GitLab

Follow upstream for pip packages that can be updated trivially...

Tarballs are already uploaded.

URL: https://trac.sagemath.org/26969
Reported by: vbraun
Ticket author(s): Volker Braun
Reviewer(s): Frédéric Chapoton

If `EXAMPLE:` introduces an indented block of examples, a second `:` is
necessary, because this block is a code block.

URL: https://trac.sagemath.org/27023
Reported by: mantepse
Ticket author(s): Martin Rubey
Reviewer(s): Frédéric Chapoton, Jeroen Demeyer

'''Tarball''':
http://sage.ugent.be/www/jdemeyer/sage/openblas-0.3.5.tar.gz

(renamed from upstream
https://github.com/xianyi/OpenBLAS/archive/v0.3.5.tar.gz)

URL: https://trac.sagemath.org/27020
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Thierry Monteil, Travis Scrimshaw

The file `src/sage/schemes/elliptic_curves/padics.py` contains only
methods which are imported in
`src/sage/schemes/elliptic_curves/ell_rational_field.py`

So there is no reason for this module to be documented.

URL: https://trac.sagemath.org/27017
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Kwankyu Lee

`uniq(X)` is just a shorthand for `sorted(set(X))`: I don't think that
we need a separate function for that. More seriously, the sorting is
problematic since arbitrary sets may not be sortable in general,
especially in Python 3 or after applying #22029.

URL: https://trac.sagemath.org/27014
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Martin Rubey, Travis Scrimshaw

URL: https://trac.sagemath.org/27013
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

Trac #27010: py3: avoid .vertices() in methods _ford_fulkerson, edge_cut, bounded_outdegree_orientation and gomory_hu_tree

We fix all doctests errors in py3 of methods
`bounded_outdegree_orientation` and `gomory_hu_tree` of `graph.py` by
avoiding calls to `.vertices()` in these methods and in methods
`edge_cut` and `_ford_fulkerson` of `generic_graph.py`. This also fixes
some doctests in `generic_graph.py`.

URL: https://trac.sagemath.org/27010
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Travis Scrimshaw

We avoid sorting vertices, edges and connected components. The code is
better this way, and this fixes a doctest error with py3.

URL: https://trac.sagemath.org/27009
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Travis Scrimshaw

Calls to `.vertices()` were performed for small graphs and are not
needed. We also avoid sorting edges when not required.

URL: https://trac.sagemath.org/27008
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Travis Scrimshaw

We change the mappings used in method `is_planar` from file
`planarity.pyx` to avoid calls to `.vertices()`.

The changes done here were inducing a doctest error in method `genus`
for
{{{
sage: cube.genus(circular=['01','10'], on_embedding=True)
}}}
As the documentation indicates that {{{If ``circular`` is defined,
``on_embedding`` is not a valid option}}}, we now raise an error in this
situation.

This patch fixes some doctests that where failing with py3 in methods
- `TutteGraph` of `smallgraphs.py`
- `apex_vertices` of `graph.py`
- `genus` of `generic_graph.py`

URL: https://trac.sagemath.org/27007
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Travis Scrimshaw

For example (in sage 8.6.b1),
{{{
sage: x = polygen(QQ,'x')
sage: M = libgap(matrix(2,2,[x,1,2,3]))
sage: M
[ [ x, 1 ], [ 2, 3 ] ]
sage: M.IsMatrix()
false
}}}
so that all matrix methods are broken on the result

URL: https://trac.sagemath.org/27005
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

The objects may not be sortable in general.

We remove one `sorted()` call and simplify the code.

For reference: this code was introduced in #25148 (but changed several
times afterwards).

URL: https://trac.sagemath.org/27003
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Frédéric Chapoton

This takes one change from upstream Sphinx autodoc: using `__qualname__`
to document aliases.

To work around https://github.com/cython/cython/pull/2773 we use this
only on Python 3.

URL: https://trac.sagemath.org/27002
Reported by: jdemeyer
Ticket author(s): Kwankyu Lee
Reviewer(s): Jeroen Demeyer

Using 8.6.beta1 with Gurobi installed and available in Sage (as
explained [http://doc.sagemath.org/html/en/thematic_tutorials/linear_pro
gramming.html#using-cplex-or-gurobi-through-sage here]), the command
{{{
sage -t --optional=sage,external
src/sage/numerical/backends/gurobi_backend.pyx
}}}

gives

{{{
Using --optional=external,memlimit,sage
External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagi
ck,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc
,scilab
Doctesting 1 file.
sage -t src/sage/numerical/backends/gurobi_backend.pyx
**********************************************************************
File "src/sage/numerical/backends/gurobi_backend.pyx", line 50, in
sage.numerical.backends.gurobi_backend.GurobiBackend
Failed example:
    TestSuite(p.get_backend()).run(skip="_test_pickling")         #
optional - Gurobi
Expected nothing
Got:
    Failure in _test_copy:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
packages/sage/misc/sage_unittest.py", line 296, in run
        test_method(tester = tester)
      File "sage/numerical/backends/generic_backend.pyx", line 1255, in
sage.numerical.backends.generic_backend.GenericBackend._test_copy
(build/cythonized/sage/numerical/backends/generic_backend.c:14740)
        self._do_test_problem_data(tester, cp)
      File "sage/numerical/backends/generic_backend.pyx", line 1229, in
sage.numerical.backends.generic_backend.GenericBackend._do_test_problem_
data (build/cythonized/sage/numerical/backends/generic_backend.c:14457)
        assert_equal_problem_data(method)
      File "sage/numerical/backends/generic_backend.pyx", line 1226, in
sage.numerical.backends.generic_backend.GenericBackend._do_test_problem_
data.assert_equal_problem_data
(build/cythonized/sage/numerical/backends/generic_backend.c:13727)
        tester.assertEqual(getattr(self, method)(), getattr(cp,
method)(),
      File
"/home/slabbe/GitBox/sage/local/lib/python2.7/unittest/case.py", line
513, in assertEqual
        assertion_func(first, second, msg=msg)
      File
"/home/slabbe/GitBox/sage/local/lib/python2.7/unittest/case.py", line
506, in _baseAssertEqual
        raise self.failureException(msg)
    AssertionError: problem_name does not match
    ------------------------------------------------------------
    Failure in _test_copy_does_not_share_data:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
packages/sage/misc/sage_unittest.py", line 296, in run
        test_method(tester = tester)
      File "sage/numerical/backends/generic_backend.pyx", line 1265, in
sage.numerical.backends.generic_backend.GenericBackend._test_copy_does_n
ot_share_data
(build/cythonized/sage/numerical/backends/generic_backend.c:14947)
        self._do_test_problem_data(tester, cpcp)
      File "sage/numerical/backends/generic_backend.pyx", line 1229, in
sage.numerical.backends.generic_backend.GenericBackend._do_test_problem_
data (build/cythonized/sage/numerical/backends/generic_backend.c:14457)
        assert_equal_problem_data(method)
      File "sage/numerical/backends/generic_backend.pyx", line 1226, in
sage.numerical.backends.generic_backend.GenericBackend._do_test_problem_
data.assert_equal_problem_data
(build/cythonized/sage/numerical/backends/generic_backend.c:13727)
        tester.assertEqual(getattr(self, method)(), getattr(cp,
method)(),
      File
"/home/slabbe/GitBox/sage/local/lib/python2.7/unittest/case.py", line
513, in assertEqual
        assertion_func(first, second, msg=msg)
      File
"/home/slabbe/GitBox/sage/local/lib/python2.7/unittest/case.py", line
506, in _baseAssertEqual
        raise self.failureException(msg)
    AssertionError: problem_name does not match
    ------------------------------------------------------------
    The following tests failed: _test_copy,
_test_copy_does_not_share_data
**********************************************************************
1 item had failures:
   1 of   3 in sage.numerical.backends.gurobi_backend.GurobiBackend
    [207 tests, 1 failure, 0.14 s]
----------------------------------------------------------------------
sage -t src/sage/numerical/backends/gurobi_backend.pyx  # 1 doctest
failed
----------------------------------------------------------------------
Total time for all tests: 0.2 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 0.1 seconds
External software detected for doctesting: gurobi
}}}

URL: https://trac.sagemath.org/26999
Reported by: slabbe
Ticket author(s): Erik Bray
Reviewer(s): Sébastien Labbé

rather easy, in fact

URL: https://trac.sagemath.org/26998
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Jori Mäntysalo

On Ubuntu 16.04, running sage-8.5.beta1, the command
{{{
sage -t --long --optional=sage,internet src/sage/databases/findstat.py
}}}

gives

{{{
...
3 items had failures:
   3 of  16 in sage.databases.findstat
   1 of   4 in sage.databases.findstat.FindStatStatistic.__repr__
   1 of   9 in sage.databases.findstat.FindStatStatistic._find_by_values
    [247 tests, 5 failures, 107.27 s]
----------------------------------------------------------------------
sage -t --long src/sage/databases/findstat.py  # 5 doctests failed
----------------------------------------------------------------------
}}}

Full failure log is long and is pasted here: https://framabin.org/p/?b9d
acda8324c7295#71YTYesLKEKBCNg1LtnDUhKkWDrcm+xiZGDI9a8bjfg=

URL: https://trac.sagemath.org/26997
Reported by: slabbe
Ticket author(s): Martin Rubey
Reviewer(s): Frédéric Chapoton

It has:
* `rational_power_parts()` fix (Isuru Fernando)
* `numeric::ratlog()` fix (Eric M Bray, #25948)
* matching improvements / fixes

https://github.com/pynac/pynac/releases/download/pynac-0.7.23/pynac-0.7.
23.tar.bz2

URL: https://trac.sagemath.org/26995
Reported by: rws
Ticket author(s): Ralf Stephan
Reviewer(s): Travis Scrimshaw

In this example

{{{
sage: K = GF(47^2)
sage: E = EllipticCurve([0, K.gen()])
sage: f = E.division_polynomial(7).factor()[4][0]
sage: E.is_supersingular()
True
sage: E.isogeny(f).codomain().is_supersingular()
False
sage: phi = E.isogeny(E.division_polynomial(7).factor()[8][0])
sage: phi(E.random_point())
------------------------------------------------------------------------
---
TypeError                                 Traceback (most recent call
last)
...
TypeError: Coordinates [16*z2 + 30, 3*z2 + 22, 1] do not define a point
on Elliptic Curve defined by y^2 = x^3 + (3*z2+36)*x over Finite Field
in z2 of size 47^2
}}}

The factors of the seventh division polynomial are not detected as bad
kernel polynomials, and a wrong isogeny is computed instead.

Tests to detect these cases are in `.isogenies_prime_degree_general()`.
They should be moved to an independent function and called before
applying Vélu's formulas.

URL: https://trac.sagemath.org/23222
Reported by: defeo
Ticket author(s): John Cremona
Reviewer(s): Luca De Feo, Frédéric Chapoton

in symbolic/ring.pyx

This fixes the last failing doctest in calculus

URL: https://trac.sagemath.org/26988
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

mostly cleaning up, and trying not to use .vertices for digraphs

URL: https://trac.sagemath.org/26985
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

In #23978 a wrong ticket number was advertised in a deprecation warning.

URL: https://trac.sagemath.org/26981
Reported by: vdelecroix
Ticket author(s): Vincent Delecroix
Reviewer(s): Frédéric Chapoton

URL: https://trac.sagemath.org/26967
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

The following crashes sage with a SIGSEGV:
{{{
sage: from sage.rings.polynomial.multi_polynomial_libsingular import
MPolynomialRing_libsingular
sage: class Foo(MPolynomialRing_libsingular):
....:     pass
sage: Foo(QQ, 2, ['x','y'], 'degrevlex')
}}}
Strangely enough this bug is triggered only when inheriting; indeed the
following works as expected:
{{{
sage: from sage.rings.polynomial.multi_polynomial_libsingular import
MPolynomialRing_libsingular
sage: MPolynomialRing_libsingular(QQ, 2, ['x','y'], 'degrevlex')
Multivariate Polynomial Ring in x, y over Rational Field
}}}

As it turns out this bug is due to a spurious call to `__init_extra__`
of `Algebras(...).parent_class`. Univariate polynomial rings avoid this
call by setting  the attribute `_no_generic_basering_coercion = True`;
now multivariate polynomial rings do so too.

URL: https://trac.sagemath.org/26958
Reported by: etn40ff
Ticket author(s): Salvatore Stella
Reviewer(s): Jeroen Demeyer

This ticket improves `sage.libs.giac` by adding support for:

- `lex`, `deglex`, as well as block orders with 2 `degrevlex` blocks in
Groebner basis computations,
- computation of elimination ideals.

Additionally, this adds an optional keyword `algorithm=...`  to
`sage.rings.polynomial.multi_polynomial_ideal.elimination_ideal` to
allow choosing between libsingular and Giac implementations.

For further information, here is the documentation of [https://www-
fourier.ujf-grenoble.fr/~parisse/giac/doc/fr/cascmd_fr/cascmd_fr282.html
giac's eliminate] and [https://groups.google.com/d/msg/sage-
devel/cxs2fNKecLo/49nl9z1MCQAJ the discussion] in which I learned that
Giac supports this.

URL: https://trac.sagemath.org/26943
Reported by: gh-mwageringel
Ticket author(s): Markus Wageringel
Reviewer(s): Vincent Delecroix

This sort can fail if the points are not comparable:
{{{
                sortkey = lambda e: [(0 if x is None else 2 if
isinstance(x, str) else 1, x) for x in e]\
                    if isinstance(e, tuple) else e
                self._points = sorted(points, key=sortkey)
}}}

The `sortkey` tries to find a clever way to "sort" the points but
hardcoding classes like that is not a general solution. In particular,
it's still comparing integers and strings when #22029 is appplied.

Instead, just don't sort.

URL: https://trac.sagemath.org/26938
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Frédéric Chapoton

In `src/sage/combinat/words/morphism.py`, there is the following code:
{{{
dom_alph.sort()
}}}
and
{{{
return FiniteWords(sorted(codom_alphabet))
}}}

These will break with #22029.

URL: https://trac.sagemath.org/26936
Reported by: jdemeyer
Ticket author(s): Sébastien Labbé
Reviewer(s): Jeroen Demeyer

It should not force sorting the set, which may be unsortable.

URL: https://trac.sagemath.org/26933
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Travis Scrimshaw

URL: https://trac.sagemath.org/26917
Reported by: chapoton
Ticket author(s): Frédéric Chapoton, Martin Rubey
Reviewer(s): Frédéric Chapoton, Travis Scrimshaw

Followup to a comment in #22148 to fix the indentation in numberfield.py
within the solve_S_unit_equation function.

URL: https://trac.sagemath.org/26864
Reported by: mwest
Ticket author(s): Mckenzie West
Reviewer(s): Jeroen Demeyer

`RealLazyField` exhibits the following bug on 8.4 stable and on
development branch:

{{{
sage: float(sin(RLF.pi()))

------------------------------------------------------------------------
---
AttributeError                            Traceback (most recent call
last)
<ipython-input-1-750e6734ef1c> in <module>()
----> 1 float(sin(RLF.pi()))

/home/pat/Software/Sage/sage-git/sage/local/lib/python2.7/site-
packages/sage/rings/real_lazy.pyx in
sage.rings.real_lazy.LazyNamedUnop.__float__
(build/cythonized/sage/rings/real_lazy.c:16203)()
   1404             0.8414709848078965
   1405         """
-> 1406         return self.eval(float)
   1407
   1408     def __call__(self, *args):

/home/pat/Software/Sage/sage-git/sage/local/lib/python2.7/site-
packages/sage/rings/real_lazy.pyx in
sage.rings.real_lazy.LazyNamedUnop.eval
(build/cythonized/sage/rings/real_lazy.c:15520)()
   1348             2.0
   1349         """
-> 1350         arg = self._arg.eval(R)
   1351         cdef bint has_extra_args = self._extra_args is not None
and len(self._extra_args) > 0
   1352         if type(R) is type:

/home/pat/Software/Sage/sage-git/sage/local/lib/python2.7/site-
packages/sage/rings/real_lazy.pyx in
sage.rings.real_lazy.LazyConstant.eval
(build/cythonized/sage/rings/real_lazy.c:16924)()
   1490                 else:
   1491                     raise TypeError("The complex constant I is
not in this real field.")
-> 1492         f = getattr(R, self._name)
   1493         if self._extra_args is None:
   1494             return f()

AttributeError: type object 'float' has no attribute 'pi'
}}}

The same issue appears with RDF replacing float.

Vincent noted that the following works fine:

{{{
sage: (sin(RLF.pi())).eval(RDF)
 1.2246467991473515e-16
}}}

On the other hand I get:
{{{
sage: (sin(RLF.pi())).eval(float)

------------------------------------------------------------------------
---
AttributeError...
}}}

URL: https://trac.sagemath.org/26839
Reported by: wphooper
Ticket author(s): Vincent Delecroix
Reviewer(s): Sébastien Labbé

URL: https://trac.sagemath.org/26834
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Vincent Klein

{{{
sage: Permutations(avoiding=[[1,3,2]])
Standard permutations
}}}
We simply implement an appropriate class.  Now
{{{
[1,3,2] in Permutations(avoiding=[1,3,2])
}}}
works as expected.

URL: https://trac.sagemath.org/26810
Reported by: mantepse
Ticket author(s): Martin Rubey
Reviewer(s): Daniel Krenn, Travis Scrimshaw

{{{
sage: P = Permutations(3, avoiding=[[1,3,2]])
sage: P.list()
[[1, 2, 3], [3, 1, 2], [2, 1, 3], [2, 3, 1], [3, 2, 1]]
sage: [1,3,2] in P
True
}}}

URL: https://trac.sagemath.org/26809
Reported by: mantepse
Ticket author(s): Martin Rubey
Reviewer(s): Daniel Krenn, Travis Scrimshaw

When running doctests in my applications of SharedMeatAxe,
`sig_on_count` reveals problems.

URL: https://trac.sagemath.org/26516
Reported by: SimonKing
Ticket author(s): Simon King
Reviewer(s): Jeroen Demeyer

This ticket adds a glucose experimental or optional package, and fixes
the old glucose interface.

Tarball: http://www.labri.fr/perso/lsimon/downloads/softwares/glucose-
syrup-4.1.tgz

URL: https://trac.sagemath.org/26361
Reported by: tmonteil
Ticket author(s): Thierry Monteil, Sébastien Labbé
Reviewer(s): Vincent Delecroix

When a line of test input tagged with e.g. `# rel tol` throws a warning
or error, the line numbers, version numbers, etc. in the tracebacks are
tested, even if there are ellipses in the test output signaling that
they should be ignored.

Here's a toy example:

{{{
def foo():
    """
    The following test fails. We should disallow this.

    TESTS::
        sage: foo() # rel tol 1e-1
        [0, ... 9]
    """
    print([j for j in range(10)])
}}}

We should throw an error if these are used in the same doctest, as this
can lead to confusing output.

URL: https://trac.sagemath.org/26183
Reported by: gh-bryangingechen
Ticket author(s): Jeroen Demeyer
Reviewer(s): Erik Bray

{{{
sage: RR(0).str(digits=3)
'0.000'
}}}

This is trivial to fix, but then it causes hundreds of doctest failures
since every real zero is printed with one less digit. To compensate for
this, we add one extra digit for 0.0 in the default case.

URL: https://trac.sagemath.org/26156
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Travis Scrimshaw

The first changes to sage in order to migrate the
https://github.com/MareoRaft/k_combinat_for_sage library (see also
#25295) involve changing `partition.py`.

This ticket is now READY FOR REVIEW :)

URL: https://trac.sagemath.org/25931
Reported by: gh-MareoRaft
Ticket author(s): Matthew Lancellotti
Reviewer(s): George H. Seelinger

This is required for compiling Python 3.7

'''Tarball''': ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz

URL: https://trac.sagemath.org/25900
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Frédéric Chapoton, Erik Bray