.cpython-38-x86_64-linux-gnu.so: undefined symbol: _bitset_issubset
> make[3]: *** [Makefile:1887 : doc-html] Erreur 1

no wonder, as this beta changes bitset stuff.

> --
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[François Bissey]

This is https://trac.sagemath.org/ticket/30675 as I mentioned to several people I am surprised
the fact this was needed was not picked up by the bots. Which version of gcc are you using.

> On 1/10/2020, at 10:13 PM, Emmanuel Charpentier <emanuel.c...@gmail.com> wrote:
>
> Upgrading from 9.2.beta13 failed : I had successfully installed the optional jupyterlab, and now make insists on installing jupyterlab_widgets2.0.0, which fails as follows :

>
> cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log
> [dochtml] Traceback (most recent call last):
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 185, in _run_module_as_main
> [dochtml] mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 144, in _get_module_details
> [dochtml] return _get_module_details(pkg_main_name, error)
> [dochtml] File "/usr/lib/python3.8/runpy.py", line 111, in _get_module_details
> [dochtml] __import__(pkg_name)
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage_setup/docbuild/__init__.py", line 58, in <module>
> [dochtml] import sage.all
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/all.py", line 129, in <module>
> [dochtml] from sage.data_structures.all import *
> [dochtml] File "/usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/all.py", line 3, in <module>
> [dochtml] from .bitset import Bitset, FrozenBitset
> [dochtml] ImportError: /usr/local/sage-9/local/lib/python3.8/site-packages/sage/data_structures/bitset.cpython-38-x86_64-linux-gnu.so: undefined symbol: _bitset_issubset
> make[3]: *** [Makefile:1887 : doc-html] Erreur 1
>

> Attempts to uninstall jupyterlab_widgets and jupyterlab, both via sage-spkg-uninstall and sage -pip uninstall... failed : makereinstalls them.

[Henri Girard]

On Ubuntu 20.04 running AMD 16 core +16 Go and SSD, Every thing passed.

As I didn't compile sage for a certain time I notice it was quick about
30 mns. I few some messages indicating I should install few libs (new
and very important, that a good idea !).

Best

Henri

[Emmanuel Charpentier]

Well… I just scratched my previous install fpr naught, since the problem was with dochtml…

Le jeudi 1 octobre 2020 à 11:16:01 UTC+2, François Bissey a écrit :

This is https://trac.sagemath.org/ticket/30675 as I mentioned to several people I am surprised
the fact this was needed was not picked up by the bots. Which version of gcc are you using.

System’s gcc 10 :

charpent@zen-book-flip:/usr/local/sage-9$ gcc  --version
gcc (Debian 10.2.0-9) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

HTH,

​

[Emmanuel Charpentier]

Trac#30675 doesn’t rebase cleanly with develop. Stuck again. Suggestions ?

​

[Kenji Iohara]

On OS X.15.7 with Xcode 12, I couldn’t compile 

       pynac-0.7.26.sage-2020-04-03.p0

. Here is its log-file.

[Dima Pasechnik]

On Thu, Oct 1, 2020 at 11:58 AM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
> Trac#30675 doesn’t rebase cleanly with develop. Stuck again. Suggestions ?

merge, not rebase. It should work. It basically changes 1 file.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/24cf3fb3-81c4-4c78-b2e0-b476ec8e0de9n%40googlegroups.com.

[Emmanuel Charpentier]

ptestlong on a rebuilt 9.2.beta14+Trac#30675results in one transient and five permanent failures, partially different from those obtained on the same machine with 9.2.beta13 :

File	Result	P/T
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py	Killed due to abort	P
src/sage/tests/parigp.py	Timed out	T
src/sage/modules/fg_pid/fgp_module.py	3 doctests failed	P
src/doc/en/constructions/algebraic_geometry.rst	1 doctest failed	P
src/doc/en/developer/coding_in_other.rst	1 doctest failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P

​

HTH,

Le jeudi 1 octobre 2020 à 01:22:01 UTC+2, Volker Braun a écrit :

[Thierry Dumont]

In my Ubuntu 20-04, upgrading from beta 13 to beta 14 did not succeed:

First, just a strange warning:
[dochtml] title = self.get_module_docstring_title(module_name)
[dochtml] Warning: Could not import sage.libs.readline libreadline.so.6:
cannot open shared object file: No such file or directory

then:

[dochtml] raise worker_exc.original_exception
[dochtml] OSError: WARNING: autodoc: failed to import module 'readline'
from module 'sage.libs';

This persists even after after a make doc-clean

Maybe make disclean and then rebuild, because:

>ldconfig -v|grep realine

libreadline.so.8 -> libreadline.so.8.0

(a security upgrade of ubuntu or something like that ?, may be).
t.d.

[Emmanuel Charpentier]

A new, interesting, and (IMHO) very serious bug :

f=function("f")
var("k")
Eq=f(x).diff(x,2)/f(x)==k
with assuming(k>0):Sp=desolve(Eq,f(x),ivar=x)
with assuming(k==0):Sz=desolve(Eq,f(x),ivar=x)
with assuming(k<0):Sn=desolve(Eq,f(x),ivar=x)
var("_K1,_K2")
# with assuming(k<0): Sn1=Sn.subs(sqrt(k)==I*sqrt(abs(k))) # Crashes Sage
# with assuming(k<0): Sn2=Sn.subs(sqrt(k)==I*sqrt(-k)) # Crashes Sage also
# Maybe "with assuming..." fails ?
assume(k<0)
# Sn3=Sn.subs(sqrt(k)==I*sqrt(abs(k))) # Crash again
# Sn4=Sn.subs(sqrt(k)==I*sqrt(-k)) # Still crashes...

Similar tricks ejusdem farinae worked up to 9.2.beta13… Did pynac handling got modified ?

What I get in a sage-shell-mode emacs session is in the attached PynacCrash.txt (too long for the post body…). Advice on how to create an informative ticket welcome...

​

.HTH,

[Emmanuel Charpentier]

1) The problem also appears in sagecell, which contradicts my constatation of having done this yesterday…

2) The problem is not in Maxima:

;;; Loading #P"/usr/local/sage-9/local/lib/ecl/sb-bsd-sockets.fas"
;;; Loading #P"/usr/local/sage-9/local/lib/ecl/sockets.fas"
Maxima 5.44.0 http://maxima.sourceforge.net
using Lisp ECL 20.4.24
Distributed under the GNU Public License. See the file COPYING.
Dedicated to the memory of William Schelter.
The function bug_report() provides bug reporting information.
(%i1) display2d:false;

(%o1) false
(%i2) assume(k<0);

(%o2) [k < 0]
(%i3) Eq:diff(f(x),x,2)/f(x)=k;

(%o3) 'diff(f(x),x,2)/f(x) = k
(%i4) S:ode2(Eq,f(x),x);

(%o4) f(x) = %i*%k1*sinh(sqrt(k)*x)+%k2*cosh(sqrt(k)*x)
(%i5) subst([sqrt(k)=%i*sqrt(-k)],S);

(%o5) f(x) = %k2*cos(sqrt(-k)*x)-%k1*sin(sqrt(-k)*x)

HTH,

​

[Emmanuel Charpentier]

The problem may reside in the backtranslation of a Maxima result to Sage:

charpent@zen-book-flip:~$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta14, Release Date: 2020-09-30              │
│ Using Python 3.8.6. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: var("k")                                                                  
k
sage: assume(k<0)                                                               
sage: f=function("f")                                                           
sage: Eq=f(x).diff(x,2)/f(x)==k                                                 
sage: S=desolve(Eq, f(x), ivar=x); S                                            
_K2*cosh(sqrt(k)*x) + I*_K1*sinh(sqrt(k)*x)
sage: SS=maxima.subst([sqrt(k)==I*sqrt(-k)], S); SS                             
_SAGE_VAR__K2*cos(sqrt(-_SAGE_VAR_k)*_SAGE_VAR_x)-_SAGE_VAR__K1*sin(sqrt(-_SAGE_VAR_k)*_SAGE_VAR_x)
sage: SS.sage()                                                                 
# CRASH :
------------------------------------------------------------------------
/usr/local/sage-9/local/lib/python3.8/site-packages/cysignals/signals.cpython-38-x86_64-linux-gnu.so(+0x842b)[0x7fac8352242b]
# Etc. ad nauseam...

HTH,

​

[Emmanuel Charpentier]

Interestingly, the problem doesn't appear when the expression to be substituted comes from Sympy :

```

charpent@zen-book-flip:~$ sage

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 9.2.beta14, Release Date: 2020-09-30              │

│ Using Python 3.8.6. Type "help()" for help.                        │

└────────────────────────────────────────────────────────────────────┘

┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓

┃ Warning: this is a prerelease version, and it may be unstable.     ┃

┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛

sage: k=var("k")                                                                

sage: assume(k<0)                                                               

sage: f=function("f")                                                           

sage: Eq=f(x).diff(x,2)/f(x)==k                                                 

sage: from sympy import sympify, dsolve                                         

sage: S=dsolve(*map(sympify, (Eq, f(x)))); S                                    

Eq(f(x), C1*exp(-sqrt(k)*x) + C2*exp(sqrt(k)*x))

sage: S._sage_()                                                                

f(x) == C2*e^(sqrt(k)*x) + C1*e^(-sqrt(k)*x)

sage: S.subs({sympify(sqrt(k)):sympify(I*sqrt(-k))})                            

Eq(f(x), C1*exp(-I*x*sqrt(-k)) + C2*exp(I*x*sqrt(-k)))

sage: S.subs({sympify(sqrt(k)):sympify(I*sqrt(-k))})._sage_()                   

f(x) == C2*e^(I*sqrt(-k)*x) + C1*e^(-I*sqrt(-k)*x)

sage: S._sage_().subs(sqrt(k)==I*sqrt(-k))                                      

f(x) == C2*e^(I*sqrt(-k)*x) + C1*e^(-I*sqrt(-k)*x)

```

[John H Palmieri]

Please also provide the top-level config.log.

[Emmanuel Charpentier]

This now [Trac#30688#ticket](https://trac.sagemath.org/ticket/30688#ticket), marked as `blocker` because this is a case of a trivial substition causing Sage to crash.

[Kenji Iohara]

Finally, I could install on Mac OS 10.15.7 with Xcode 12 on zsh-mode,
but make ptestlong didn’t pass.

[Thierry Dumont]

afeter a make distclean, building was ok.

[Sébastien Labbé]

On Ubuntu 16.04, testing few optional and external package, I get

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

----------------------------------------------------------------------
sage -t --long --random-seed=0 src/doc/en/constructions/interface_issues.rst  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/arith/misc.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/lfunctions/sympow.py  # 4 doctests failed
sage -t --long --random-seed=0 src/sage/misc/package.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/integral.py  # 1 doctest failed
Doctests interrupted: 2231/4210 files tested

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I don't know why it got interupted. don't have time to check this now.

Above failures were already reported. Follow up at: https://trac.sagemath.org/ticket/25536