Sage 8.8.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 

baff1c42dd (tag: 8.8.beta5) Updated SageMath version to 8.8.beta5

71ded1d112 Trac #27797: remove one old note, and pep cleanup of zariski_vankampen

2735ee2c04 Trac #27786: yet another harvest of typos

bdffff56d9 Trac #27796: get rid of dollar signs in elliptic curves

52fdfad1d7 Trac #27795: spkg-configure.m4 for perl_term_readline_gnu

595929f120 Trac #27794: py3: doctests in sets

8fa7e9c235 Trac #27782: 1 pynormaliz doctest failing in src/sage/geometry/polyhedron/backend_normaliz.py

ddbf8517cd Trac #27779: Py3: Fix dynamics.arithmetic_dynamics for python3

3f3f9f8fc6 Trac #27776: some py3 fixes in ext

41b531ebb0 Trac #27755: some fixes and pep cleanup in number fields orders

51b11e4f33 Trac #27680: MR11: Lazy initialization of libgap

28b02c41ef Trac #27642: Re-run configure+make after installing an SPKG with sage -i

2512f066d4 Trac #27284: spkg-configure.m4 for pcre

11ce0d345d Trac #24905: Upgrade polymake to version 3.4

320848ca5d Trac #2693: Sage should have generic resultant implementation for multivariate polynomials

dde47f6924 Trac #27771: py3: matroid/unpickling.pyx fix

b7f85e720c Trac #27768: py3: fix a flaky doctest in multipoly element

adc54ac6cb Trac #27767: py3: fix regression in qqbar.py

027201ea48 Trac #27766: Add a few more 'optional - build' tags

080beb1a9c Trac #27748: avoid using is_package_installed in generic_graph.py

2cc376afb3 Trac #27711: Remove deprecated parameter "implementation" from Graph and DiGraph constructors

2a23b96573 Trac #27706: building doc: u'\xe9' in position 19: ordinal not in range(128)

7073b50509 Trac #27559: py3: maxint to maxsize in cryptominisat interface

b26d1ad7f4 Trac #26982: remove dynamics/interval_exchanges and dynamics/flat_surfaces

b38af08e41 Trac #24082: Genus from a TorsionQuadraticModules and a signature pair

ba0f482123 Trac #27236: PariError: bug in gerepile when factoring polynomials

2264f560b8 Trac #27756: pyflakes and pep cleanup for free monoids

55699b1a57 Trac #27743: Hyperplane Arrangement enhancements

9cd0936c52 Trac #27739: commutative rings have commutative monoids of ideals

b5ebee39f2 Trac #27622: Minor import fix in misc/package.py

c63bda62ab Trac #27759: cleanup pyflakes warnings in sage.rings.asymptotic

b317ba9555 Trac #27758: py3: remaining fixes in doc/en

e57105d5a2 Trac #27757: py3: remaining fixes in categories

b4f31996cd Trac #27746: Upgrade LiDIA to v2.3.0+latte-patches-2019-05-01

c78e8ce544 Trac #27742: PolymakeElement._sage_: Handle polymake type Polyhedron

c1b8bd1bcf Trac #27741: bug in sympy conversion of hypergeometric with tuple arg of length 1

4fb11501c4 Trac #27740: pyflakes and pep8 cleanup in features

b607472081 Trac #27735: Support matrix input in @interact

5dbc7ced54 Trac #27732: py3: fix one doctest in semigroups category

76b3fb388f Trac #27674: py3: some fixes to rings/polynomial

3b73058655 Trac #27653: Update sympy to 1.4

1363b54194 Trac #27641: SAGE_SPKG_CONFIGURE macro: Add new pre-check and post-check optional arguments

9c129a313c Trac #27588: Py3: Fix libs.ntl.ntl_ZZ_pX.pyx doctests.

027d0c5e6c Trac #27487: spkg-configure.m4 for cmake

cba1d16698 Trac #27479: Univariate PolynomialRing with 'negdegrevlex' order does not get 'ds' order in Singular

d8c5874b48 Trac #27262: remove "Replacing library search directory in linker " in src/setup.py

86c5bb0002 Trac #26718: Upgrade to three.js r100

46912716a3 Trac #26592: py3: combinat/designs: bytes-like object is required, not 'str'

40f87c92b6 Trac #25989: PolynomialSequence should handle iterator as input

37c2490525 Trac #27753: Fix patchbot on Python 3

5c0b498fb2 Trac #27656: py3: Fix table display in Jupyter notebook with Sage kernel

b9782553cc Trac #27751: barvinok spkg-install syntax error

d765ee2917 (tag: 8.8.beta4) Updated SageMath version to 8.8.beta4

[Dima Pasechnik]

there are tickets listed here but still not marked as merged n trac, eg #27795

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[Emmanuel Charpentier]

On Debian testing running on core i7+16 GB RAM, upgrading from 8.8.beta3 (Python 2) builds and passes ptestlong with the usual transient failure (already reported) :

sage -t --long --warn-long 147.3 src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py

which passes when ran standalone.

HTH,

[Emmanuel Charpentier]

Sorry, I forgot to add that tis is on 8.8.beta5+Trac#27738.

[darwin doppelganger]

Sage 8.8.beta5 build succeeds on my MacBook Pro, Mojave 10.14.4.

[Sébastien Labbé]

Runing optional/external doctests, more specifically with the following ones:

Using --optional=4ti2,bliss,cbc,ccache,cmake,cryptominisat,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,mpir,ninja_build,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,qhull,rst2ipynb,sage,topcom

External software detected for doctesting: ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

I get All test passed except these ones:

----------------------------------------------------------------------
sage -t --long src/sage/sat/boolean_polynomials.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 5 doctests failed
sage -t --long src/sage/databases/oeis.py  # 6 doctests failed
sage -t --long src/sage/combinat/designs/ext_rep.py  # 2 doctests failed
sage -t --long src/sage/combinat/designs/covering_design.py  # 2 doctests failed
sage -t --long src/sage/combinat/designs/design_catalog.py  # 3 doctests failed
----------------------------------------------------------------------

The boolean_polynomial failure is not reproducible. I can reproduce the other ones with:

sage -tp --long --optional=sage,optional,external src/sage/sat/boolean_polynomials.py  src/sage/databases/findstat.py  src/sage/databases/oeis.py  src/sage/combinat/designs/ext_rep.py  src/sage/combinat/designs/covering_design.py  src/sage/combinat/designs/design_catalog.py

New issues are copied below. In particular, the following error is raised by designs/*.py :

AttributeError: addinfourl instance has no attribute '__exit__'

which is not the same as before if I remember well.

sage -t --long src/sage/databases/findstat.py
**********************************************************************
File "src/sage/databases/findstat.py", line 1416, in sage.databases.findstat.FindStatStatistic.generating_functions
Failed example:
    st.generating_functions()                                     # optional -- internet
Expected:
    {2: q + 1,
     3: q^3 + 2*q^2 + 2*q + 1,
     4: q^6 + 3*q^5 + 5*q^4 + 6*q^3 + 5*q^2 + 3*q + 1,
     5: q^10 + 4*q^9 + 9*q^8 + 15*q^7 + 20*q^6 + 22*q^5 + 20*q^4 + 15*q^3 + 9*q^2 + 4*q + 1,
     6: q^15 + 5*q^14 + 14*q^13 + 29*q^12 + 49*q^11 + 71*q^10 + 90*q^9 + 101*q^8 + 101*q^7 + 90*q^6 + 71*q^5 + 49*q^4 + 29*q^3 + 14*q^2 + 5*q + 1}
Got:
    {1: 1,
     2: q + 1,
     3: q^3 + 2*q^2 + 2*q + 1,
     4: q^6 + 3*q^5 + 5*q^4 + 6*q^3 + 5*q^2 + 3*q + 1,
     5: q^10 + 4*q^9 + 9*q^8 + 15*q^7 + 20*q^6 + 22*q^5 + 20*q^4 + 15*q^3 + 9*q^2 + 4*q + 1,
     6: q^15 + 5*q^14 + 14*q^13 + 29*q^12 + 49*q^11 + 71*q^10 + 90*q^9 + 101*q^8 + 101*q^7 + 90*q^6 + 71*q^5 + 49*q^4 + 29*q^3 + 14*q^2 + 5*q + 1}
**********************************************************************
File "src/sage/databases/findstat.py", line 1423, in sage.databases.findstat.FindStatStatistic.generating_functions
Failed example:
    st.generating_functions(style="dictionary")                   # optional -- internet
Expected:
    {2: {0: 1, 1: 1},
     3: {0: 1, 1: 2, 2: 2, 3: 1},
     4: {0: 1, 1: 3, 2: 5, 3: 6, 4: 5, 5: 3, 6: 1},
     5: {0: 1, 1: 4, 2: 9, 3: 15, 4: 20, 5: 22, 6: 20, 7: 15, 8: 9, 9: 4, 10: 1},
     6: {0: 1,
      1: 5,
      2: 14,
      3: 29,
      4: 49,
      5: 71,
      6: 90,
      7: 101,
      8: 101,
      9: 90,
      10: 71,
      11: 49,
      12: 29,
      13: 14,
      14: 5,
      15: 1}}
Got:
    {1: {0: 1},
     2: {0: 1, 1: 1},
     3: {0: 1, 1: 2, 2: 2, 3: 1},
     4: {0: 1, 1: 3, 2: 5, 3: 6, 4: 5, 5: 3, 6: 1},
     5: {0: 1, 1: 4, 2: 9, 3: 15, 4: 20, 5: 22, 6: 20, 7: 15, 8: 9, 9: 4, 10: 1},
     6: {0: 1,
      1: 5,
      2: 14,
      3: 29,
      4: 49,
      5: 71,
      6: 90,
      7: 101,
      8: 101,
      9: 90,
      10: 71,
      11: 49,
      12: 29,
      13: 14,
      14: 5,
      15: 1}}
**********************************************************************
File "src/sage/databases/findstat.py", line 1445, in sage.databases.findstat.FindStatStatistic.generating_functions
Failed example:
    st.generating_functions(style="list")                         # optional -- internet
Expected:
    {2: [1, 1],
     3: [1, 2, 2, 1],
     4: [1, 3, 5, 6, 5, 3, 1],
     5: [1, 4, 9, 15, 20, 22, 20, 15, 9, 4, 1],
     6: [1, 5, 14, 29, 49, 71, 90, 101, 101, 90, 71, 49, 29, 14, 5, 1]}
Got:
    {1: [1],
     2: [1, 1],
     3: [1, 2, 2, 1],
     4: [1, 3, 5, 6, 5, 3, 1],
     5: [1, 4, 9, 15, 20, 22, 20, 15, 9, 4, 1],
     6: [1, 5, 14, 29, 49, 71, 90, 101, 101, 90, 71, 49, 29, 14, 5, 1]}
**********************************************************************
File "src/sage/databases/findstat.py", line 1492, in sage.databases.findstat.FindStatStatistic.oeis_search
Failed example:
    st.oeis_search()                                              # optional -- internet
Expected:
    Searching the OEIS for "1,1  1,2,2,1  1,3,5,6,5,3,1  1,4,9,15,20,22,20,15,9,4,1  1,5,14,29,49,71,90,101"
    0: A008302: Triangle of Mahonian numbers T(n,k)...
Got:
    Searching the OEIS for "1  1,1  1,2,2,1  1,3,5,6,5,3,1  1,4,9,15,20,22,20,15,9,4,1  1,5,14,29,49,71,90"
    0: A008302: Triangle of Mahonian numbers T(n,k): coefficients in expansion of Product_{i=0..n-1} (1 + x + ... + x^i), where k ranges from 0 to A000217(n-1). Also enumerates permutations by their major index.
    1: A274887: Triangle read by rows: coefficients of the q-factorial.
**********************************************************************
File "src/sage/databases/findstat.py", line 1496, in sage.databases.findstat.FindStatStatistic.oeis_search
Failed example:
    st.oeis_search(search_size=13)                                # optional -- internet
Expected:
    Searching the OEIS for "1,1  1,2,2,1  1,3,5,6,5,3,1"
    0: A008302: Triangle of Mahonian numbers T(n,k)...
    1: A115570: Array read by rows: row n (n>= 1) gives the Betti numbers...
    2: A187447: Array for all multiset choices...
Got:
    Searching the OEIS for "1  1,1  1,2,2,1  1,3,5,6,5,3"
    0: A008302: Triangle of Mahonian numbers T(n,k): coefficients in expansion of Product_{i=0..n-1} (1 + x + ... + x^i), where k ranges from 0 to A000217(n-1). Also enumerates permutations by their major index.
    1: A115570: Array read by rows: row n (n>= 1) gives the Betti numbers for the n-th element of the Weyl group of type A3 (in Goresky's standard ordering).
    2: A187447: Array for all multiset choices (multiset repetition class representatives in Abramowitz-Stegun order).
**********************************************************************
2 items had failures:
   3 of   5 in sage.databases.findstat.FindStatStatistic.generating_functions
   2 of   4 in sage.databases.findstat.FindStatStatistic.oeis_search
    7 webbrowser tests not run
    0 tests not run because we ran out of time
    [249 tests, 5 failures, 54.68 s]


sage -t --long src/sage/combinat/designs/design_catalog.py
**********************************************************************
File "src/sage/combinat/designs/design_catalog.py", line 22, in sage.combinat.designs.design_catalog
Failed example:
    C = designs.best_known_covering_design_from_LJCR(7, 3, 2)   # optional - internet
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.combinat.designs.design_catalog[1]>", line 1, in <module>
        C = designs.best_known_covering_design_from_LJCR(Integer(7), Integer(3), Integer(2))   # optional - internet
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/combinat/designs/covering_design.py", line 527, in best_known_covering_design_www
        with urlopen(url) as f:
    AttributeError: addinfourl instance has no attribute '__exit__'
**********************************************************************
File "src/sage/combinat/designs/design_catalog.py", line 23, in sage.combinat.designs.design_catalog
Failed example:
    C                            # optional - internet
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.combinat.designs.design_catalog[2]>", line 1, in <module>
        C                            # optional - internet
    NameError: name 'C' is not defined
**********************************************************************
File "src/sage/combinat/designs/design_catalog.py", line 28, in sage.combinat.designs.design_catalog
Failed example:
    C.incidence_structure()      # optional - internet
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1095, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.combinat.designs.design_catalog[3]>", line 1, in <module>
        C.incidence_structure()      # optional - internet
    NameError: name 'C' is not defined
**********************************************************************
1 item had failures:
   3 of   5 in sage.combinat.designs.design_catalog
    1 gap_packages test not run
    0 tests not run because we ran out of time
    [4 tests, 3 failures, 0.77 s]

[E. Madison Bray]

make ptestlong passes on Cygwin 64 *with* the fixes from the following
tickets merged in as well:

https://trac.sagemath.org/ticket/27721
https://trac.sagemath.org/ticket/27724
https://trac.sagemath.org/ticket/27514

[Eric Gourgoulhon]

On Ubuntu 18.04 running on bi-Xeon E5-2623 (8 cores) + 16 GB RAM:

- python2:

  - incremental build (from 8.8.beta4, with -j16) completed, with Sphinx complaining during the doc build:

     formatargspec() is now deprecated.  Please use sphinx.util.inspect.Signature instead

  - all tests from ptestlong passed, except for one transient timed-out failure:

    sage -t --long --warn-long 51.4 src/sage/rings/finite_rings/finite_field_constructor.py  # Timed out

    The test is passed when run standalone though, as well as in a second run of make ptestlong.

- python3:

  - incremental build (from 8.8.beta4, with -j16) completed, with the same Sphinx deprecation warning as with python 2.

  - all tests from ptest-python3 passed

Eric.

[Sébastien Labbé]

2 items had failures:
   3 of   5 in sage.databases.findstat.FindStatStatistic.generating_functions
   2 of   4 in sage.databases.findstat.FindStatStatistic.oeis_search
    7 webbrowser tests not run
    0 tests not run because we ran out of time
    [249 tests, 5 failures, 54.68 s]

I just created

https://trac.sagemath.org/ticket/27838

for the 5 internet failures in findstat.

[David Joyner]

Installed fine with on a 2014 mini-mac running 10.14.5.