Sage 9.0.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 

93db4cc438 (tag: 9.0.beta5, trac/develop) Updated SageMath version to 9.0.beta5

9d8ca86b1e Trac #28657: Build Sage without "python"

6e157378e7 Trac #28702: Three.js: Add option to render only single side of surface

dd2f597b29 Trac #28699: Three.js: Upgrade to r110

6512528983 Trac #28669: Unnecessary coordinate check while initializing an integrated curve

5bf0c36e04 Trac #27195: slightly faster highest_weight_vectors_iterator

8cf66c860a Trac #28691: Xcode 11 breaks gfortran build

9296d51ea4 Trac #28690: Vector Bundles: Section Module Name Fix

64cf3b03da Trac #28687: Demote scons to experimental

3e5c24e5dd Trac #28245: Implement center of a HyperplaneArrangement

f362bea55f Trac #28693: Update sagenb exporter 3.3

c26dd23b46 Trac #28681: py3: Construction of (A#A)+(A#A) fails for CombinatorialFreeModules

43a77880b6 Trac #28678: Bug in CombinatorialPolyhedron of empty Lattice polytope

20da4fadea Trac #28674: RecursivelyEnumeratedSet: certified enumeration order

b5e6a225eb Trac #28645: Error in precision of Tate elliptic curves over Qp

3c16c6a771 Trac #28578: Mixed Forms Code Improvements

75294da5d9 Trac #28574: conversion of nested polynomial rings to Macaulay2

3145f5344c Trac #28506: Direct sum of polyhedron is broken, so is minkowski difference and face truncation

0976a5cf93 Trac #28502: MR36: Use Sphinx hash function

b90b558fc9 (tag: 9.0.beta4) Updated SageMath version to 9.0.beta4

[Emmanuel Charpentier]

FWIW, upgrading a Python 3-based 9.0.beta4 to 9.0.beta5 on Debian testing running on core i7 + 16 GB Ram gives me ptestalllong results quite close to those already reported for previous betas:

• No failure for ptestlong-related doctests
• One permanent failure on src/sage/tests/gap_packages.py
• Eleven transient failures:

File                                          | Result           

----------------------------------------------+------------------

src/sage/graphs/generators/smallgraphs.py     | 6 doctests failed

src/sage/combinat/posets/posets.py            | 1 doctest failed 

src/sage/plot/animate.py                      | 7 doctests failed

src/sage/combinat/matrices/hadamard_matrix.py | 2 doctests failed

src/sage/misc/latex.py                        | 1 doctest failed 

src/sage/coding/databases.py                  | 2 doctests failed

src/sage/misc/persist.pyx                     | 2 doctests failed

src/sage/repl/load.py                         | 1 doctest failed 

src/sage/graphs/graph_latex.py                | 2 doctests failed

src/sage/misc/remote_file.py                  | 2 doctests failed

src/sage/databases/findstat.py                | 9 doctests failed

HTH,

[Eric Gourgoulhon]

On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer and for a python3 build:

  - incremental build (from 9.0.beta4, with -j16) OK

  - all tests from ptestlong passed

Eric.

[Emmanuel Charpentier]

Similar results on  smaller machine (Debian testing, core i5, 8 GB RAM, no gap_packages). Transient failures:

File                                          | Result           

----------------------------------------------+------------------

src/sage/combinat/posets/posets.py            | 1 doctest failed 

src/sage/plot/animate.py                      | 7 doctests failed

src/sage/combinat/matrices/hadamard_matrix.py | 2 doctests failed

src/sage/misc/latex.py                        | 1 doctest failed 

src/sage/misc/persist.pyx                     | 2 doctests failed

src/sage/coding/databases.py                  | 2 doctests failed

src/sage/repl/load.py                         | 1 doctest failed 

src/sage/graphs/graph_latex.py                | 2 doctests failed

src/sage/misc/remote_file.py                  | 2 doctests failed

src/sage/databases/findstat.py                | 9 doctests failed

src/sage/interfaces/magma_free.py             | 2 doctests failed

HTH,

[Justin C. Walker]

> On Nov 10, 2019, at 15:59 , Volker Braun <vbrau...@gmail.com> wrote:
>
> 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

Built from a fresh clone of the develop tree on three macOS platforms: 10.11.6 (mid-2015 MBP, Quad-core Core i7), 10.13.6 (2017 iMac Pro, 18-core Xeon W), 10.14.6 (2017 MBP, Quad-core Core i7). All builds completed w/o problems.

Testing (‘ptestlong’) went as follows:

10.11.6: all tests passed!
10.13.6: one failure, good ol’ polynomials.pyx. Stand-alone runs passed.
10.14.6: all tests passed!

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
I'm beginning to like the cut of his jibberish.
-----------

[E. Madison Bray]

Testing this on Windows + Python 3 for the first time in a while.
During the docbuild it crashes while generating one of the plots, with
some call to maxima resulting in:

RuntimeError: ECL says: #<a FLOATING-POINT-OVERFLOW>

I'll see if I can get this in any other context. Has anyone else seen
problems like this on Python 3?

> --
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[E. Madison Bray]

On Wed, Nov 13, 2019 at 6:15 PM E. Madison Bray <erik....@gmail.com> wrote:
>
> Testing this on Windows + Python 3 for the first time in a while.
> During the docbuild it crashes while generating one of the plots, with
> some call to maxima resulting in:
>
> RuntimeError: ECL says: #<a FLOATING-POINT-OVERFLOW>
>
> I'll see if I can get this in any other context. Has anyone else seen
> problems like this on Python 3?

How to reproduce:

sage: f = piecewise([((0,pi/2), -1), ((pi/2,pi), 2)])
sage: s5 = f.fourier_series_partial_sum(5)
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-2-9ea0d6ecd263> in <module>()
----> 1 s5 = f.fourier_series_partial_sum(Integer(5))

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/expression.pyx
in sage.symbolic.expression._eval_on_operands.new_f
(build/cythonized/sage/symbolic/expression.cpp:67434)()
12688 new_args = list(ex._unpack_operands())
12689 new_args.extend(args)
> 12690 return f(ex, *new_args, **kwds)
12691 return new_f
12692

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/functions/piecewise.py
in fourier_series_partial_sum(self, parameters, variable, N, L)
1347 L = (self.domain().sup() - self.domain().inf()) / 2
1348 x = self.default_variable()
-> 1349 a0 = self.fourier_series_cosine_coefficient(0, L)
1350 result = a0/2 +
sum([(self.fourier_series_cosine_coefficient(n, L)*cos(n*pi*x/L) +
1351
self.fourier_series_sine_coefficient(n, L)*sin(n*pi*x/L))

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/expression.pyx
in sage.symbolic.expression._eval_on_operands.new_f
(build/cythonized/sage/symbolic/expression.cpp:67434)()
12688 new_args = list(ex._unpack_operands())
12689 new_args.extend(args)
> 12690 return f(ex, *new_args, **kwds)
12691 return new_f
12692

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/functions/piecewise.py
in fourier_series_cosine_coefficient(self, parameters, variable, n, L)
1179 a = interval.lower()
1180 b = interval.upper()
-> 1181 result += (f*cos(pi*x*n/L)).integrate(x, a, b)
1182 return SR(result/L0).simplify_trig()
1183

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/expression.pyx
in sage.symbolic.expression.Expression.integral
(build/cythonized/sage/symbolic/expression.cpp:64542)()
12370 R = ring.SR
12371 return R(integral(f, v, a, b, **kwds))
> 12372 return integral(self, *args, **kwds)
12373
12374 integrate = integral

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/integration/integral.py
in integrate(expression, v, a, b, algorithm, hold)
921 return indefinite_integral(expression, v, hold=hold)
922 else:
--> 923 return definite_integral(expression, v, a, b, hold=hold)
924
925

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/function.pyx
in sage.symbolic.function.BuiltinFunction.__call__
(build/cythonized/sage/symbolic/function.cpp:12262)()
1025 res = self._evalf_try_(*args)
1026 if res is None:
-> 1027 res = super(BuiltinFunction, self).__call__(
1028 *args, coerce=coerce, hold=hold)
1029

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/function.pyx
in sage.symbolic.function.Function.__call__
(build/cythonized/sage/symbolic/function.cpp:6938)()
484 for i from 0 <= i < len(args):
485 vec.push_back((<Expression>args[i])._gobj)
--> 486 res = g_function_evalv(self._serial, vec, hold)
487 elif self._nargs == 1:
488 res = g_function_eval1(self._serial,

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/function.pyx
in sage.symbolic.function.BuiltinFunction._evalf_or_eval_
(build/cythonized/sage/symbolic/function.cpp:13412)()
1113 res = self._evalf_try_(*args)
1114 if res is None:
-> 1115 return self._eval0_(*args)
1116 else:
1117 return res

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/integration/integral.py
in _eval_(self, f, x, a, b)
195 for integrator in self.integrators:
196 try:
--> 197 A = integrator(*args)
198 except (NotImplementedError, TypeError):
199 pass

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/symbolic/integration/external.py
in maxima_integrator(expression, v, a, b)
44 result = maxima.sr_integral(expression,v)
45 else:
---> 46 result = maxima.sr_integral(expression, v, a, b)
47 return result._sage_()
48

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx
in sage.misc.lazy_import.LazyImport.__getattr__
(build/cythonized/sage/misc/lazy_import.c:3536)()
319 True
320 """
--> 321 return getattr(self.get_object(), attr)
322
323 # We need to wrap all the slot methods, as they are not forwarded

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx
in sage.misc.lazy_import.LazyImport.get_object
(build/cythonized/sage/misc/lazy_import.c:2347)()
186 if likely(self._object is not None):
187 return self._object
--> 188 return self._get_object()
189
190 cpdef _get_object(self):

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/misc/lazy_import.pyx
in sage.misc.lazy_import.LazyImport._get_object
(build/cythonized/sage/misc/lazy_import.c:2586)()
218 elif self._at_startup and not startup_guard:
219 print('Option ``at_startup=True`` for lazy import
{0} not needed anymore'.format(self._name))
--> 220 self._object = getattr(__import__(self._module, {},
{}, [self._name]), self._name)
221 name = self._as_name
222 if self._deprecation is not None:

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/interfaces/maxima_lib.py
in <module>()
106 ecl_eval("(require 'maxima \"{}\")".format(MAXIMA_FAS))
107 else:
--> 108 ecl_eval("(require 'maxima)")
109 ecl_eval("(in-package :maxima)")
110 ecl_eval("(setq $nolabels t))")

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/libs/ecl.pyx
in sage.libs.ecl.ecl_eval (build/cythonized/sage/libs/ecl.c:10133)()
1323
1324 #convenience routine to more easily evaluate strings
-> 1325 cpdef EclObject ecl_eval(str s):
1326 """
1327 Read and evaluate string in Lisp and return the result

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/libs/ecl.pyx
in sage.libs.ecl.ecl_eval (build/cythonized/sage/libs/ecl.c:10072)()
1338 cdef cl_object o
1339 o=ecl_safe_read_string(str_to_bytes(s))
-> 1340 o=ecl_safe_eval(o)
1341 return ecl_wrap(o)
1342

/home/embray/src/sagemath/sage-python3/local/lib/python3.7/site-packages/sage/libs/ecl.pyx
in sage.libs.ecl.ecl_safe_eval
(build/cythonized/sage/libs/ecl.c:5130)()
347 if ecl_nvalues > 1:
348 s = si_coerce_to_base_string(ecl_values(1))
--> 349 raise RuntimeError("ECL says: {}".format(
350 char_to_str(ecl_base_string_pointer_safe(s))))
351 else:

RuntimeError: ECL says: #<a FLOATING-POINT-OVERFLOW>

[E. Madison Bray]

On Wed, Nov 13, 2019 at 6:23 PM E. Madison Bray <erik....@gmail.com> wrote:
>
> On Wed, Nov 13, 2019 at 6:15 PM E. Madison Bray <erik....@gmail.com> wrote:
> >
> > Testing this on Windows + Python 3 for the first time in a while.
> > During the docbuild it crashes while generating one of the plots, with
> > some call to maxima resulting in:
> >
> > RuntimeError: ECL says: #<a FLOATING-POINT-OVERFLOW>
> >
> > I'll see if I can get this in any other context. Has anyone else seen
> > problems like this on Python 3?
>
> How to reproduce:
>
> sage: f = piecewise([((0,pi/2), -1), ((pi/2,pi), 2)])
> sage: s5 = f.fourier_series_partial_sum(5)

False alarm, I guess. I did a `./sage -f ecl && make build` and now
everything works. Slightly disconcerting, but possibly attributable
to reusing an old Python 3 build that was left in a dubious state.

I'm very impressed, and congratulations to Frédéric et al. for getting
things this far! I'm sorry I couldn't have been of more help in the
final push.

[Sébastien Labbé]

Testing with few optional and external packages, I get

Using --optional=4ti2,awali,cbc,ccache,cryptominisat,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,python2,rst2ipynb,sage

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

sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/schemes/cyclic_covers/cycliccover_finite_field.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 1824.4 seconds
    cpu time: 11665.0 seconds
    cumulative wall time: 14121.7 seconds
External software detected for doctesting: ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

New error copied below:

sage -t --long src/sage/schemes/cyclic_covers/cycliccover_finite_field.py
**********************************************************************
File "src/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1131, in sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial
Failed example:
    CyclicCover(11, PolynomialRing(GF(1129), 'x')([-1] + [0]*(5-1) + [1])).frobenius_polynomial() # long time
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 681, 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 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial[23]>", line 1, in <module>
        CyclicCover(Integer(11), PolynomialRing(GF(Integer(1129)), 'x')([-Integer(1)] + [Integer(0)]*(Integer(5)-Integer(1)) + [Integer(1)])).frobenius_polynomial() # long time
      File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (build/cythonized/sage/misc/cachefunc.c:12712)
        self.cache = f(self._instance)
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1257, in frobenius_polynomial
        cp = charpoly_frobenius(F, charpoly_prec, self._p, 1, self._n, denom.list())
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-packages/sage/schemes/cyclic_covers/charpoly_frobenius.py", line 202, in charpoly_frobenius
        assert cp[-1] == 1
    AssertionError
**********************************************************************
1 item had failures:
   1 of  54 in sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial
    0 tests not run because we ran out of time
    [162 tests, 1 failure, 130.61 s]

But I can not reproduce it:

----------------------------------------------------------------------
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: internet

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