Sage 9.3.beta5 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 

9d686f22f4 (trac/develop, tag: 9.3.beta5) Updated SageMath version to 9.3.beta5

0c355ddc52 Trac #31106: refresh combinat.py

951ab8ca9f Trac #31096: some flake8 cleanup in abvar/

871b530c62 Trac #30979: Remove duplication of options handled in src/bin/sage and build/bin/sage-site

86310bfbfe Trac #31095: tox.ini, GH Actions: Remove ubuntu-eoan

57f462dd34 Trac #31001: Some bugs concerning the trivial knot diagram

0e64d005b6 Trac #28746: Developer's Guide: Add instructions for sagelib development in a conda environment

789604ecea Trac #27122: Compile with -march=native

6e0f7d9b48 Trac #31082: Upgrade: OpenSSL 1.1.1i

0d79fd60d4 Trac #31025: FPLLL 5.4.0 and FPyLLL 0.5.4

89351e77c6 Trac #31034: Fix sage -package download --allow-upstream, add option --on-error=warn, add filtering to sage -package upload

76840e0962 Trac #31089: detect_poles puts a gap in function plots (even if there are no poles)

709603316c Trac #31073: typos in graphs, matroids, logic

3e26b6bc58 Trac #31072: Allow conversion of Sequence into function fields

6fa14926ed Trac #31068: some typos in rings/ and schemes/

6384225e3b Trac #31067: another bunch of typos

372959f4c2 Trac #31066: a few typos

17b176f183 Trac #31060: some details in fraction field of Fp[T]

93e2f09871 Trac #30964: partial flake8 cleanup for repl/

33e237fe60 Trac #31085: fix conversion of sign function to fricas

e5425a6253 Trac #31081: get rid of _multiply

2336f9b254 Trac #31080: Replace startup exception by warning

08e430229a Trac #31079: refresh Symmetric Group representations

32c4f04ac9 Trac #31070: add some type hints in parking functions

e63f65cef0 Trac #31063: Fix a test failure with readline 8.1

f455241f5a Trac #31061: Upgrade: GLPK 5.0

792340f539 Trac #31059: refresh dirichlet.py

4766dfe650 Trac #31057: more cleanup in pbori

e310f55ae1 Trac #31056: Guard against an empty SAGE_LOCAL

1608ba96f2 Trac #31051: Fix gp2c spkg-configure to let configure succeed on Fedora 32

fdcb0a1160 Trac #30993: add pre processing for treewidth

557ba32733 Trac #30971: Update to pillow 8.0.1

3d9a1babd9 Trac #30901: sage.env._get_shared_lib_filename: Fix for MULTIARCH

0a08e12aa5 Trac #30750: Implementation of semistandard tableaux as pathtableaux

c3643ef633 Trac #30356: Graphs: grouped sporadic distance-regular graphs in a function

8d4d3f3d90 Trac #30343: Graphs: point-graph of generalised polygons

44b6d7584b Trac #30199: Prime degree isogeny (di)graphs of elliptic curves

c073c753ba Trac #29973: Make sets doctests ready for random seeds

e50d12df76 Trac #29853: Do not go through Python for gf2e dense matrices in word_to_poly

ac908e83e8 Trac #29364: Bug in S-class groups of number fields

f1ccdc0505 Trac #29031: Actions cannot be pickled

81aebb9649 Trac #11590: Integrating the sgn() function can produce incorrect results

df2adf8c67 Trac #31058: src/bin/sage-venv-config: Do not fail if sage_conf is not available

7388d57159 Trac #30764: Adapt to float factorial deprecation in Python 3.9

e8fe2ecb32 Trac #31042: build/pkgs/_recommended: Remove duplication of the pandoc system package in debian, homebrew

3460a4ac4a Trac #31039: refresh the Knutson-Tao puzzles file

4d8bd8aef0 Trac #31028: flake8 for two files in modular/hecke

b235baa8f3 Trac #30989: add some typing information to interval-posets

38fabbc781 Trac #30870: Add path_tableaux/frieze module to documentation

d2edce9ab4 Trac #31038: Improve the zonotope construction

389a88783c Trac #31050: Upgrade wheel

c4a802d2b6 (tag: 9.3.beta4) Updated SageMath version to 9.3.beta4

[Thierry Dumont]

On my Ubuntu 20-10, compilation ok;

make ptestlong produced one error:


sage: a = singular(1) ## line 503 ##
sage: _ = singular._expect.sendline('1+') # unfinished input ## line 504 ##
sage: try:
alarm(0.5)
singular._expect_expr('>') # interrupt this
except KeyboardInterrupt:
pass ## line 505 ##
Control-C pressed. Interrupting Singular. Please wait a few seconds...
sage: 2*a ## line 514 ##

[David Coudert]

Hello,

On macOS 10.15.7 and fedora 32, I have an error compiling fpylll-0.5.4. See attached log file.

This is apparently non blocking to finalize the compilation of 9.3.beta5. I can run it.

Best wishes,

David.

[Dima Pasechnik]

it seems you have a conflicting install of fplll in /usr/local

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[Kenji Iohara]

I have compiled from the first built on my Mac with OS 10.15.7 which worked perfectly and on OS 11.1 it stopped with the problem on Cython…

28/12/2020 15:05、Dima Pasechnik <dim...@gmail.com>のメール:

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[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.3.beta5 (configured to use all available system packages) to 9.3.beta5 leads to :

• ./configure still insists on installing texlive-latex-extra, texlive-xetex, latexmk, dvipng, default-jdk, ffmpeg, libavdevice-dev and pari-gp2c , notwithstanding the fact that all of them are already installed and up-to-date.

• ptestlong results in tree permanent failures, already seen and reported in previous versions, two being likely cosmetic :

File	Results	P/T
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/misc/package.py	1 doctest failed	P
src/sage/groups/abelian_gps/abelian_group_gap.py	1 doctest failed	P

HTH,

​

[Kenji Iohara]

On mac OS10.15.7, MAKE PTESTLONG passed without problem. 

28/12/2020 15:07、Kenji Iohara <simplye...@gmail.com>のメール:

[John H Palmieri]

I've been having problems with computers running Mac OS for several Sage releases now. With OS X 10.15.7 and a pretty full homebrew installation, cypari fails:

  cypari2/gen.c:23742:70: error: too many arguments to function call, expected 3, have 4
    __pyx_v__ret = asympnum0(__pyx_v__expr, __pyx_v_k, __pyx_v__alpha, __pyx_v_precision);
                   ~~~~~~~~~                                           ^~~~~~~~~~~~~~~~~
  /usr/local/include/pari/paripriv.h:101:1: note: 'asympnum0' declared here
  GEN  asympnum0(GEN u, GEN alpha, long prec);
  ^
  cypari2/gen.c:28023:18: error: implicit declaration of function 'bnfcompress' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    __pyx_v__ret = bnfcompress(__pyx_v__bnf);
                   ^
  cypari2/gen.c:28023:16: warning: incompatible integer to pointer conversion assigning to 'GEN' (aka 'long *') from 'int' [-Wint-conversion]
    __pyx_v__ret = bnfcompress(__pyx_v__bnf);
                 ^ ~~~~~~~~~~~~~~~~~~~~~~~~~
  cypari2/gen.c:79145:52: error: too few arguments to function call, expected 3, have 2
    __pyx_v__ret = lfuntwist(__pyx_v__L, __pyx_v__chi);
                   ~~~~~~~~~                         ^
  /usr/local/include/pari/paridecl.h:4164:1: note: 'lfuntwist' declared here
  GEN     lfuntwist(GEN ldata1, GEN ldata2, long bitprec);
  ^
  cypari2/gen.c:80115:70: error: too many arguments to function call, expected 3, have 4
    __pyx_v__ret = limitnum0(__pyx_v__expr, __pyx_v_k, __pyx_v__alpha, __pyx_v_precision);
                   ~~~~~~~~~                                           ^~~~~~~~~~~~~~~~~
  /usr/local/include/pari/paripriv.h:125:1: note: 'limitnum0' declared here
  GEN  limitnum0(GEN u, GEN alpha, long prec);
  ^
  cypari2/gen.c:101823:18: error: implicit declaration of function 'nfbasis_gp' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    __pyx_v__ret = nfbasis_gp(__pyx_v__T);
                   ^
  cypari2/gen.c:101823:18: note: did you mean 'nfbasis'?
  /usr/local/include/pari/paridecl.h:2231:9: note: 'nfbasis' declared here
  GEN     nfbasis(GEN x, GEN *y);
          ^
  cypari2/gen.c:101823:16: warning: incompatible integer to pointer conversion assigning to 'GEN' (aka 'long *') from 'int' [-Wint-conversion]
    __pyx_v__ret = nfbasis_gp(__pyx_v__T);
                 ^ ~~~~~~~~~~~~~~~~~~~~~~
  cypari2/gen.c:112854:16: warning: incompatible pointer to integer conversion assigning to 'long' from 'GEN' (aka 'long *'); dereference with * [-Wint-conversion]
    __pyx_v__ret = permorder(__pyx_v__x);
                 ^ ~~~~~~~~~~~~~~~~~~~~~
                   *
  cypari2/gen.c:116073:18: error: implicit declaration of function 'isirreducible' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    __pyx_v__ret = isirreducible(__pyx_v__pol);
                   ^
  cypari2/gen.c:116073:18: note: did you mean 'polisirreducible'?
  /usr/local/include/pari/paridecl.h:4812:9: note: 'polisirreducible' declared here
  long    polisirreducible(GEN x);
          ^
  cypari2/gen.c:124325:49: error: too few arguments to function call, expected 3, have 2
    __pyx_v__ret = qfbsolve(__pyx_v__Q, __pyx_v__p);
                   ~~~~~~~~                       ^
  /usr/local/include/pari/paridecl.h:1880:1: note: 'qfbsolve' declared here
  GEN     qfbsolve(GEN Q, GEN n, long flag);
  ^
  cypari2/gen.c:134243:69: error: too many arguments to function call, expected 3, have 4
    __pyx_v__ret = rnfkummer(__pyx_v__bnr, __pyx_v__subgp, __pyx_v_d, __pyx_v_precision);
                   ~~~~~~~~~                                          ^~~~~~~~~~~~~~~~~
  /usr/local/include/pari/paridecl.h:4110:1: note: 'rnfkummer' declared here
  GEN     rnfkummer(GEN bnr, GEN subgroup, long prec);
  ^
  cypari2/gen.c:145599:18: error: implicit declaration of function 'zetamult0' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    __pyx_v__ret = zetamult0(__pyx_v__s, __pyx_v__T, __pyx_v_precision);
                   ^
  cypari2/gen.c:145599:18: note: did you mean 'zetamult'?
  /usr/local/include/pari/paridecl.h:5345:9: note: 'zetamult' declared here
  GEN     zetamult(GEN avec, long prec);
          ^
  cypari2/gen.c:145599:16: warning: incompatible integer to pointer conversion assigning to 'GEN' (aka 'long *') from 'int' [-Wint-conversion]
    __pyx_v__ret = zetamult0(__pyx_v__s, __pyx_v__T, __pyx_v_precision);
                 ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  cypari2/gen.c:167603:15: error: implicit declaration of function 'isirreducible' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    __pyx_v_t = isirreducible(__pyx_v_self->__pyx_base.g);
                ^
  4 warnings and 10 errors generated.
  error: command '/usr/bin/gcc' failed with exit code 1

If I use `./configure --with-system-python3=no`, then the build succeeds but I get a bunch of doctest failures, I think all of the form

File "src/sage/misc/sagedoc.py", line 646, in sage.misc.sagedoc.format
Failed example:
    cython('\n'.join(cython_code))
Expected nothing
Got:
    ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (10.15) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (10.15) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (10.15) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer macOS version (10.15) than being linked (10.9)

[David Coudert]

Hello,

So, I first ensured that I have homebrew install of fplll 5.4.0 and glpk 5.0.

Then I made a distclean, bootstrap, source .homebrew…, configure, and make, but it fails to detect that I have fplll 5.4.0 and then to build fpylll.

After a small edit of build/pkgs/fplll/spkg-configure.m4 and the addition of missing homebrew.txt file in distros/

And distclean again… I succeed to compile without error.

I will comment on that on https://trac.sagemath.org/ticket/31025

However, on fedora 32, we don’t have fplll 5.4.0, but .configure for incremental upgrade says that I have a correct version of fplll installed and so it proceeds and later it fails on building fpylll.

I assume that a distclean will fix the issue (at the cost of installing the fplll spkg).

Best,

David.

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[John H Palmieri]

With OS X 11.1, I am unable to build Sage at all. With 9.3.beta5 as well as earlier releases, cffi fails:

Installing cffi-1.14.3
Traceback (most recent call last):
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta5/local/var/tmp/sage/build/cffi-1.14.3/src/setup.py", line 152, in <module>
    if 'darwin' in sys.platform and macosx_deployment_target() >= (10, 15):
  File "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta5/local/var/tmp/sage/build/cffi-1.14.3/src/setup.py", line 76, in macosx_deployment_target
    return tuple(map(int, get_config_var("MACOSX_DEPLOYMENT_TARGET").split('.')))
AttributeError: 'int' object has no attribute 'split'
Error: could not determine package name

numpy fails with a similar error. If I patch both to handle this (by calling 'str', as in 'str(get_config_var(...))'), then scipy fails with an error that I don't know how to fix, as reported at https://trac.sagemath.org/ticket/30651.

[Samuel Lelièvre]

2020-12-28 00:11 UTC, Volker Braun:

>
> 9d686f22f4 (trac/develop, tag: 9.3.beta5) Updated SageMath version to 9.3.beta5

Thanks for this new release. It built fine here:

- macOS 10.14.6 with lots of Homebrew packages installed
- make: ok; make testlong: All tests passed!

whereas for Sage 9.3.beta4, SciPy would not build ---
luckily, that did not prevent Sage from working;
only functions that rely on SciPy would give errors
but Sage remained otherwise usable, which is nice.
Now on to installing some extra packages. --Samuel

[Sébastien Labbé]

On Ubuntu 18.04, testing various optional and external packages, I get:

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

----------------------------------------------------------------------
sage -t --long --warn-long 72.7 --random-seed=0 src/sage/databases/findstat.py  # 2 doctests failed
sage -t --long --warn-long 72.7 --random-seed=0 src/sage/combinat/designs/ext_rep.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

Rerunning failed tests, I obtain:

----------------------------------------------------------------------
sage -t --long --warn-long 72.1 --random-seed=0 src/sage/databases/findstat.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: internet

The issue with ext_rep.py which does not reproduce is:

sage -t --long --warn-long 72.7 --random-seed=0 src/sage/combinat/designs/ext_rep.py
**********************************************************************
File "src/sage/combinat/designs/ext_rep.py", line 1049, in sage.combinat.designs.ext_rep.designs_from_XML_url
Failed example:
    ext_rep.designs_from_XML_url("http://designtheory.org/database/v-b-k/v3-b6-k2.icgsa.txt.bz2") # optional - internet
Expected:
    [(3, [[0, 1], [0, 1], [0, 1], [0, 1], [0, 1], [0, 2]]),
     (3, [[0, 1], [0, 1], [0, 1], [0, 1], [0, 2], [0, 2]]),
     (3, [[0, 1], [0, 1], [0, 1], [0, 1], [0, 2], [1, 2]]),
     (3, [[0, 1], [0, 1], [0, 1], [0, 2], [0, 2], [0, 2]]),
     (3, [[0, 1], [0, 1], [0, 1], [0, 2], [0, 2], [1, 2]]),
     (3, [[0, 1], [0, 1], [0, 2], [0, 2], [1, 2], [1, 2]])]
Got:
    []
**********************************************************************
1 item had failures:
   1 of   7 in sage.combinat.designs.ext_rep.designs_from_XML_url
    0 tests not run because we ran out of time
    [102 tests, 1 failure, 17.82 s]

The issue with findstat was already reported. Follow-up at: https://trac.sagemath.org/ticket/25536