Sage 5.9 released

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Sage 5.9 released Jeroen Demeyer 5/3/13 6:54 AM
Sage 5.9 was released on 30 April 2013. It is available in
source and binary form from:

   * http://www.sagemath.org/download.html

Sage (http://www.sagemath.org/) is developed by volunteers and combines
over 90 open source packages. For instructions about installing Sage, see

   * http://www.sagemath.org/doc/installation

The following page lists the platforms on which Sage should work:

   * http://wiki.sagemath.org/SupportedPlatforms

If you have any questions and/or problems, please report them to any of
these Google groups:

   * sage-support: http://groups.google.com/group/sage-support
   * sage-devel: http://groups.google.com/group/sage-devel

You can also drop by in #sagemath on freenode or post your questions
at http://ask.sagemath.org/

The following 68 people contributed to this release. Of those, 4 made
their first contribution to Sage:

   - Adrien Brochier [first contribution]
   - Alejandro Morales
   - Alexander Dreyer
   - Alexandre Blondin Massé
   - Amnon Besser [first contribution]
   - Andrey Novoseltsev
   - Anna Haensch
   - Burcin Erocal
   - Chris Berg
   - Christian Stump
   - Christopher Schwan
   - Dan Drake
   - David Coudert
   - David Loeffler
   - David Roe
   - Dmitrii Pasechnik
   - Eviatar Bach
   - Florent Hivert
   - Franco Saliola
   - François Bissey
   - Frédéric Chapoton
   - Gregg Musiker
   - Hans Schoenemann
   - Hayden Stainsby [first contribution]
   - Jason Grout
   - Jean-Pierre Flori
   - Jeroen Demeyer
   - John Cremona
   - John Palmieri
   - Jordi Gutiérrez Hermoso [first contribution]
   - Julian Rueth
   - Julien Puydt
   - Kannappan Sampath
   - Karl-Dieter Crisman
   - Keshav Kini
   - Kevin Halasz
   - Leif Leonhardy
   - Luis Felipe Tabera Alonso
   - Maarten Derickx
   - Marc Masdeu
   - Marco Streng
   - Marshall Hampton
   - Martin Albrecht
   - Miguel Marco
   - Mike Hansen
   - Mike Zabrocki
   - Minh Van Nguyen
   - Nathann Cohen
   - Nicolas M. Thiéry
   - Nils Bruin
   - Paul Zimmermann
   - Peter Müller
   - Punarbasu Purkayastha
   - R. Andrew Ohana
   - Rob Beezer
   - Robert Bradshaw
   - Robert Harron
   - Salvatore Stella
   - Sebastien Gouezel
   - Simon King
   - Stepan Starosta
   - Stephen Montgomery-Smith
   - Sébastien Labbé
   - Thierry Monteil
   - Timo Kluck
   - Travis Scrimshaw
   - Vincent Delecroix
   - Volker Braun

* Release manager: Jeroen Demeyer.

* We closed 197 tickets in this release. For details, see

   http://boxen.math.washington.edu/home/release/sage-5.9/tickets.html

Closed tickets:

#4750: make it so sage -t foo.sage pulls in the preparsed version of all
the code in foo.sage before doctesting foo.py; make it so "sage -t
foo.py" has an option to pull in all code from foo.py before doctesting
it. [Reviewed by David Roe]
#8699: allow doctest coverage script to handle triple single quotes
[Reviewed by Minh Van Nguyen, Mike Hansen]
#8708: allow doctest script to handle docstrings with triple single
quotes [Reviewed by John Palmieri, Burcin Erocal]
#9225: New doctesting features [Reviewed by David Roe, Jeroen Demeyer]
#9273: doctest elliptic_curves/BSD.py reports "file not found" [Reviewed
by Jeroen Demeyer]
#9772: unify doctest commands, especially for 'long' and 'parallel'
options [Reviewed by Jeroen Demeyer]
#11336: Update doctest tolerance to work with print statement. [Reviewed
by Jeroen Demeyer]
#11338: Fix signals/interrupts in sage-doctest [Reviewed by Jeroen Demeyer]
#13928: Problematic file filter in skip() from sage-ptest [Reviewed by
Nils Bruin, John Palmieri]
#2630: Python API for sage-ptest [Reviewed by David Roe]
#4790: sage -t does not take into account the current directory
[Reviewed by David Roe]
#4943: make sage -tp run sage -t when only one file is specified
[Reviewed by David Roe]
#9164: cygwin: gap.cputime() does not work [Reviewed by Jean-Pierre
Flori, Karl-Dieter Crisman]
#9602: Fix gap on FreeBSD [Reviewed by Stephen Montgomery-Smith, Volker
Braun]
#9642: sage-maketest and sage-test-new should be able to run tests in
parallel [Reviewed by David Roe]
#14106: slicing p-adic elements [Reviewed by David Roe]
#14181: Add wireframe=False option for rendering 2d polyhedron plots
[Reviewed by Volker Braun, Nicolas M. Thiéry]
#14313: Christian Stump: spkg containing precomputed data for
exceptional finite and affine mutation types of quiver [Reviewed by
Gregg Musiker]
#3007: gap.Factorization? is useless [Reviewed by Travis Scrimshaw]
#3320: Gap <-> Sage interface for Dense Matrices over GF(2) [Reviewed by
Travis Scrimshaw]
#3355: invoke the libdir rewrite script on "sage -upgrade" [Reviewed by
Jeroen Demeyer]
#4259: use Modular<float> instead of Modular<double> for small primes in
LinBox [Reviewed by Martin Albrecht]
#5084: speed regression in number of partitons [Reviewed by Travis
Scrimshaw]
#6415: "sage -t foo.pyx" should not by default dynamically build foo.so
[Reviewed by David Roe]
#7026: linbox 1.1.6.p0 says GMP is not installed, even though MPIR is
[Reviewed by Jeroen Demeyer]
#7185: bug in FFT object in Sage -- segfault [Reviewed by Travis Scrimshaw]
#8895: symbolic unit conversion function should ignore non-unit symbolic
variables [Reviewed by Eviatar Bach, Burcin Erocal]
#10298: Cluster Algebra and Quiver Package: Overview [Reviewed by
Christian Stump]
#11633: Tutorial on programming in python and sage [Reviewed by Florent
Hivert]
#12592: plot error for message for too large figsize [Reviewed by
Karl-Dieter Crisman]
#13020: Upgrade palp to upstream 2.1 [Reviewed by Andrey Novoseltsev]
#13636: %timeit unpickle_all() causes a SEGABRT [Reviewed by Travis
Scrimshaw]
#14005: Span of vectors over ZZ fails with "maximum recursion depth
exceeded" [Reviewed by Travis Scrimshaw]
#14247: bell numbers in mpmath is incorrect [Reviewed by Travis Scrimshaw]
#14315: Matrices _matrix_() method is inconsistent with expected
arguments [Reviewed by Travis Scrimshaw]
#14352: Bug in parsing Maxima output with factorial [Reviewed by Eviatar
Bach, Karl-Dieter Crisman]
#8854: sage -upgrade segfaults on Cygwin [Reviewed by Karl-Dieter
Crisman, Jean-Pierre Flori]
#9176: cygwin: various heegner_index errors involving interval
arithmetic on cygwin [Reviewed by Jean-Pierre Flori, Dmitrii Pasechnik,
Karl-Dieter Crisman]
#9447: "except:" count in sage too high [Reviewed by Andrey Novoseltsev]
#10896: Strongly Regular Graph [Reviewed by Travis Scrimshaw]
#12095: integral_points missing solutions [Reviewed by Travis Scrimshaw]
#12148: random_digraph fails with ZeroDivisionError [Reviewed by Travis
Scrimshaw]
#13858: update M4RI to newest upstream release [Reviewed by Travis
Scrimshaw]
#14404: Create $SAGE_ROOT/logs for upgrades [Reviewed by Jeroen Demeyer]
#14407: Test for a GNU tar on Solaris is broken [Reviewed by Jeroen Demeyer]
#4824: speed up conversion of matrices from sage to pari [Reviewed by
Travis Scrimshaw]
#9151: build multithreaded version of ATLAS [Reviewed by Jean-Pierre Flori]
#10138: Doctest failure in trace.py with 64-bit OS X build [Reviewed by
David Roe]
#10360: Polyhedron.vertex_adjacencies() gives different answers because
of a side effect [Reviewed by Volker Braun, Andrey Novoseltsev]
#11776: Holding an expression unevaluated: Something like hold_all()
would be nice. [Reviewed by Travis Scrimshaw]
#12516: Cython compile error in optional package
p_group_cohomology-2.0.spkg [Reviewed by Travis Scrimshaw]
#13766: No conversion from unit group to number field. [Reviewed by
Marco Streng, Maarten Derickx]
#1465: the maple interface is broken in some configurations [Reviewed by
Karl-Dieter Crisman]
#5322: Sage 3.3.rc2: mandriva 32/64 bit fails with mysterious error 139
in make [Reviewed by Jeroen Demeyer]
#10231: Don't repackage examples and extcode on sage-*dist [Reviewed by
Jeroen Demeyer]
#13016: Creating a trac ticket is not doctested [Reviewed by Volker Braun]
#13918: systemwide install of cremona database permission issues
[Reviewed by Jeroen Demeyer]
#14374: recover from doctest timings cache corruption [Reviewed by
Volker Braun]
#14440: bug in max? [Reviewed by Karl-Dieter Crisman]
#14458: indentation problem with "except" in doctests [Reviewed by Paul
Zimmermann]
#6984: cygwin port: make lapack into a dummy spkg that requires
systemwide lapack [Reviewed by Karl-Dieter Crisman]
#9520: scipy_sandbox does not exit if there are build failures, but
spkg-install looks OK [Reviewed by Karl-Dieter Crisman]
#10259: success error code returned when spkg install fails [Reviewed by
Karl-Dieter Crisman]
#12054: crash in digraph.py [Reviewed by Nathann Cohen]
#12622: Jason Grout: cliquer memory leaks [Reviewed by David Coudert,
Nathann Cohen]
#13666: openssl as a default package [Reviewed by Jeroen Demeyer]
#14450: MPIR build is broken on arm with ubuntu raring [Reviewed by
Jean-Pierre Flori, Julien Puydt]

Merged in sage-5.9.beta0:

#2235: Jeroen Demeyer: doctest issue -- combining # long and # 32-bit /
# 64-bit [Reviewed by David Roe]
#11863: Anna Haensch, Frédéric Chapoton: Bilinear Map [Reviewed by
Kannappan Sampath]
#12415: David Roe, Robert Bradshaw, Jeroen Demeyer: Update doctesting
framework [Reviewed by Jeroen Demeyer, David Roe]
#12708: Punarbasu Purkayastha: limit not correctly computed by maxima
[Reviewed by Karl-Dieter Crisman]
#12828: Stephen Montgomery-Smith: get_memory_usage and top under FreeBSD
[Reviewed by Karl-Dieter Crisman]
#13209: Kannappan Sampath: Fix some minor Cayley table documentation
problems [Reviewed by Karl-Dieter Crisman]
#13262: Sebastien Gouezel: Update doctests after bug correction in pynac
[Reviewed by Burcin Erocal]
#13351: Jean-Pierre Flori: Cannot import sage.libs.lcalc.lcalc_Lfunction
[Reviewed by Dmitrii Pasechnik]
#13424: Christian Stump, Gregg Musiker: Compute Mutation Class for
Cluster Algebra Seed or Cluster Quiver [Reviewed by Gregg Musiker,
Salvatore Stella]
#13432: R. Andrew Ohana: add sage/env.py and fix many inappropriate
references to SAGE_ROOT [Reviewed by François Bissey]
#13729: Burcin Erocal, Sebastien Gouezel: Update pynac to 0.2.6
[Reviewed by François Bissey]
#13743: Travis Scrimshaw: Bug in k-bounded symmetric functions [Reviewed
by Mike Zabrocki]
#14079: Jeroen Demeyer: Cython interface to pselect() system call
[Reviewed by Volker Braun]
#14175: Volker Braun, Nicolas M. Thiéry: More plot options for polytopes
[Reviewed by Volker Braun, Nicolas M. Thiéry]
#14197: Chris Berg, Christian Stump: Add map from PerfectMatchings to
Permutations. Fix string representation in perfect matchings. [Reviewed
by Alejandro Morales, Christian Stump]
#14238: Nathann Cohen: a polyhedron() method for Linear Programs
[Reviewed by Dmitrii Pasechnik]
#14241: Timo Kluck: Patch to FLINT fails to apply because of double path
separator // in filenames [Reviewed by Leif Leonhardy]
#14242: Jeroen Demeyer: Race condition in gap_reset_workspace()
[Reviewed by Volker Braun]
#14251: Nathann Cohen: Circulant digraphs [Reviewed by David Coudert]
#14253: Jeroen Demeyer: sage.misc.sage_ostools.have_program: use
os.access() [Reviewed by David Roe]
#14257: Nathann Cohen: Implements the Wells graph [Reviewed by Dmitrii
Pasechnik]
#14263: John Palmieri: if build fails, print message about which spkgs
failed [Reviewed by Volker Braun]

Merged in sage-5.9.beta1:

#9877: Thierry Monteil, Frédéric Chapoton: Add is_sturmian_factor,
is_tangent methods for finite words [Reviewed by Alexandre Blondin
Massé, Sébastien Labbé, Vincent Delecroix]
#11715: Rob Beezer, Hayden Stainsby: Upgrade matrix set_row() and
set_column() [Reviewed by Karl-Dieter Crisman, David Loeffler, Hayden
Stainsby]
#12281: David Roe: Many doctest options are undocumented [Reviewed by
Jeroen Demeyer]
#12997: Adrien Brochier: LyndonWords from composition beginning by 0's
[Reviewed by Travis Scrimshaw, Frédéric Chapoton]
#13078: Punarbasu Purkayastha: Make it easier to do custom tick
formatting [Reviewed by Volker Braun, Karl-Dieter Crisman]
#13249: Marshall Hampton, Franco Saliola, Volker Braun: Volume
computation of polyhedra [Reviewed by Frédéric Chapoton]
#13299: Julian Rueth: Fix slice and __getitem__ methods of padics
[Reviewed by Robert Harron, David Roe]
#13507: Frédéric Chapoton: implements the order polytope and chain
polytope of a poset [Reviewed by Alejandro Morales]
#13587: Burcin Erocal: automatic simplification can lose some infinities
[Reviewed by Jean-Pierre Flori]
#13617: Julian Rueth: SEGFAULT in matrix_mod_pn for padic extensions
[Reviewed by David Roe, Punarbasu Purkayastha]
#14016: Kannappan Sampath: Tiny touchup on tour of calculus in tutorial
[Reviewed by Karl-Dieter Crisman]
#14026: Jeroen Demeyer: PolyBoRi should depend on IPython [Reviewed by
Alexander Dreyer]
#14183: Kannappan Sampath: Unnecessary replication of Code in
sage/logic/boolformula.py [Reviewed by Punarbasu Purkayastha]
#14250: Nathann Cohen: GenericGraph.is_circulant() test [Reviewed by
Frédéric Chapoton]
#14255: Christian Stump: Provides some further functionalities for
combinatorial maps [Reviewed by Travis Scrimshaw]
#14285: David Roe: Add __len__ and cardinality to
cartesian_product_iterator and CartesianProduct [Reviewed by Julian Rueth]
#14289: Jeroen Demeyer: Doctest debugger doesn't work on OS X [Reviewed
by David Roe]
#14294: David Roe: make absprec argument of p-adics lift_to_precision
optional [Reviewed by Julian Rueth]
#14295: Leif Leonhardy: Singular 3-1-5 fails to build on Solaris with
GCC 4.7.x [Reviewed by Jeroen Demeyer]
#14303: John Palmieri: "sage -i" should only run sage-location if it
exists [Reviewed by Jeroen Demeyer]
#14307: Jeroen Demeyer: The new doctesting framework doesn't like being
run with nohup [Reviewed by François Bissey]

Merged in sage-5.9.beta2:

#9847: Jeroen Demeyer: Handle preset R_PROFILE or R_HOME variables
[Reviewed by Leif Leonhardy, Karl-Dieter Crisman]
#12575: Amnon Besser, Marc Masdeu, Julian Rueth: Generic p-adic log and
exp [Reviewed by David Loeffler, David Roe, Julian Rueth]
#13062: David Roe, Jeroen Demeyer: Change parsing of nodoctest [Reviewed
by Jeroen Demeyer, David Roe]
#13183: Andrey Novoseltsev: Implement index(cone) for fan morphisms
[Reviewed by Volker Braun]
#13278: David Roe: Allow reporting of skipped optional tests [Reviewed
by Jeroen Demeyer]
#13425: Gregg Musiker, Christian Stump: Compute mutation type of a
ClusterSeed or ClusterQuiver [Reviewed by Christian Stump, Gregg Musiker]
#13685: Travis Scrimshaw: More doctests for sage.rings [Reviewed by
Volker Braun]
#14172: Leif Leonhardy: mpir-2.6.0.p0 fails to build on Intel "Core" and
Pentium4 Prescott CPUs [Reviewed by Thierry Monteil, Jean-Pierre Flori]
#14206: Jeroen Demeyer: random_element() of number fields ignores
exceptions [Reviewed by Luis Felipe Tabera Alonso]
#14246: Dan Drake: installation guide has wrong location for SageTeX
documentation [Reviewed by Karl-Dieter Crisman]
#14271: Nathann Cohen: Sylvester and Sims-Gewirtz graphs [Reviewed by
Frédéric Chapoton]
#14278: Simon King: Clear the cache of a cached representation [Reviewed
by Travis Scrimshaw]
#14284: David Roe: Sampling in unit tests [Reviewed by Julian Rueth]
#14286: Jeroen Demeyer: Remove unreliable get_memory_usage() test
[Reviewed by François Bissey]
#14290: David Roe: Running doctests from within Sage doesn't work
[Reviewed by Volker Braun]
#14310: Nathann Cohen: CBC compilation problem -- optional arguments in
a .pxd file [Reviewed by Peter Müller]
#14322: Dan Drake: improve documentation for Integer bits(); negative
numbers have "negative bits" [Reviewed by David Roe]
#14323: Volker Braun: libGAP messes with Python subprocesses [Reviewed
by Jeroen Demeyer]
#14331: R. Andrew Ohana: remove explict references to SAGE_ROOT in the
doctesting framework [Reviewed by David Roe]
#14332: Keshav Kini: Octave nomenclature [Reviewed by Jordi Gutiérrez
Hermoso]
#14338: Nils Bruin: Fix debug() in notebook [Reviewed by Andrey Novoseltsev]
#14342: John Palmieri: Remove references to `DOT_SAGE/tmp` [Reviewed by
Keshav Kini, Jeroen Demeyer]
#14344: Keshav Kini: Fix packages test [Reviewed by Karl-Dieter Crisman]
#14351: David Coudert: Fix overflow error in hyperbolicity [Reviewed by
Nathann Cohen]
#14354: John Palmieri: simplicial complexes: add_face doesn't clear
enough cached data [Reviewed by Travis Scrimshaw]
#14359: Volker Braun: doctest spurious UnicodeWarning [Reviewed by
Jeroen Demeyer]
#14362: Jeroen Demeyer: Fix more optional tags [Reviewed by Karl-Dieter
Crisman]

Merged in sage-5.9.beta3:

#5039: Travis Scrimshaw: Improve DisjointSet documentation [Reviewed by
Nathann Cohen]
#14094: Mike Hansen: Iterating through Partitions(n) for n>=1000.
[Reviewed by Travis Scrimshaw]
#14140: Travis Scrimshaw: Reorganization of set partitions [Reviewed by
Chris Berg]
#14265: Jeroen Demeyer: Compile Python with -D__C99FEATURES__ on Solaris
[Reviewed by François Bissey]
#14314: Travis Scrimshaw: Matrices _matrix_() method is inconsistent
with expected arguments [Reviewed by Andrey Novoseltsev]
#14316: R. Andrew Ohana: remove explict references to SAGE_ROOT in
docbuilding [Reviewed by Robert Bradshaw]
#14369: Jeroen Demeyer: Misc doctesting improvements [Reviewed by David Roe]
#14370: Jeroen Demeyer, Volker Braun: Run IPython tests with
--colors=NoColor [Reviewed by John Palmieri, David Roe]
#14376: John Palmieri: Add doctest directory to the reference manual
[Reviewed by Jeroen Demeyer]
#14379: R. Andrew Ohana: remove unused head in polybori mecurial
repository [Reviewed by Jeroen Demeyer]
#14380: Jean-Pierre Flori: Add $SAGE_LOCAL/bin to LD_LIBRARY_PATH on
Cygwin [Reviewed by Karl-Dieter Crisman]
#14383: Jeroen Demeyer: Use wget -nv instead of wget --no-verbose
[Reviewed by R. Andrew Ohana]
#14386: Jean-Pierre Flori: Fix Cygwin inline fortran issue [Reviewed by
Karl-Dieter Crisman]
#14387: Jean-Pierre Flori: Fix Cygwin Cython compilation issue [Reviewed
by Karl-Dieter Crisman]

Merged in sage-5.9.beta4:

#1191: Robert Harron: wrap pari's matsolvemodn for A.solve_right over
Z/nZ [Reviewed by Martin Albrecht]
#5814: Timo Kluck: %prun doesn't work in the notebook [Reviewed by
Travis Scrimshaw]
#10054: Travis Scrimshaw: Provide an alphabet to the parent of any
generated word [Reviewed by Sébastien Labbé]
#12466: Stepan Starosta: test whether a polynomial is cyclotomic
[Reviewed by Frédéric Chapoton, Travis Scrimshaw]
#12951: Simon King: Support cached_methods on extension types [Reviewed
by Travis Scrimshaw]
#13031: Robert Bradshaw, R. Andrew Ohana: Use cythonize() from cython
for Sage module building. [Reviewed by Jeroen Demeyer, R. Andrew Ohana]
#13194: Volker Braun: FaceFan and NormalFan should work with
(non-lattice) polyhedra [Reviewed by Andrey Novoseltsev]
#13610: David Roe: Make sage -t --debug trigger on an incorrect doctest
in addition to an unexpected error [Reviewed by Jeroen Demeyer]
#13989: Alexander Dreyer: Updating PolyBoRi to release 0.8.3 [Reviewed
by Martin Albrecht, Julien Puydt, Jean-Pierre Flori]
#14081: Miguel Marco: Solve bug in BraidGroup [Reviewed by Travis
Scrimshaw, Volker Braun]
#14152: Jeroen Demeyer: Add sig_on_count() check check [Reviewed by
David Roe]
#14179: Jean-Pierre Flori: Increase harcoded timeouts default values
[Reviewed by Jeroen Demeyer]
#14220: Mike Zabrocki: Cleanup of symmetric function code [Reviewed by
Frédéric Chapoton]
#14226: R. Andrew Ohana: add SAGE_SPKG_INST environment variable
[Reviewed by Robert Bradshaw, Leif Leonhardy, Jeroen Demeyer]
#14264: Simon King: Fix negation of Jacobian morphisms [Reviewed by
Travis Scrimshaw]
#14292: Jeroen Demeyer: Race conditions in doctester [Reviewed by Volker
Braun]
#14328: Jeroen Demeyer, John Palmieri: Simplify test* targets in
top-level Makefile and move logs to logs/ [Reviewed by R. Andrew Ohana]
#14377: John Palmieri: Move spkg logs to logs/pkgs [Reviewed by R.
Andrew Ohana, Jeroen Demeyer]
#14378: Jeroen Demeyer: Upgrade GCC to 4.7.2 [Reviewed by Volker Braun,
Jean-Pierre Flori]
#14385: Robert Bradshaw: auto-generate package list in setup.py
[Reviewed by Nicolas M. Thiéry]
#14388: Nils Bruin, Jean-Pierre Flori: Fix plural polynomials overflow
error [Reviewed by Jean-Pierre Flori, Karl-Dieter Crisman]
#14391: Robert Harron: Add pari function matsolvemod to C-library
interface [Reviewed by Martin Albrecht]
#14398: Jeroen Demeyer: Add warning when downloading
experimental/archive packages [Reviewed by Nathann Cohen]
#14399: Leif Leonhardy: MPIR 2.6.0's test suite fails with GCC 4.8.0
[Reviewed by Jean-Pierre Flori]
#14406: Jeroen Demeyer, Jean-Pierre Flori: Various prereq fixes
[Reviewed by Jean-Pierre Flori, Jeroen Demeyer]
#14415: Jeroen Demeyer: Singular link problems on OS X PPC with GCC
4.7.2 [Reviewed by Hans Schoenemann]

Merged in sage-5.9.beta5:

#13151: Jeroen Demeyer: fix pickling of Matrix_modn_dense_double on
SPARC [Reviewed by Jean-Pierre Flori]
#13715: Dan Drake: documentation for "attach" should mention
load_attach_path() [Reviewed by David Roe, Travis Scrimshaw]
#14030: Volker Braun: Switch order in automatic backtrace [Reviewed by
Jeroen Demeyer]
#14393: François Bissey: Clean SAGE_ROOT from module_list.py (again)
[Reviewed by Christopher Schwan]
#14409: Volker Braun: sage_input support for some geometry objects
[Reviewed by Andrey Novoseltsev]
#14429: Jeroen Demeyer: Singular omalloc requires 8-byte alignment on
SPARC [Reviewed by Volker Braun]
#14430: Volker Braun: doctesting enhancements [Reviewed by Jeroen Demeyer]

Merged in sage-5.9.rc0:

#9668: John Palmieri: Fix hardcoding of paths in R binary [Reviewed by
Karl-Dieter Crisman, Jeroen Demeyer]
#13614: Kevin Halasz: Add Table Explaining How To Create Every Group of
Order < 32 [Reviewed by Volker Braun]
#13826: Volker Braun, Jeroen Demeyer: Race condition in star_imports
cache [Reviewed by Volker Braun]
#14371: Jeroen Demeyer, Volker Braun: Race condition in singular doctest
[Reviewed by Volker Braun, Jeroen Demeyer]
#14400: Jeroen Demeyer: Run sage-location before installing spkgs
[Reviewed by Karl-Dieter Crisman]
#14426: Jeroen Demeyer: Runaway/Segfaulting ECL processes [Reviewed by
Volker Braun, John Cremona]
#14447: Jean-Pierre Flori, Jeroen Demeyer: Add Cygwin as supported
platform [Reviewed by Jeroen Demeyer, Jean-Pierre Flori]
#14452: Jeroen Demeyer: Upgrade to Cython 0.19 [Reviewed by Robert Bradshaw]
#14460: Jeroen Demeyer: GCC-4.8.0 miscompiles some sig_on() statements
[Reviewed by Jean-Pierre Flori]
#14470: Jeroen Demeyer: Relax PARI warnings [Reviewed by Leif Leonhardy]

Merged in sage-5.9.rc1:

#14031: Dmitrii Pasechnik, Jean-Pierre Flori: provide proper cygwin
rebasing scripts [Reviewed by Jean-Pierre Flori, Karl-Dieter Crisman]
#14465: Jean-Pierre Flori: Clean source.rst and include instructions for
Cygwin [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer]
#14495: Jeroen Demeyer: Improvement to --optional doctests [Reviewed by
Volker Braun]