Trac 7099: mark two doctests with "abs tol 2e-10"
Merge branch 'develop' of trac.sagemath.org:sage into u/malb/t15915_discrete_gaussians
trac #16655: resolvable OA/TD
Extended the method to the case of non-strongly-connected digraphs
Added a "SEEALSO" to .period into .is_aperiodic()
trac #16662: doc + test
trac #16604: on the doc again
trac #16662: New assertion
Apply pyparsing patch in binary mode
added further doctests to check the evaluation and modularity of modular forms
trac #16604: small check of dimensions
rewrote to avoid copying subgraphs.
Trac #7099: serious incomplete gamma function precision bugs

{{{
sage: C = ComplexField(1000)
sage: C(2+I).gamma_inc(C(3+I))
0.1215156446645086956511068454478419198494520969688892364501953125000000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
00000000000000 +
0.1015339090798260332775427433604775728781532961875200271606445312500000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
000000000000000000000000000000000000000000000000000000000000000000000000
\
00000000000000*I
}}}

What's with all the zeros?   Same bad behavior for higher precision and
any other random input.  This is undoubtedly the typical mistake of not
setting the pari precision correctly, etc., etc.

URL: http://trac.sagemath.org/7099
Reported by: was
Ticket author(s): Peter Bruin
Reviewer(s): Ralf Stephan
Trac #16538: FiniteStateMachine.process: follow all paths if machine is non-deterministic

Prior to #16539, a (more or less) random path was chosen in case of
ambiguity
in {{{FiniteStateMachine.process}}}. In #16539, this undesired behaviour
is replaced by a {{{NonImplementedError}}}.

However, ideally, in the case of non-deterministic machines, all
possible paths should be considered. This shall be implemented in this
ticket.

URL: http://trac.sagemath.org/16538
Reported by: cheuberg
Ticket author(s): Daniel Krenn
Reviewer(s): Clemens Heuberger, Sara Kropf
Trac #16598: New empty design classes for a better user interface and new is_group_divisible_design Cython function

This branch defines:

- `GroupDivisibleDesign`
- `PairwiseBalancedDesign`
- `BalancedIncompleteBlockDesign`
- `TransversalDesign`

All these classes (which inherit from `IncidenceStructure`) make it
easier to do things like compute the `automorphism_group` of a
transversal design.

The branch also adds a function `is_group_divisible_design` in
`designs_pyx.pyx`, and an empty `is_pairwise_balanced_design` that call
it. We can thus get rid of the ugly `_check_pbd`.

Nathann

URL: http://trac.sagemath.org/16598
Reported by: ncohen
Ticket author(s): Nathann Cohen
Reviewer(s): Vincent Delecroix
Trac #16725: Implement a general monoid_generators for groups

As discussed on #16718, not all groups have a `monoid_generators` method
but we can define them by taking the generators as a group and their
inverses.

URL: http://trac.sagemath.org/16725
Reported by: tscrim
Ticket author(s): Travis Scrimshaw
Reviewer(s): Nathann Cohen
Trac #16756: Fully make lrcalc standard

`build/deps` should reflect the dependency of `sage` on `lrcalc`.

URL: http://trac.sagemath.org/16756
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): John Palmieri
Trac #16785: derivative operator translation to maxima

Currently, we are failing to properly convert certain expressions to
maxima when they contain differential operators:
{{{
sage: function('f')
sage: maxima_calculus(f(x).diff(x))
'diff(f(_SAGE_VAR_x),_SAGE_VAR_x,1)
sage: maxima_calculus(f(x+1).diff(x)) #this is bad!
?%at('diff(f(t0),t0,1),[t0=x+1])
}}}
note the bare `x` in the bottom line. That should be a `_SAGE_VAR_`.

As it turns out, a lot of conversion here is happening with string
manipulations, circumventing the standard conversion machinery. That
also means that functions that have a non-trivial `_maxima_init_evaled_`
will not get translated using it. It's better to do everything using the
standard conversion.

URL: http://trac.sagemath.org/16785
Reported by: nbruin
Ticket author(s): Nils Bruin
Reviewer(s): Ralf Stephan
Trac #15672: Computing degree bound GBs with Magma is broken

This should work:

{{{
sage: R.<a,b,c,d,e,f,g,h,i,j> = PolynomialRing(GF(127),10)
sage: I = sage.rings.ideal.Cyclic(R,6)
sage: gb = I.groebner_basis('magma:GroebnerBasis', deg_bound=4)
}}}

The culprit is that !PolynomialSequence casts to an ideal in Magma, but
we need a sequence.

URL: http://trac.sagemath.org/15672
Reported by: malb
Ticket author(s): Martin Albrecht
Reviewer(s): Jakob Kroeker
Trac #16795: Update sage-mode to 0.12

0.12 has an important fix for viewing inline plots.

Tarball: http://trac.sagemath.org/raw-
attachment/ticket/16795/sage_mode-0.12.tar.bz2

URL: http://trac.sagemath.org/16795
Reported by: iandrus
Ticket author(s): Ivan Andrus
Reviewer(s): Volker Braun