Bug in AffineGeometryDesign
Fix for phi in tensor_product.py
Merge branch 'develop' into public/combinat/crystals/fix_phi_tensor_product

* develop: (375 commits)
  Updated Sage version to 6.1.beta2
  fix latex
  fix documentation
  minor typography
  Trac 13101: mark doctest as "long time"
  trac 13101 better doctest
  Trac 13101: Fix bug in enumerate_totallyreal_fields_all
  #9706: review patch.
  trac 9706: Propose new class structure
  Symbolic Chebyshev polynomials: reviewer patch
  trac 9706: Collective patch. Bugfixes, extensions, optimizations, documentation, doctests for chebyshev_T, chebyshev_U and base class for ortho polys
  Updated Sage version to 6.1.beta1
  Fixing Whitespace errors
  Use bash as SHELL for build/Makefile
  allow numpy arrays in list_plot, line, points
  Run Jmol from current directory
  Trac #12322: Add a doctest for the correct behavior introduced in trac #12737.
  Trac #14186 coerce_binop errors with keyword arguments
  trac #15553: Broken links in the doc of graph/ and numerical/
  bug fix : importing BooleanPolynomialRing at the top-level prevents sage from starting
  ...
workaround for maxima hanging on emacs
Merge branch 'develop' into public/combinat/crystals/fix_phi_tensor_product

* develop: (95 commits)
  Trac #14858: more robust type checks for arith.py
  Updated Sage version to 6.1.beta3
  Trac #11271: making the curve inaccessible + documentation
  Trac #11271: Corrections to is_surjective in Galois representations over Q.
  sage-sdist: copy upstream tarballs using sage-spkg
  Fixed docbuild.
  Removed removed file from doc.
  Fix wrong NOTE block.
  Where possible, remove optional - database_stein_watkins
  Stein-Watkins database: reviewer patch
  buid/deps : added a dependency of freetype on libpng in order to work around a build-time race condition.
  Replace bytes_to_long/long_to_bytes by ord/chr.
  Revert "Filter pycrypto warning about insecure modular exponentiaiton."
  first version of the git-trac package
  Filter pycrypto warning about insecure modular exponentiaiton.
  Update PyCrypto to version 2.6.1.
  Let PyCrypto build on FreeBSD.
  trac #15435: WeylGroup and CoxeterGroup to groups.<tab>
  trac #15369: Alias groups.misc.AdditiveCyclic to IntegerModRing
  Fix for comparison of padics.
  ...
trac 15285: rebase on 6.1.beta4
trac #15285: Rebase on updated #15107
Do not import sagenb at Sage startup
Fixed doctest.
Changed type of BasisExchangeMatroid._E and SetSystem._groundset from `list' to `tuple'.
Changed several methods that manipulated these fields to use `tuple' methods.
Only add sagenb globals if actually testing a sagenb file
Merge branch 'u/tscrim/ticket/15335' of git://trac.sagemath.org/sage into ticket/15335
trac #14589: binary matrices, dense graphs, and faster is_strongly_regular
Changed docstring of BasisExchangeMatroid.groundset_list() to include a test verifying that ticket 15290 was fixed.
trac #15285: Doc of AffineGeometryDesign
Merge branch 'develop' into public/combinat/crystals/fix_phi_tensor_product

* develop: (166 commits)
  Updated Sage version to 6.1.beta5
  Don't use "missing"
  trac 15265: various changes, finishing review.
  allow disabling of maintainer mode
  trac 15265: Additional change to farey.cpp.
  trac 15265: Minor changes to farey_symbol.pyx
  trac 15265: Minor changes to sl2z.cpp and sl2z.hpp.
  trac 15265: Minor changes to farey.cpp and farey.hpp.
  Run "missing" using bash
  fix tarball url
  trac 15265: Add some further examples and one test to _acton_ of elements of arithmetic groups.
  Source sage-env inside configure
  Improved Karatsuba: more thorough tests
  bootstrap configure: small fixes
  make saving of the confball optional in bootstrap
  fix typos in SPKG.txt
  also commit changes to confball in sage-update-version
  add a SPKG.txt file
  rename to bootstrap, run during version bump
  trac 15265: correct mistakes done while converting to git branch.
  ...
Trac #14589: binary matrices, dense graphs, and faster is_strongly_regular

As the title says !!

With the patch applied
{{{
sage: g = graphs.PaleyGraph(primes_first_n(70)[-1])
sage: %time g.is_strongly_regular()
CPU times: user 0.16 s, sys: 0.00 s, total: 0.16 s
Wall time: 0.16 s
True
}}}

Without it
{{{
sage: g = graphs.PaleyGraph(primes_first_n(70)[-1])
sage: %time g.is_strongly_regular()
CPU times: user 20.43 s, sys: 0.00 s, total: 20.43 s
Wall time: 20.44 s
True
}}}

Ahhhh.. It is so nice to implement an algorithm with the right data
structure ! `:-P`

Nathann

URL: http://trac.sagemath.org/14589
Reported by: ncohen
Ticket author(s): Nathann Cohen
Reviewer(s): Jernej Azarija
Trac #15285: Bug in AffineGeometryDesign

A `List` is used instead of a `Set`, and as a result blocks are returned
several times. Example :

Before
{{{
sage: print designs.AffineGeometryDesign(2, 1, GF(2)).blocks()
[[0, 1], [0, 1], [0, 2], [0, 2], [0, 3], [0, 3], [1, 2],
 [1, 2], [1, 3], [1, 3], [2, 3], [2, 3]]
}}}

After
{{{
sage: print designs.AffineGeometryDesign(2, 1, GF(2)).blocks()
[[0, 1], [0, 2], [0, 3], [1, 2], [1, 3], [2, 3]]
}}}

URL: http://trac.sagemath.org/15285
Reported by: ncohen
Ticket author(s): Nathann Cohen
Reviewer(s): Stefan van Zwam
Trac #15290: BasisExchangeMatroid.groundset_list() should return a copy

The following will break the matroid M:

{{{
sage: M = matroids.named_matroids.Fano()
sage: len(M.dependent_r_sets(3))
7
sage: L = M.groundset_list()
sage: x = L.pop()
sage: list(M.dependent_r_sets(3))
Traceback (most recent call last)
...
IndexError: list index out of range
}}}

Solution 1: BasisExchangeMatroid.groundset_list() should return a copy
of self._E
Solution 2: BasisExchangeMatroid._E should be a tuple instead of a list.

I think Solution 2 is the preferred one, but it should be tested for
speed.

Additional suggestion: update the docstrings of groundset() and
groundset_list() in BasisExchangeMatroid so they refer to each other.

URL: http://trac.sagemath.org/15290
Reported by: Stefan
Ticket author(s): Rudi Pendavingh
Reviewer(s): Michael Welsh
Trac #15335: Do not import sagenb at startup

URL: http://trac.sagemath.org/15335
Reported by: chapoton
Ticket author(s): Jeroen Demeyer
Reviewer(s): Travis Scrimshaw