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Let us remove some bad uses of comparison to True or False.

URL: http://trac.sagemath.org/20459
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

some problems (about future transition to py3) can be found using
{{{
export PYTHONIOENCODING="utf-8"
python -Qwarnall $(which sage-runtests) src/sage/combinat/*.py
}}}
let us try to correct a few of them.

see also #18659 and #15995

URL: http://trac.sagemath.org/20468
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

here:
{{{
sage: W=CoxeterGroup(('A1',['H',3]))
}}}
is not working. This comes from
{{{
sage: from sage.groups.matrix_gps.coxeter_group import *
sage: Z=CartanType(('A1',['H',3]))
sage: CoxeterMatrixGroup(Z)
}}}

URL: http://trac.sagemath.org/20425
Reported by: chapoton
Ticket author(s): Travis Scrimshaw
Reviewer(s): Frédéric Chapoton

Trac #20414: Add copy/__copy__ methods to CVXOPT, PPL, InteractiveLP backends, and __deepcopy__ to MixedIntegerLinearProgram and backends

The COIN, CPLEX, GLPK, and Gurobi backends supply a `copy` method.
But it's not documented as a backend interface method in
`GenericBackend`, and the CVXOPT, PPL, InteractiveLP backends do not
implement it.
It is used by `MixedIntegerLinearProgram.__copy__`.

The backend method should actually probably be called `__copy__` as well
-- see https://docs.python.org/2/library/copy.html

The branch on the ticket does this.

We also add `__deepcopy__` methods to `MixedIntegerLinearProgram` and
the backends.
This fixes #15159, though the semantics of `copy` and `deepcopy` of a
`MixedIntegerLinearProgram` remains questionable due to its interaction
with `MIPVariable`; see #15159 and #19523.

See also #20323 (in which copying a backend could be the basis for more
diverse tests).

URL: http://trac.sagemath.org/20414
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

Some easy updates

URL: http://trac.sagemath.org/20450
Reported by: vbraun
Ticket author(s): Volker Braun
Reviewer(s): François Bissey

In generic implementations of `f.quo_rem(g)`, an exception
{{{#!python
ArithmeticError: Nonunit leading coefficient
}}}
is raised as soon as the leading coefficient of `g` is not invertible.
This was introduced by ticket #11593, and I mimicked the behavior in
#16544.

The change I propose is to try to compute the Euclidean division, and
raise an exception
{{{#!python
ArithmeticError: division not exact (consider coercing to polynomials
over the fraction field first)
}}}
when the computation is not possible. Then, `quo_rem` would produce less
exceptions, and in particular give an answer each time the answer is not
controversial (see below).

'''Note on the controverse.''' There is a debate to know whether one
should raise an exception when the division is not exact (as it is done
for dense integer polynomials with the `NTL` implementation), or if one
should silently return a result that has a mathematical meaning though
it is not a Euclidean division (as it is done with the `flint`
implementation). See #16276 as well as https://groups.google.com/d/msg
/sage-devel/UVrx5CG4qA0/WUz2RItJtF8J for this debate. My proposition is
to already implement a more capable algorithm, and not to wait for the
debate to be closed.

URL: http://trac.sagemath.org/16649
Reported by: bruno
Ticket author(s): Bruno Grenet
Reviewer(s): Frédéric Chapoton, Ralf Stephan

The color default should work for single AND multiband images, so a
tuple is a bad choice.

This ticket changes SageNB from a distribution to a normal Python
package. This means unbundling everything which used to be part of the
SageNB distribution.

The package `webassets` is simply removed, since it doesn't seem to be
used by anything in Sage or SageNB.
[https://groups.google.com/forum/#!msg/sage-
devel/fEeGgVWuk7I/nDOHbclqLUAJ This thread] indicates that `webassets`
is used by the `newui` branch of SageNB but not in vanilla SageNB. So it
has no reason being in Sage currently.

'''New upstream tarballs''':

* http://sage.ugent.be/www/jdemeyer/sage/sagenb-0.12.tar.bz2
* ​https://pypi.python.org/packages/source/B/Babel/Babel-2.2.0.tar.gz
* https://pypi.python.org/packages/source/F/Flask/Flask-0.10.1.tar.gz
* http://sage.ugent.be/www/jdemeyer/sage/Flask_AutoIndex-0.5.tar.gz
(renamed `-` -> `_`)
* http://sage.ugent.be/www/jdemeyer/sage/Flask_Babel-0.9.tar.gz (renamed
`-` -> `_`)
* http://sage.ugent.be/www/jdemeyer/sage/Flask_OldSessions-0.10.tar.gz
(renamed `-` -> `_`)
* http://sage.ugent.be/www/jdemeyer/sage/Flask_OpenID-1.2.5.tar.gz
(renamed `-` -> `_`)
* http://sage.ugent.be/www/jdemeyer/sage/Flask_Silk-0.2.tar.gz (renamed
`-` -> `_`)
* https://pypi.python.org/packages/source/i/itsdangerous/itsdangerous-0.
24.tar.gz
* http://sage.ugent.be/www/jdemeyer/sage/python_openid-2.2.5.tar.gz
(renamed `-` -> `_`)
* ​http://sage.ugent.be/www/jdemeyer/sage/pytz-2016.3.tar.bz2 (upstream
version with sanitized permissions)
* https://pypi.python.org/packages/source/s/speaklater/speaklater-1.3.ta
r.gz
*
https://pypi.python.org/packages/source/T/Twisted/Twisted-15.5.0.tar.bz2
* https://pypi.python.org/packages/source/W/Werkzeug/Werkzeug-0.11.5.tar
.gz
* https://pypi.python.org/packages/source/z/zope.interface/zope.interfac
e-4.1.3.tar.gz

URL: http://trac.sagemath.org/14840
Reported by: felixs
Ticket author(s): Jeroen Demeyer
Reviewer(s): Salvatore Stella, Dima Pasechnik

This enables the use of fpylll from within Sage.

tarball: http://trac.sagemath.org/raw-
attachment/ticket/20291/libfplll-20160331.tar.gz

URL: http://trac.sagemath.org/20291
Reported by: malb
Ticket author(s): Martin Albrecht
Reviewer(s): François Bissey, Jeroen Demeyer

By implementing a non-recursive iterator, we avoid some overhead. With
this branch, we get the following:
{{{
sage: I = IntegerVectors(12,7)
sage: %timeit list(I.__iter__())
10 loops, best of 3: 20.8 ms per loop
sage: I = WeightedIntegerVectors(12, [4,1,2,2])
sage: %timeit list(I.__iter__())
1000 loops, best of 3: 291 µs per loop
sage: I = WeightedIntegerVectors(12, [2,1,1,2])
sage: %timeit list(I.__iter__())
1000 loops, best of 3: 556 µs per loop
sage: I = WeightedIntegerVectors(17, [2,1,1,2,1,1,2])
sage: %timeit list(I.__iter__())
10 loops, best of 3: 56.4 ms per loop
sage: I = WeightedIntegerVectors(26, [2,1,1,2,1,1,2])
sage: %timeit list(I.__iter__())
1 loop, best of 3: 443 ms per loop
}}}
versus the current version:
{{{
sage: I = IntegerVectors(12,7)
sage: %timeit list(I.__iter__())
10 loops, best of 3: 50.3 ms per loop
sage: %timeit list(I.__iter__())
The slowest run took 8.13 times longer than the fastest. This could mean
that an intermediate result is being cached.
1000 loops, best of 3: 301 µs per loop
sage: I = WeightedIntegerVectors(12, [2,1,1,2])
sage: %timeit list(I.__iter__())
1000 loops, best of 3: 554 µs per loop
sage: I = WeightedIntegerVectors(17, [2,1,1,2,1,1,2])
sage: %timeit list(I.__iter__())
10 loops, best of 3: 68.1 ms per loop
sage: I = WeightedIntegerVectors(26, [2,1,1,2,1,1,2])
sage: %timeit list(I.__iter__())
1 loop , best of 3: 528 ms per loop
}}}

URL: http://trac.sagemath.org/20166
Reported by: tscrim
Ticket author(s): Travis Scrimshaw
Reviewer(s): Vincent Delecroix

On the online documentation for setting up a fork, the D is left off of
Detail.

http://doc.sagemath.org/html/en/developer/sagenb/set_up_fork.html#set-
up-fork

I plan on fixing this to learn how to use the system.

URL: http://trac.sagemath.org/20290
Reported by: tara
Ticket author(s): Tara Fife
Reviewer(s): Stefan van Zwam

We need to support running both sagenb and ipynb notebooks.  Moreover,
we need to support exporting sagenb to ipynb to ease the transition.
Auto-detection of existing sagenb notebooks and smartly offering to
upgrade would be nice as well.

URL: http://trac.sagemath.org/19881
Reported by: iandrus
Ticket author(s): Ivan Andrus
Reviewer(s): Volker Braun

In the symbolic ring, cmp implements the print comparison which is
probably not what you envisioned:
{{{
sage: cmp(1, sqrt(2))     # mathematically correct, uses rich comparison
-1
sage: cmp(SR(1), sqrt(2)) # unexpectedly, you get the print sort order
1
sage: cmp(log(8), 3*log(2))
-1
}}}
Everybody who coerces to same parents internally before comparing trips
over this, for example the real lazy field:
{{{
sage: RLF(1) < RLF(sqrt(2))
False
}}}
This also makes `RealSet` unusable with symbolics:
{{{
sage: RealSet((0, pi),[pi, pi],(pi,4))
[pi, 4)
sage: RealSet((0, pi),[0, pi],(pi,4))
[pi, 4)
sage: RealSet((0, pi),[0, 3.5],(pi,4))
(pi, 4)
}}}

URL: http://trac.sagemath.org/16397
Reported by: vbraun
Ticket author(s): Volker Braun, Ralf Stephan
Reviewer(s): Ralf Stephan, Volker Braun

The functions `inject_on`/`inject_off` are most likely used by nobody:
they are superseded by the `K.<x> = ...` syntax and not all constructors
are supported.

URL: http://trac.sagemath.org/20442
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Frédéric Chapoton

`generic_graph.py` contains several functions where documentation says
that there are several algorithms available. However there is no
explanation of their difference. Is some faster, other uses less memory?
Better for sparse/dense graphs?

As an example `flow()` has three algorithm and no clear explanation when
to choose `FF` or `LP`.

URL: http://trac.sagemath.org/19599
Reported by: jmantysalo
Ticket author(s): Jori Mäntysalo
Reviewer(s): Frédéric Chapoton

libSingular functions require a ring parameter set. But for some
functions the ring parameter is redundant.

Martin Albrecht answers to this issue:

We could do this:

- if no ring is given, we try to find one as we do currently.
- if that fails because the inputs are not polynomials of any kind, we
could use a dummy ring.

We implement this.

URL: http://trac.sagemath.org/19084
Reported by: klee
Ticket author(s): Kwankyu Lee
Reviewer(s): Volker Braun

I have frequently encountered computer setups where one has access to a
Sage installation locally, but Magma is only installed in a remote
machine (say with address 'remote'). Typically one either:
1) Logs into 'remote' via ssh and does some computation in Magma.
2) uses the ssh command
{{{
    $> ssh -t remote 'magma'
}}}
to pretend having magma installed locally.

Actually Sage has functionality to use (2) in its interface with Magma,
but it is currently broken and not advertised. It presumes that 'remote'
also has sage installed (in fact it presumes that sage-native-execute is
in the default PATH), for example.

This ticket fixes this, and makes a command like
{{{
    sage: magma = Magma(server = 'remote', command = 'magma-myversion')
}}}
work, and provide the user with an interface to a particular version of
Magma installed in 'remote'.

URL: http://trac.sagemath.org/20388
Reported by: mmasdeu
Ticket author(s): Marc Masdeu
Reviewer(s): Nils Bruin, Vincent Delecroix

Add a function to see if a poset is series-parallel (or "N-free").

First wait for #19659 to get closed. Series-parallel decomposition is
just recursive applying of `connected_components()` and
`ordinal_sum_decomposition()`.

URL: http://trac.sagemath.org/19215
Reported by: jmantysalo
Ticket author(s): Jori Mäntysalo
Reviewer(s): Frédéric Chapoton

The definition allows a choice of a general c,,ij,, matrix such that
c,,ij,, + c,,ji,, = 1 for all `i != j`.

We also perform some cleanup:

- Remove the trailing whitespace at the end of the monomial printing.
- Only needing to input the dominant weight.
- Better handling of dictionaries in monomial methods.

URL: http://trac.sagemath.org/18895
Reported by: tscrim
Ticket author(s): Travis Scrimshaw
Reviewer(s): Ben Salisbury

{{{
sage: x,y=polygen(ZZ,'x,y')
sage: p=x**2-y**2
sage: p.parent()
Multivariate Polynomial Ring in x, y over Integer Ring
sage: factor(p)
(x - y) * (x + y)
sage: factor(p)[0][0].parent()
Multivariate Polynomial Ring in x, y over Multivariate Polynomial Ring
in x, y over Integer Ring
}}}
but no problem over QQ

URL: http://trac.sagemath.org/20435
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Bruno Grenet