Sage 5.1 was released on 09 July 2012. 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 85 people contributed to this release. Of those, 13 made their first contribution to Sage: - Alex Ghitza - Alexander Dreyer - Alexei Sheplyakov - Andrey Novoseltsev - Andrzej Giniewicz - André Apitzsch - Anne Schilling - Antonio Russo [first contribution] - Benjamin Jones - Bjarke Hammersholt Roune - Burcin Erocal - Charles Bouillaguet [first contribution] - Christian Stump - Damiano Testa [first contribution] - Dan Drake - Daniel Krenn - Darij Grinberg [first contribution] - David Coudert - David Eklund - David Loeffler - David Roe - Douglas McNeil - Ethan Van Andel - Florent Hivert - Francis Clarke - Franco Saliola - Fredrik Johansson - Frithjof Schulze - Frédéric Chapoton - Harald Schilly - Hugo Tremblay [first contribution] - Itai Bar-Natan - Ivan Andrus - Jan Pöschko [first contribution] - Jan Vonk - Jason Grout - Jean-Pierre Flori - Jeroen Demeyer - Jim Stark - Johan Sebastian Rosenkilde Nielsen - John Connor [first contribution] - John Cremona - John Palmieri - John Perry - Julian Rueth - Karl-Dieter Crisman - Keshav Kini - Kevin Halasz [first contribution] - Leif Leonhardy - Maarten Derickx - Marco Streng - Mariah Lenox - Marshall Hampton - Martin Albrecht - Mathieu Guay-Paquet - Michael Orlitzky - Mike Hansen - Nathann Cohen - Nick Alexander - Nicolas Borie - Nicolas M. Thiéry - Nils Bruin - Oriol Castejon - Paul Zimmermann - Peter Jeremy - Punarbasu Purkayastha - R. Andrew Ohana - Rob Beezer - Robert Bradshaw - Robert Gerbicz [first contribution] - Ryan Grout - Sebastian Pancratz - Simon King - Stefan Reiterer - Stephen Montgomery-Smith [first contribution] - Sébastien Labbé - ThanhVu Nguyen [first contribution] - Timo Kluck [first contribution] - Titus Nicolae [first contribution] - Tom Boothby - Tom Denton - Travis Scrimshaw - Viviane Pons - Volker Braun - William Stein * Release manager: Jeroen Demeyer. * We closed 206 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.1/tickets.html Closed tickets: #1206: doc testing support for numerical computations with randomish output is insufficient [Reviewed by Maarten Derickx] #2210: make checkversion.pl complain about old XCode releases [Reviewed by Jeroen Demeyer] #3524: Buildbot [Reviewed by Maarten Derickx] #5774: running "make" on a -bdisted binary is broken [Reviewed by Jeroen Demeyer] #7205: fix the list of old sage releases website [Reviewed by Harald Schilly, Jeroen Demeyer] #8975: Methods missing for reducible root systems [Reviewed by Keshav Kini] #9621: Fix GAP interface problem in sylow_subgroup method [Reviewed by Simon King, Johan Sebastian Rosenkilde Nielsen, Mike Hansen] #10696: SymmetricGroup function doesn't seem to do arbitrary sets [Reviewed by Mike Hansen] #11831: multivariate factorization over finite fields and Proof=false [Reviewed by Paul Zimmermann] #7436: frobby optional spkg doesn't build on a lot of machines [Reviewed by Benjamin Jones] #8783: frobby optional spkg doesn't build with newer GCC's [Reviewed by Benjamin Jones, Bjarke Hammersholt Roune] #12843: Volker Braun, William Stein: Make zeromq and pyzmq optional packages [Reviewed by Benjamin Jones] #12870: Mariah Lenox: update optional package openssl to version 1.0.1a [Reviewed by William Stein] #13007: Mike Hansen: Update to Frobby 0.9.0 [Reviewed by Benjamin Jones] #8151: wrong file permissions in lie-2.2.2.p3.spkg [Reviewed by Keshav Kini] #9950: Oriol Castejon: Change Brian package from experimental to optional [Reviewed by Karl-Dieter Crisman] #11433: Mike Hansen: Move graphviz-2.16.1.p0.spkg from optional to experimental [Reviewed by Benjamin Jones] #12983: Keshav Kini: Fix LiE optional SPKG [Reviewed by R. Andrew Ohana] #1842: clean up sage repositories [Reviewed by R. Andrew Ohana] #7357: Add non-offset logarithmic integral, Li [Reviewed by Karl-Dieter Crisman] #8591: Support for Gurobi [Reviewed by R. Andrew Ohana] #9627: converting from symbolic ring to int is broken [Reviewed by Burcin Erocal] #9953: int(symbolic expr) off by 1 [Reviewed by Burcin Erocal] #10198: Homsets of schemes are wrong [Reviewed by Andrey Novoseltsev] #10204: cddlib fails to build on iras [Reviewed by Volker Braun] #11773: Elliptic curve constructor with no arguments gives an obscure error message [Reviewed by John Cremona] #12839: reduced Groebner basis not unique [Reviewed by John Perry] #12987: When comparing ideals, try to avoid computing the Gröbner basis of a copy of the ideal [Reviewed by Simon King] #13002: Fix Singular interrupt timeout [Reviewed by Jeroen Demeyer] #13096: find_maximum_on_interval fails when used with a sage function [Reviewed by Andrzej Giniewicz] #8073: deprecation version number should say "After version ..." [Reviewed by Volker Braun, Karl-Dieter Crisman] #8546: add section on deprecating functions to developer's guide [Reviewed by Volker Braun] #12214: polygon documentation in error [Reviewed by Karl-Dieter Crisman] #13176: Nick Alexander: Upgrade sage-mode to 0.7 [Reviewed by Ivan Andrus] Merged in sage-5.1.beta0: #10113: Simon King: Calling seed() incorrectly causes Sage to crash with SIGSEGV (Segmentation Fault) [Reviewed by Volker Braun] #10217: Mike Hansen, André Apitzsch: bug in rings/fast_arith.pyx [Reviewed by Mike Hansen, André Apitzsch] #10902: Martin Albrecht: proof=False unnecessary in factor() [Reviewed by Paul Zimmermann] #10993: John Cremona: Update eclib to latest upstream release [Reviewed by Frithjof Schulze, Jeroen Demeyer, Volker Braun, Leif Leonhardy] #11233: Michael Orlitzky: failing calculation of an integral [Reviewed by Paul Zimmermann] #11880: Nathann Cohen: ISGCI in Sage (a Graph Classes database http://www.graphclasses.org/ ) [Reviewed by Nicolas M. Thiéry] #11932: John Palmieri: Allow running Sage with a temporary DOT_SAGE directory [Reviewed by Jeroen Demeyer] #11943: Simon King: The category graph should comply with Python's method resolution order [Reviewed by Nicolas M. Thiéry] #12292: Michael Orlitzky: charpoly is recomputed when called with a different variable [Reviewed by Paul Zimmermann] #12361: Volker Braun: Fix normalization in cohomology ring of orbifold toric varieties [Reviewed by David Eklund, Andrey Novoseltsev] #12469: Hugo Tremblay: RuntimeError raised by standard_factorization of a finite word [Reviewed by André Apitzsch] #12716: David Coudert: MILP formulation and test functions for vertex separation [Reviewed by Nathann Cohen] #12724: David Loeffler: Allow different normalizations for Eisenstein series q-expansion [Reviewed by Alex Ghitza, Martin Albrecht, David Roe] #12736: John Perry, Nathann Cohen: More solver options for GLPK [Reviewed by Nathann Cohen, John Perry] #12743: David Coudert: Addition of reduction rules as pre-processing of the vertex cover function [Reviewed by Nathann Cohen] #12748: Martin Albrecht: An inconsistent term order must not be accepted as input of a polynomial ring construction [Reviewed by Simon King] #12773: William Stein, John Palmieri: include R interface in reference manual [Reviewed by Andrey Novoseltsev] #12777: Jeroen Demeyer: Add signal handling to libecm.pyx [Reviewed by Paul Zimmermann] #12787: Jeroen Demeyer: R spkg: use -### instead of -v to detect linker options [Reviewed by Volker Braun] #12808: Florent Hivert, Simon King: Optimize ClassCallMetaClass using Cython [Reviewed by Simon King, Florent Hivert] #12826: Julian Rueth: minpoly() of quadratic number field element ignores var argument [Reviewed by Francis Clarke] #12838: Christian Stump: Root poset should treat type A1 properly [Reviewed by Frédéric Chapoton] #12869: Florent Hivert: The warn-links option shouldn't always trigger full doc compilation [Reviewed by Andrey Novoseltsev] #12872: Nathann Cohen: A show method for permutations [Reviewed by David Coudert] #12873: Jeroen Demeyer: Clear FPU in i386/x86_64 longjmp() [Reviewed by Volker Braun] #12875: Nicolas M. Thiéry: Fix the homset category initialization for ModularAbelianVariety's homspaces [Reviewed by Simon King] #12889: Punarbasu Purkayastha: Make is_irreducible() for polynomials consistent across all fields [Reviewed by Francis Clarke] #12893: Benjamin Jones: Increase doctest coverage in sage/coding/linear_code.py to 100% [Reviewed by William Stein] #12903: Nathann Cohen: Memory leaks with CPLEX [Reviewed by David Coudert] Merged in sage-5.1.beta1: #6338: Jeroen Demeyer: Support sage --sdist sage-VERSION [Reviewed by Volker Braun] #8901: Travis Scrimshaw: negative integers in IntegerVectors() [Reviewed by Tom Denton] #11693: Ivan Andrus: Edges are doubled when creating Graphs with multiedges=True [Reviewed by Nathann Cohen] #11817: Simon King: Use sage_getdoc in sage interpreter when doing "?" [Reviewed by Volker Braun] #11919: Michael Orlitzky: Issue when pickling a formal function [Reviewed by Nils Bruin, Burcin Erocal] #12445: John Palmieri, Jeroen Demeyer: revise Sage banner, help message [Reviewed by Jeroen Demeyer, Karl-Dieter Crisman] #12614: John Palmieri: prereq should clean up its build directory [Reviewed by Keshav Kini] #12663: Travis Scrimshaw: Partitions(-1).list() goes into infinte recursion [Reviewed by Tom Denton] #12770: David Coudert: cartesian product of directed graphs [Reviewed by Frédéric Chapoton, Nicolas M. Thiéry] #12816: Nathann Cohen: Documentation and list of Graph functions [Reviewed by David Coudert] #12823: John Perry, Nathann Cohen: Allow constants for objective function & deletion of rows in MixedIntegerLinearProgram [Reviewed by David Coudert, Nathann Cohen] #12831: Frédéric Chapoton: implement product of posets [Reviewed by Itai Bar-Natan] #12836: Jason Grout: arrows are shortened too much [Reviewed by Michael Orlitzky] #12877: Nicolas M. Thiéry: Categories for padics, schemes, and some more rings [Reviewed by Simon King] #12897: Benjamin Jones: Increase doctest coverage in coding/sd_codes.py to 100% [Reviewed by Punarbasu Purkayastha] #12910: Jim Stark: Graph construction of empty list fails [Reviewed by Daniel Krenn] #12919: Nicolas M. Thiéry, Mathieu Guay-Paquet: Typo in Parent.discover_coerce_map_from [Reviewed by André Apitzsch] #12929: Viviane Pons: Changing default color option for posets [Reviewed by Franco Saliola] #12936: Michael Orlitzky: Adding plots should (at least attempt to) preserve legend options [Reviewed by Andrey Novoseltsev] #12937: William Stein: sqlite sometimes picks up the wrong libraries (e.g., readline) since we forgot to set LDFLAGS [Reviewed by John Connor] #12939: Keshav Kini: Allow evaluation of univariate polynomials at singleton lists [Reviewed by Francis Clarke] #12942: Nathann Cohen: Balaban's 10-Cage [Reviewed by Keshav Kini] #12944: Nathann Cohen: Inconcistencies in the documentation of traveling_salesman_problem [Reviewed by Keshav Kini] #12945: Keshav Kini, Nathann Cohen: Balaban 11-cage [Reviewed by Nathann Cohen, Keshav Kini] #12953: Nicolas M. Thiéry: Bindable classes [Reviewed by Franco Saliola] #12956: Nicolas M. Thiéry: Let categories override the default implementation of __getitem__ in Parent [Reviewed by Franco Saliola] #12961: Nathann Cohen: Documentation of the facade argument in Poset contructor [Reviewed by Nicolas M. Thiéry] #12975: Burcin Erocal: Fix misleading typo in the doc of "cython" [Reviewed by Simon King] Merged in sage-5.1.beta2: #10566: Stefan Reiterer: Update openmpi docu [Reviewed by Volker Braun] #11028: Ethan Van Andel: More Modular ComplexPlot [Reviewed by Karl-Dieter Crisman] #11383: Ryan Grout, Itai Bar-Natan, Jan Pöschko: Color('red') == Color('red') returns False [Reviewed by Itai Bar-Natan, Karl-Dieter Crisman, André Apitzsch, Jan Pöschko] #11459: Sébastien Labbé: Implement sage -rst2txt and sage -rst2sws [Reviewed by Keshav Kini] #11930: Daniel Krenn, Marco Streng, Damiano Testa: disallow non-smooth hyperelliptic curves, and let hyperelliptic curves know they are not singular [Reviewed by Marco Streng, Damiano Testa, David Eklund] #11974: Jason Grout: transformations don't work with a function that returns a singleton numpy array [Reviewed by Karl-Dieter Crisman] #12334: Michael Orlitzky: mark all Lie tests as optional "requires LiE" (this is a *very* easy ticket!) [Reviewed by Benjamin Jones] #12335: Dan Drake: change "#optional - jones_database" to "#optional - database_jones_numfield", and several other similar renames needed [Reviewed by Benjamin Jones] #12383: David Roe: Doctest for sage.categories.category.__repr_object_names fails interactively [Reviewed by Dan Drake] #12393: David Roe: Reseting doctesting state [Reviewed by Volker Braun] #12740: David Loeffler: Revamp code for finding generators of modular forms spaces [Reviewed by Jan Vonk] #12767: David Loeffler: Clean up dead links in sage/rings/number_field documentation [Reviewed by Karl-Dieter Crisman, William Stein, Benjamin Jones] #12776: Michael Orlitzky: Add maxima_lib to the reference documentation [Reviewed by Karl-Dieter Crisman] #12821: Jeroen Demeyer: testcc.sh: allow $CC to contain multiple words [Reviewed by Leif Leonhardy, R. Andrew Ohana] #12874: Nathann Cohen: Recognition of Comparability graphs and Permutation graphs [Reviewed by David Coudert] #12950: Volker Braun, Burcin Erocal, Jean-Pierre Flori, Titus Nicolae, Alexei Sheplyakov: update to Pynac 0.2.4 [Reviewed by Jean-Pierre Flori, Burcin Erocal, Benjamin Jones] #12952: Nathann Cohen: DoubleStarSnark, FosterGraph, GrayGraph and HarriesGraph [Reviewed by Keshav Kini] #12960: Punarbasu Purkayastha: legend not properly set in Graphics().matplotlib() [Reviewed by Karl-Dieter Crisman] #12966: Rob Beezer: Indefinite factorization for exact matrices [Reviewed by Andrey Novoseltsev] #12988: Julian Rueth: characteristic() should be an integer [Reviewed by David Roe, Jeroen Demeyer] #12991: John Palmieri: Don't doctest autogenerated rst files [Reviewed by Keshav Kini] #13001: Benjamin Jones: Rebase documentation improvements in #1173 to sage-5.0 [Reviewed by Dan Drake] #13010: William Stein: Mathematica interface message on OS X is out of date [Reviewed by Mike Hansen] #13033: Jeroen Demeyer: Conversion PARI -> RR fails for large exponents [Reviewed by William Stein] #13037: Jeroen Demeyer: Remove remaining traces of real quad double field [Reviewed by William Stein] #13043: Julian Rueth: dir(RIF) contains duplicates [Reviewed by Mike Hansen] Merged in sage-5.1.beta3: #7041: Leif Leonhardy: GAP purposely unsets CC which screws up Sun Studio build. [Reviewed by R. Andrew Ohana] #7597: Michael Orlitzky: segfault in libsingular [Reviewed by Mike Hansen] #7685: Douglas McNeil: integer.pyx: factor docstring lies about output -- fix this [Reviewed by William Stein] #10164: Robert Gerbicz, Douglas McNeil: Few digits of precision in N(). [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #10272: Timo Kluck: laurent series truncate behaviour different from power series truncate [Reviewed by Marshall Hampton, Jeroen Demeyer, Karl-Dieter Crisman] #11309: Keshav Kini, Burcin Erocal: Sage sees - x + y > 0, - y + x >= 0, and x - y > 0 as equivalent [Reviewed by Karl-Dieter Crisman, ThanhVu Nguyen] #12340: Benjamin Jones: the optional polymake doctests are seriously misformatted so never run [Reviewed by Mike Hansen] #12404: Julian Rueth: is_squarefree() incorrect over imperfect fields [Reviewed by Paul Zimmermann, Jeroen Demeyer] #12438: Andrey Novoseltsev: Definite integral should not depend on the dummy variable [Reviewed by Karl-Dieter Crisman, Benjamin Jones, Douglas McNeil] #12557: Volker Braun: RDF(1e-17).log() gives NaN [Reviewed by Douglas McNeil] #12845: Michael Orlitzky: Incorrect doctest in sage/misc/functional.py [Reviewed by Karl-Dieter Crisman] #13000: David Roe: Creating integers with very large base [Reviewed by Keshav Kini] #13035: Rob Beezer: Cholesky decomposition over RDF/CDF [Reviewed by William Stein] Merged in sage-5.1.beta4: #6812: Nicolas Borie, Simon King: Enumerate integer vectors modulo the action of a Permutation Group [Reviewed by Karl-Dieter Crisman, Simon King, Nicolas Borie] #10514: Douglas McNeil: legend_label doesn't work when plotting multiple functions at the same time [Reviewed by Karl-Dieter Crisman] #10678: Dan Drake: properly link "derivative" in sage.symbolic.expression.derivative documentation [Reviewed by Benjamin Jones] #11155: Alexei Sheplyakov, Titus Nicolae: abs(pi+I) = pi+I [Reviewed by Burcin Erocal] #11311: Franco Saliola, John Palmieri: engine="pdflatex" in view is ignored [Reviewed by Karl-Dieter Crisman, Franco Saliola, John Palmieri] #11608: Rob Beezer: RDF/CDF eigenvalues: symmetric matrices, multiplicities [Reviewed by Volker Braun] #11888: Benjamin Jones: Sage is missing the lambert_w function [Reviewed by Keshav Kini, Karl-Dieter Crisman, Fredrik Johansson, Burcin Erocal, Douglas McNeil, William Stein] #11951: Douglas McNeil: nth_prime is badly documented [Reviewed by Karl-Dieter Crisman] #12076: Mike Hansen: sage-location doesn't deal with packages after initialize_pkgconfig_files has run [Reviewed by Dan Drake, Karl-Dieter Crisman] #12195: Robert Bradshaw, Rob Beezer, William Stein: numerical_approx broken for vectors [Reviewed by Rob Beezer, William Stein, Dan Drake] #12345: Douglas McNeil: Sympy minus infinity doesn't convert to Sage [Reviewed by Karl-Dieter Crisman] #12671: Punarbasu Purkayastha: attaching files which have spaces in absolute path name fails on second run [Reviewed by William Stein] #12756: Jeroen Demeyer: interrupt.pyx test: flush buffers before fork() [Reviewed by Volker Braun] #12789: Jeroen Demeyer: Move local/bin/sage-check-64 to spkg/bin/sage-arch-env [Reviewed by Volker Braun] #12813: Antonio Russo: contour_plot region option [Reviewed by Jason Grout, Karl-Dieter Crisman, Jeroen Demeyer] #12971: Nathann Cohen: Biggs-Smith graph [Reviewed by Keshav Kini] #12980: Nathann Cohen: Harries-Wong graph [Reviewed by Keshav Kini] #12981: Nathann Cohen: Ljubljana Graph [Reviewed by Keshav Kini] #12999: Keshav Kini: Color('red') > Color('red') returns True [Reviewed by Karl-Dieter Crisman] #13006: Dan Drake: All-paths in a graph blows up when start and end are identical vertices [Reviewed by Rob Beezer, William Stein] #13009: Dan Drake: Add blank lines for a couple plots in reference manual [Reviewed by Karl-Dieter Crisman] #13018: Rob Beezer: Positive definite check for exact matrices [Reviewed by Dan Drake] #13023: Andrey Novoseltsev: Move toric varieties to a dedicated folder [Reviewed by William Stein] #13030: Robert Bradshaw: Use pxd file for pynac declarations [Reviewed by Mike Hansen] #13095: John Cremona: Update Cremona's table of elliptic curves to 240000 [Reviewed by R. Andrew Ohana] Merged in sage-5.1.beta5: #4735: Mike Hansen, Karl-Dieter Crisman: Make e^A for A a generic matrix work [Reviewed by Karl-Dieter Crisman, Mike Hansen] #8659: Burcin Erocal: another broken square root simplification [Reviewed by Karl-Dieter Crisman, Mike Hansen] #8969: Douglas McNeil: problems with maxima inequalities [Reviewed by Karl-Dieter Crisman] #9260: Karl-Dieter Crisman: missing pointer in documentation [Reviewed by Keshav Kini] #10617: Sebastian Pancratz: Make polynomial over ZZ call FLINT for composition and evaluation [Reviewed by Tom Boothby, Mike Hansen] #11274: Rob Beezer: Cholesky matrix decomposition breaks over the rationals [Reviewed by Dan Drake] #11775: Punarbasu Purkayastha: Make pretty_print take multiple arguments [Reviewed by Keshav Kini, William Stein] #11793: John Palmieri, Mike Hansen: autogenerate doc directories in sage-maketest [Reviewed by Mike Hansen, John Palmieri] #11998: Douglas McNeil: Duplicate legends when plotting partial function with detect_poles=True [Reviewed by Keshav Kini, Karl-Dieter Crisman] #12088: Andrey Novoseltsev, Volker Braun: Make use of PALP for different dimensions [Reviewed by Volker Braun, Andrey Novoseltsev] #12293: Douglas McNeil: Graph(n) is not documented [Reviewed by Dan Drake] #12605: Karl-Dieter Crisman: Change the default color of circle and ellipses, etc. back to be the same shade of blue as for all other graphics objects [Reviewed by William Stein] #12688: Rob Beezer: Improve documentation of span method [Reviewed by Andrey Novoseltsev] #12693: Douglas McNeil: bug in jordan_form(transformation=true) for integer matrices [Reviewed by Rob Beezer] #12746: Mike Hansen: Another coercion problem with QQbar [Reviewed by Robert Bradshaw] #12810: Nathann Cohen: Broken links in the documentation of graph/ files [Reviewed by Karl-Dieter Crisman] #12862: Stephen Montgomery-Smith: The partition function under FreeBSD [Reviewed by Mike Hansen] #12884: John Perry: Fix problems introduced by remove_constraint functionality in MIP [Reviewed by Nathann Cohen] #12904: André Apitzsch: colors from rainbow don't work in 3d plots [Reviewed by Karl-Dieter Crisman] #12933: Nathann Cohen: Speedup in DiGraph.stronly_connected_components_digraph [Reviewed by David Coudert] #12968: Mike Hansen: round of symbolic expression (precision issue due to RR) [Reviewed by Burcin Erocal, Karl-Dieter Crisman] #12982: Nathann Cohen: McGeeGraph, Tutte12Cage, TutteCoxeterGraph, WagnerGraph [Reviewed by Keshav Kini] #12993: Darij Grinberg, Anne Schilling: Bug in computing the rank function a poset [Reviewed by Christian Stump, Franco Saliola] #13005: R. Andrew Ohana: "maximum recursion depth exceeded" when doing change_ring(RR) on an elliptic curve [Reviewed by William Stein] #13011: William Stein: several optional tests fail in the sage/mathematica interface with mathematica 8.0 [Reviewed by Mike Hansen, Volker Braun] #13012: Andrey Novoseltsev: MatrixSpace is too eager to construct zero matrices [Reviewed by William Stein] #13019: Nathann Cohen: longest_path broken for digraphs [Reviewed by Mike Hansen] #13045: Rob Beezer: Deprecate cholesky_decomposition() in favor of cholesky() [Reviewed by Dan Drake] #13057: John Palmieri: introspection is slow and causes a significant memory leak [Reviewed by Keshav Kini] #13091: Jason Grout: Bug in graph tensor_product [Reviewed by David Coudert] #13105: William Stein: fix some copyright headers in c_lib [Reviewed by Keshav Kini] Merged in sage-5.1.beta6: #10655: John Palmieri: Fix optional animate.py doctests [Reviewed by John Palmieri, Karl-Dieter Crisman] #11871: John Palmieri: Fix cellular automata function [Reviewed by Karl-Dieter Crisman] #12009: Mike Hansen: optional package gnuplotpy-1.8.spkg causes test failure on sage-4.7.2 [Reviewed by Douglas McNeil, Karl-Dieter Crisman] #12634: Punarbasu Purkayastha: detach list of files and also be able to detach relative filenames [Reviewed by William Stein] #12911: John Palmieri: fix failing ipython test in tests/cmdline [Reviewed by Keshav Kini] #12964: Robert Bradshaw: multiply matrix of matrices by a scalar: boom [Reviewed by Mike Hansen] #13034: Andrey Novoseltsev: Fix index in saturation of zero matrices [Reviewed by William Stein] #13104: Charles Bouillaguet: BooleanPolynomial.variables() consider "1" as a variable [Reviewed by Alexander Dreyer, Martin Albrecht] #13108: Kevin Halasz: A one letter typo in the documentation for the class DiCyclicGroup [Reviewed by Rob Beezer] #13116: John Palmieri: The :trac: sphinx role does not work on the commandline [Reviewed by Volker Braun] #13118: Jeroen Demeyer: Support GCC version "4.7" in LinBox [Reviewed by R. Andrew Ohana] #13122: R. Andrew Ohana: Remove last vestiges of darcs from Sage [Reviewed by Karl-Dieter Crisman] #13133: Charles Bouillaguet: BooleanMonomial.index() SEGFAULT on constant monomials [Reviewed by Alexander Dreyer] #13134: Jeroen Demeyer: real_double logarithm test fails due to ulp() bug [Reviewed by Volker Braun] #13138: John Palmieri: stopgap for #13137: don't run MPIR's self-tests [Reviewed by R. Andrew Ohana] Merged in sage-5.1.rc0: #1172: Keshav Kini: change the watkins license in SAGE_ROOT/COPYING [Reviewed by R. Andrew Ohana] #9544: Peter Jeremy, Jeroen Demeyer: Fix flintqs on FreeBSD [Reviewed by Stephen Montgomery-Smith, Jeroen Demeyer, Karl-Dieter Crisman] #12855: Jeroen Demeyer: FLINTQS fails to build on Solaris (with GCC 4.7.x) [Reviewed by Karl-Dieter Crisman] #13152: John Palmieri: add vsyasm, yasm, and ytasm to .hgignore [Reviewed by Jeroen Demeyer] Merged in sage-5.1.rc1: #13195: Jeroen Demeyer: import shutil in sage-ptest [Reviewed by Volker Braun]