imported patch root_systems-ts.patch
imported patch root_system_data-ts.patch
Merge branch 'master' into public/combinat/root_systems/improvements-15384
Fixed indentation error.
Changed horizontal to basic_untwisted.
Merge branch 'master' into public/combinat/root_systems/improvements-15384
Merge branch 'master' into public/combinat/root_systems/improvements-15384
Merge branch 'master' into public/combinat/root_systems/improvements-15384

* master: (25 commits)
  [FIXUP] 5.13.beta4: update git specific files
  5.13.beta4
  5.13.beta4
  Trac #15402: fix eint1() precision
  #14706: fix visibility of symbols for built-in libintl.
  #14706: Move previous install of R on OS X.
  #14706: Add $SAGE_LOCAL/lib to LDFLAGS.
  #14706: update to 3.0.2.
  Trac #13951: fix bug in local height
  #14706: Use --disable-long-double on Cygwin.
  Trac #13951: polish height functions and documentation
  #14706 (r-3.0.1.p0): Upgrade to new upstream version 3.0.1
  Trac #13951: computing local heights of QQ-rational points fails
  Trac #15311: Implemented the classical Hall algebra. * * * trac #15311: new review patch, fixing q=0 case
  Trac #15299: replace page number by section number in Cohen reference
  Trac #15299: Use arbitrary precision reals instead of Python floats in L series
  Trac #14706: Upgrade R to version 3.0.2.
  Trac #15402: omit page number (editions of Cohen's book differ)
  Trac #15402: Compute exponential_integral_1() with higher precision
  Trac #15434: Fix bug in endomorphisms of elliptic curves with j=1728
  ...
Merge branch 'public/combinat/root_systems/improvements-15384' of trac.sagemath.org:sage into public/combinat/root_systems/improvements-15384

* 'public/combinat/root_systems/improvements-15384' of trac.sagemath.org:sage:
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (274 commits)
  Updated Sage version to 6.1.beta1
  Run Jmol from current directory
  bug fix : importing BooleanPolynomialRing at the top-level prevents sage from starting
  Trac #15445: review + broken doctests
  trac #15054: reviewer's comments
  Update installation guide for installation with OS X Mavericks
  also changed the order of options, as requested in comment 1, and few other minor edits
  Updated Sage version to 6.1.beta0
  removed isinteger option in delsarte_bound_hamming_space, as (mathematically) incorrect.
  gen.eval() documentation: mention that f(x) == f.eval(x)
  Allow default arguments in closures
  Mention that PARI supports conversion from tuples
  Document sig_error()
  Trac #15403: knapsack's docstring doesn't document an useful feature
  Trac 12217: correctly handle division by zero
  Update signals section of developer manual
  Revert parts of 67a76032fda3ee140c3bc52422020ef722cbee52
  #14912: fix leaking print statement when running doctests.
  #14912: Fix two doc tests concerning unique representation.
  trac #14912: more changes, hopefully adding a systematic intro to factories
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (101 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
  Fixing Whitespace errors
  Use bash as SHELL for build/Makefile
  allow numpy arrays in list_plot, line, points
  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/
  Improve handling of make targets sage, csage, extcode, scripts
  Reorded all.py to match original (so fewer changes).
  Fixed minor typo in cobminat/crystals/letters.pyx.
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* 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.
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (59 commits)
  Updated Sage version to 6.1.beta4
  trac #15572: DiGraph.is_directed_acyclic handles loops pretty well
  Fixed bug in uniform matroid.
  trac #15619: Pickling multigraphs with loops and labels
  Trac 15619: Review commit
  Trac 15603: More doctests, nicer error message
  No need to specify caller_name in verbose()
  Add comments, small cosmetic changes
  Make q monic before computing cubic resolvent
  Implement splitting fields for number fields
  trac #15619: bug in the former definition; exception to avoid it in the future
  trac 8723: fix one line in isogeny_small_degree
  Use "in" instead of PyDict_Contains()
  test for membership with `x in self`; minor doc formatting change
  trac #15619: Pickling of immutable graphs
  Rebased on sage-6.1.beta2
  # User Thomas Feulner <thomas.feulner@uni-bayreuth.de>
  Implemented IntegerVectors_nk.rank(). Fixes #15609
  Trac #5153: small change in documentation.
  Trac 7695: Variable name for all subfields where the name ends with a digit
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (107 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.
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (120 commits)
  Updated Sage version to 6.1.rc0
  only use CONFVERSION after it has been incremented
  note that the E6->A5 rule is now implemented
  document the glibc bug workaround patch
  Avoid scanf instead of just ignoring rest of file
  bump confball version
  fix for the m4_divert_push error
  sage-clone-source: allow downloading the configure tarball
  Require autoconf 2.64
  revised thematic tutorial regarding maximal_subgroup(s) method
  reference: branching_rules: minor fixup
  bump confball version
  removed bogus commits
  LinearMatroid.is_field_equivalent now tests if self is other before calling LinearMatroid._is_field_isomorphism.
  implemented maximal_subgroup(s) as a WeylCharacterRing method etc.
  Updated Sage version to 6.1.beta6
  Do not use the GNU extension chmod --recursive
  Workaround for glibc-2.18 scanf bug when building ATLAS
  Added  free_group and finitely_presented_group
  Made the repr sorted for the rules.
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (188 commits)
  Updated Sage version to 6.2.beta1
  Use posix locale for regex
  Let ncurses build again on Solaris.
  Tweaks for speed in sparse graph backend for #15715.
  Updated Sage version to 6.1.1
  trac #14508: better now?
  Trac 14508: bugfix in jordan_form
  Update README.txt re installation with OS X Mavericks
  Fix test for empty string in FLINT build system.
  Update to version 0.10.8.2
  Update sagenb to 0.10.8.1
  Replace two more "except StandardError:"
  Updated Sage version to 6.2.beta0
  Fix documentation syntax
  GSL FFT: indentation (& related) fixes in docstrings
  Minor documentation fixes.
  #Documentation for gsl/fft.pyx
  #10058: Segfault in backward and inverse FFT for 2**n elements
  Regression test for #7475
  Trac #8499: reviewer patch
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (58 commits)
  Updated Sage version to 6.2.beta2
  fix doctest error
  Limit the GAP command line history
  integrate better with Integer.is_prime
  Combine ECM-GMP with Baillie-PSW for prime factorization
  Cleaned up documentation and formatting.
  add doctesr
  Trac 15262: fix combine function
  trac #15810: The graph data structures may have a ._directed but no .directed
  ignore randomness in assertion
  trac #15810: Immutable directed graphs should know that they are directed
  Trac 15166: regression test
  Fix representation of RIF elements with large exponent
  docbuilding: suppress warnings during latex build
  workaround for the utf8 code points in the Sage banner
  Trac 15798: fix mwrank doctest for Solaris
  do not abbreviate 3.99999... to 3.99 with # abs tol 1e-2
  setuptools: export PYTHON_EGG_CACHE and silence a warning about it
  Remove .hgignore files
  PARI: fix pow, mod and shift operators
  ...
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (163 commits)
  Updated Sage version to 6.2.beta3
  fix incorrect permissions for install-sh
  Prevent python from using system hg and svn during its installation.
  Do not hardcode the non-posix install program
  poison proxy environment variables
  Slight modifications of gap related pkgs SPKG.txt files. * Remove now git recorded old changelog. * Put patches description into subsections.
  remove nose from dependencies
  undefine FORTIFY_SOURCE
  udpate to GAP-4.7.4
  reviewer changes with Travis
  added the affine factorization crystal to the documentation
  Fix modular exponentiation of polynomials over finite field extensions.
  Reenable previously failing doctests for modular exponentiation of polynomials over finite field extensions.
  fix trivial doctest failure
  apply sparc patch also to libgap
  add SPARC alignment fix
  remove duplicated changelog
  reverted changes in k_tableaux
  finished affine factorization crystal
  fixed rep
  ...

Conflicts:
	src/sage/combinat/root_system/root_lattice_realizations.py
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (100 commits)
  Updated Sage version to 6.2.beta4
  added documentation, patchlevel bump
  trac #15894 modif of two warnings
  delete cruft from the guava package
  trac #15893 review patch
  trac #15894 another backward change
  trac #15894 changin back the category names
  trac #15xxx proper names should start by a capital letter
  Fix changelog entry for ell_wp
  trac #15893: graphs.petersen_family
  Fixes to code from #9505.
  Fix the banner displayed by sage -h
  trac #15466: remove dead import
  trac #15795 line wrap
  trac #15795 redone with ( ::)
  Fraction to power series: doctests
  Fraction to power series conversion when the fraction coerces into the base ring
  15698: Allow construction of power series from fractions
  Create *unevaluated* integrals when converting sage integrals to sympy
  Use evaluate=False in SympyConverter too
  ...

Conflicts:
	src/sage/combinat/root_system/root_lattice_realizations.py
Merge branch 'develop' into public/combinat/root_systems/improvements-15384

* develop: (121 commits)
  Updated Sage version to 6.2.beta5
  in docstring: added ``
  OSX 10.4 build fix
  Only accepts fields as input for change_ring
  FiniteStateMachine.determine_alphabets: one more small correction in docstring
  add definition
  use pydoc.pager on _sage_doc_unformatted instead
  FiniteStateMachine.determine_alphabets: corrected description of parameter reset
  Trac #13174: sagedoc.help() didn't discriminate cachedfuncs from funcs
  trac #15951 correct one raise statement towards python3
  Added destruction of pool in parallel_iter
  separate absolute from local (implicit relative) imports
  microfixes
  Added global options to rigged configurations to improve printing.
  Trac 13609: fix symbolic expression auto evaluation when content is in GF(2^k)
  Trac 13048: fixed division without remainder for polynomials over QQbar
  allow Singular to build with recent versions of Xcode
  removed k from init
  remove the avoid section "Function" in the intial comment and implement a function are_mutually_orthogonal_latin_squares
  Do not forget to define ambient_field before computing its algebraic closure.
  ...