May 03, 2013 ------------ 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 instead of Modular 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] March 18, 2013 -------------- Sage 5.8 was released on 15 March 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 76 people contributed to this release. Of those, 10 made their first contribution to Sage: - Alejandro Morales [first contribution] - Alexander Dreyer - Aly Deines - Andrew Mathas - André Apitzsch - Anne Schilling - Ben Hutz - Ben Salisbury [first contribution] - Benjamin Jones - Chris Berg - Christian Nassau - Christian Stump - Dan Orr [first contribution] - Darij Grinberg - David Coudert - David Harvey - David Joyner - David Loeffler - David Roe - Dmitrii Pasechnik - Emily Gunawan [first contribution] - Eric Rowland [first contribution] - Florent Hivert - Francis Clarke - Franco Saliola - François Bissey - Frithjof Schulze - Frédéric Chapoton - Gregg Musiker - Ivan Andrus - Jason Bandlow - Javier López Peña - Jean-Pierre Flori - Jeroen Demeyer - John Palmieri - John Perry - Julian Rueth - Kannappan Sampath - Karl-Dieter Crisman - Kevin Halasz - Kwankyu Lee - Leif Leonhardy - Lucas David-Roesler [first contribution] - Luis Felipe Tabera Alonso - Mario Pernici - Mark Shimozono - Martin Albrecht - Michael Orlitzky - Michelle Manes [first contribution] - Miguel Marco - Mike Hansen - Mike Zabrocki - Mitesh Patel - Nathann Cohen - Nicholas Kirchner [first contribution] - Nicolas M. Thiéry - Niles Johnson - Nils Bruin - Paul Zimmermann - Paul-Olivier Dehaye - Punarbasu Purkayastha - R. Andrew Ohana - Robert Miller - Salvatore Stella [first contribution] - Samuel Lelièvre - Sara Billey [first contribution] - Simon King - Simon Spicer - Stepan Starosta - Sébastien Labbé - Timo Kluck - Travis Scrimshaw - Vincent Delecroix - Volker Braun - Wai Yan Pong - William Stein * Release manager: Jeroen Demeyer. * We closed 144 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.8/tickets.html Closed tickets: #2694: Hecke algebra basis not implemented [Reviewed by Travis Scrimshaw] #3426: bessel_K function is broken [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #4230: implement arbitrary precision Bessel Y function [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #12349: linbox fails to builds in sage-5.0_beta1 [Reviewed by François Bissey] #13603: .DS_Store garbage in rpy2-2.0.8.p0 [Reviewed by Karl-Dieter Crisman] #14074: saving fill in eps doesn't work right for some reason [Reviewed by Punarbasu Purkayastha] #4294: sage -t under %pdb [Reviewed by David Roe] #7493: Implement sage -t --time [Reviewed by Jeroen Demeyer] #9224: Unify sage-test and sage-ptest [Reviewed by David Roe] #9449: The summary printed after running doctests is inaccurate. [Reviewed by Jeroen Demeyer] #10760: Improve coverage test for gsl/interpolation.pyx [Reviewed by Kannappan Sampath] #12024: 90% doctest coverage thrust metaticket [Reviewed by Travis Scrimshaw] #13383: Fix missing documentation of sage/rings/real_lazy in doc/en/reference/rings_numerical.rst [Reviewed by Volker Braun] #13652: Error in pari when dealing with algebraic numbers [Reviewed by Jeroen Demeyer] #14113: affine root system ambient lattice issue [Reviewed by Nicolas M. Thiéry] #12357: Make groupoids garbage collectable [Reviewed by Simon King, Jean-Pierre Flori] #13904: Better deletion of items of TripleDict [Reviewed by Simon King, Jean-Pierre Flori] #11525: file name conflict in SageTeX using sage.tex [Reviewed by Ivan Andrus, Karl-Dieter Crisman] #12253: SVD segfaults on complex matrices [Reviewed by Luis Felipe Tabera Alonso] #12686: Add sage.rings.finite_rings to the reference manual [Reviewed by Travis Scrimshaw] #9194: Expose and extend the thematic tutorial on symmetric functions [Reviewed by Jason Bandlow, Anne Schilling, Mike Zabrocki, Nicolas M. Thiéry] #13296: unicode default encoding is not utf-8 in command line [Reviewed by John Palmieri] #13991: Mitigate speed regressions in symmetric function related code due to #12313 [Reviewed by Simon King] #14201: During upgrade to sage 5.7 ppl is using gmpxx headers from the system [Reviewed by Wai Yan Pong, Volker Braun] Merged in sage-5.8.beta0: #6495: Mitesh Patel, John Palmieri, Florent Hivert: Build the reference manual incrementally [Reviewed by Volker Braun, Florent Hivert] #9235: Simon King: Doctest coverage for sage.categories.homset [Reviewed by Niles Johnson, Travis Scrimshaw] #10834: Mario Pernici: faster creation of an ETuple from a list or tuple [Reviewed by Travis Scrimshaw] #11026: Ivan Andrus: Add double clicking of sws files for Mac app [Reviewed by Karl-Dieter Crisman, Nicholas Kirchner, John Palmieri] #12774: Mark Shimozono: various enhancements for Coxeter and Weyl groups [Reviewed by Christian Stump, Anne Schilling] #13079: Frédéric Chapoton, Franco Saliola: Use a ranked poset's rank function to determine heights for plotting [Reviewed by Christian Stump] #13369: Christian Stump, Gregg Musiker: Implementation of the class ClusterSeed [Reviewed by Salvatore Stella] #13370: Simon King: Do not cache the result of is_Field externally [Reviewed by Nils Bruin] #13440: Emily Gunawan: Adding reverse_edge() function to DiGraph [Reviewed by Gregg Musiker, Nathann Cohen] #13732: John Perry: Fix alpha in disk() graphics object so that we can save PDF's [Reviewed by Karl-Dieter Crisman] #13787: Nathann Cohen: Bug in GenericGraph.line_graph() when the vertices cannot be compared [Reviewed by Frédéric Chapoton] #13801: Vincent Delecroix: Fix facade set category initialisation [Reviewed by Travis Scrimshaw] #13856: Christian Nassau: Add a top_class method to the Steenrod algebra [Reviewed by John Palmieri] #13960: Dmitrii Pasechnik: nef.x segfaults on Cygwin [Reviewed by Jean-Pierre Flori] #14033: Jean-Pierre Flori: Let Singular link to termcap on Cygwin [Reviewed by Dmitrii Pasechnik] #14038: Volker Braun, Jean-Pierre Flori: Let libgap build a shared library on Cygwin [Reviewed by Jean-Pierre Flori, Dmitrii Pasechnik] #14065: Travis Scrimshaw: Element overrides python behavior of cmp [Reviewed by Mike Hansen] #14070: Jeroen Demeyer: Problems with get_test_shell() [Reviewed by David Roe] #14075: Karl-Dieter Crisman: remove annoying printing of primes in conway polynomials spkg [Reviewed by François Bissey, R. Andrew Ohana] #14080: Jeroen Demeyer: Simplify cdefs.pxi using Cython's libc module [Reviewed by David Roe] #14084: Simon King: Wrong domain of the fraction field construction functor [Reviewed by Julian Rueth] #14089: Anne Schilling: Speed improvements in affine crystals and fix of optional doctest failure [Reviewed by Nicolas M. Thiery, Travis Scrimshaw] #14096: Jean-Pierre Flori: Let GSL build a shared library on Cygwin [Reviewed by Dmitrii Pasechnik] #14115: Frédéric Chapoton: missing log attribute for power series [Reviewed by Travis Scrimshaw] #14129: John Palmieri: Incorrect notebook typesetting due to '\texttt' [Reviewed by Luis Felipe Tabera Alonso] Merged in sage-5.8.beta1: #5978: Travis Scrimshaw: Can't construct the quotient of an univariate polynomial ring by its zero ideal [Reviewed by Luis Felipe Tabera Alonso] #10556: Ivan Andrus: Add button to Mac App to add sage executable to PATH [Reviewed by Karl-Dieter Crisman, John Palmieri] #11490: Simon King: Add a thematic tutorial on coercion and categories [Reviewed by Vincent Delecroix, Travis Scrimshaw, Dmitrii Pasechnik] #11696: Leif Leonhardy, Jean-Pierre Flori: The libpng12 spkg should also create symbolic links from `libpng.*` for its libraries [Reviewed by Dmitrii Pasechnik] #12175: Frithjof Schulze: Missing *args and **kwds in SL2Z.random_element() [Reviewed by Frédéric Chapoton] #12912: Mike Hansen: Interface to Fokko Ducloux's Coxeter 3 [Reviewed by Anne Schilling, Nicolas M. Thiéry, Jean-Pierre Flori] #13254: John Palmieri: compute fundamental groups of simplicial complexes [Reviewed by Miguel Marco] #13367: Kevin Halasz: Add Holomorph method for Permutation Groups [Reviewed by Frédéric Chapoton, Benjamin Jones] #13600: Julian Rueth: pAdicZZpXCAElement can not be initialized from fraction field element [Reviewed by David Roe] #13618: Travis Scrimshaw: Doctest coverage for rings [Reviewed by Kannappan Sampath, Volker Braun] #13688: Travis Scrimshaw: FiniteEnumeratedSets cardinality override [Reviewed by Andrew Mathas] #13839: Jean-Pierre Flori: Let lrcalc build as a shared library on Cygwin. [Reviewed by Dmitrii Pasechnik] #13894: Michael Orlitzky, Jean-Pierre Flori: Fix ArithmeticError: 0^0 in rings/finite_rings/integer_mod.pyx [Reviewed by Travis Scrimshaw] #14011: Florent Hivert: Add various new sphinx roles [Reviewed by Frédéric Chapoton] #14041: Christian Nassau: Give the SteenrodAlgebra a proper basis object [Reviewed by John Palmieri] #14098: Francois Bissey, David Harvey: zn_poly-0.9.p9 fails at least one its tests on power7 [Reviewed by Paul Zimmermann, Jeroen Demeyer] #14108: Robert Miller: bug in is_isomorphic with multiple edges [Reviewed by Paul Zimmermann] #14118: Jean-Pierre Flori: Compiling universal_cyclotomic_field_c.pyx fails on Cygwin [Reviewed by Dmitrii Pasechnik] #14122: Nathann Cohen: Tournament and directed path constructors [Reviewed by David Coudert] #14128: Nathann Cohen: Very bad mistakes in linear_arboricity [Reviewed by David Coudert] #14138: Nathann Cohen: some cleanup in sage.combinat.combinat [Reviewed by Punarbasu Purkayastha, Nicolas M. Thiéry] #14139: Frédéric Chapoton, Travis Scrimshaw: doc of prandom.py [Reviewed by Frédéric Chapoton] #14148: John Palmieri: Print location of output from documentation building [Reviewed by Anne Schilling] #14157: Travis Scrimshaw: Latex output for barred letters [Reviewed by Anne Schilling] #14160: Mike Zabrocki: Fix bug with the antipode in NonCommutativeSymmetricFunctions [Reviewed by Franco Saliola] #14162: Franco Saliola: fix parent coefficients for elements of NCSF / QSym [Reviewed by Mike Zabrocki] #14163: Mike Zabrocki, Franco Saliola: add counit method to QSym [Reviewed by Franco Saliola, Mike Zabrocki] Merged in sage-5.8.beta2: #7886: Javier López Peña: Implement conjugacy classes [Reviewed by David Joyner, Travis Scrimshaw] #8920: Vincent Delecroix, Stepan Starosta: Factor code between words's alphabets and sets/enumerated sets/ordered sets [Reviewed by Travis Scrimshaw] #11593: Kwankyu Lee: `quo_rem` for divisor of leading unit coefficient [Reviewed by Frédéric Chapoton] #12313: Simon King, Jean-Pierre Flori: Fix yet another memory leak caused by caching of coercion data [Reviewed by Simon King, Jean-Pierre Flori, John Perry, Nils Bruin] #13054: Jeroen Demeyer: PARI polred() bug [Reviewed by David Roe] #13387: Nils Bruin: Improve MonoDict and TripleDict data structures [Reviewed by Simon King] #13539: Julian Rueth: Add inverse_of_unit() for padics [Reviewed by David Roe] #13780: Kannappan Sampath: Typo in the docstring for echelon_coordinate_vector in FreeModules Documentation [Reviewed by Julian Rueth] #13786: Michael Orlitzky: Fix remaining instances of ArithmeticError: 0^0 is undefined [Reviewed by Travis Scrimshaw] #13895: Michael Orlitzky: Fix ArithmeticError: 0^0 in rings/polynomial/polynomial_modn_dense_ntl.pyx [Reviewed by Travis Scrimshaw] #13897: Michael Orlitzky: Fix ArithmeticError: 0^0 in rings/finite_rings/element_givaro.pyx [Reviewed by Travis Scrimshaw] #13941: Michael Orlitzky: Fix ArithmeticError: 0^0 in rings/padics/padic_capped_absolute_element.pyx [Reviewed by Travis Scrimshaw] #14000: Nathann Cohen: Speedup in GenericGraph.relabel() and two new options [Reviewed by Anne Schilling] #14040: Volker Braun: Configurable "tall list" output style [Reviewed by Travis Scrimshaw] #14063: Travis Scrimshaw: Remove CombinatorialClass from Compositions [Reviewed by Vincent Delecroix] #14085: Nicolas M. Thiéry: Ambient spaces for dual and affine root systems [Reviewed by Dan Orr, Anne Schilling] #14100: Simon King: Make raising attribute errors faster [Reviewed by Volker Braun] #14105: Alejandro Morales, Eric Rowland: all_graph_colorings should have an option to use integer colors. [Reviewed by Chris Berg, Nathann Cohen] #14120: Travis Scrimshaw: Add constant_coefficient method for Laurent polynomials [Reviewed by Kannappan Sampath] #14142: Travis Scrimshaw: Making mutable copies of simplicial complexes [Reviewed by John Palmieri] #14150: Jeroen Demeyer: Fix wait() in @parallel [Reviewed by David Roe] #14156: John Palmieri: New docbuilder always rebuilds everything [Reviewed by Volker Braun] #14158: Jeroen Demeyer: _is_Field() ignores exceptions [Reviewed by David Roe] #14166: John Palmieri: Use "tar", not "cp -pr", to copy files in spkg-install [Reviewed by Jeroen Demeyer] #14173: Nathann Cohen: Stopgap warning in Graph.modular_decomposition [Reviewed by Luis Felipe Tabera Alonso] #14174: Nicolas M. Thiéry: Remove coxeter matrix implementation for type H (the generic implementation is just as good) [Reviewed by Anne Schilling] #14176: Nicolas M. Thiéry: Use standard Python operators for intersection of polyhedrons and membership testing [Reviewed by Volker Braun] #14177: Nicolas M. Thiéry: More uniform handling of color_by_labels for graph plot, plot3d, graphviz, and reference fix [Reviewed by Nathann Cohen] #14182: Jeroen Demeyer: Fix whitespace in coercion_and_categories.rst [Reviewed by Simon King] #14185: Nathann Cohen: Stopgap warning in Poset.relabel [Reviewed by Luis Felipe Tabera Alonso] Merged in sage-5.8.beta3: #6567: David Roe: function to test whether or not some integer is a primitive root modulo n [Reviewed by Julian Rueth, Simon Spicer] #12109: David Roe: Function for faster evaluation of cyclotomic polynomials [Reviewed by André Apitzsch, Simon Spicer] #12116: David Roe: perfect_power for integers [Reviewed by David Loeffler, Aly Deines, Simon Spicer] #12543: Vincent Delecroix: improve import_statements [Reviewed by Nicolas M. Thiéry] #13102: Nathann Cohen: PermutationGroup.all_blocks from GAP [Reviewed by Benjamin Jones] #13130: Ben Hutz: Ring support for projective space points and morphisms [Reviewed by Michelle Manes] #13605: Travis Scrimshaw: Partition options and cleanup partitions documentation [Reviewed by Andrew Mathas, Nicolas M. Thiéry] #13767: Timo Kluck: upgrade boost to version 1.52.0 [Reviewed by Volker Braun, François Bissey, Alexander Dreyer] #13798: Frédéric Chapoton: q-Bernoulli numbers of Carlitz [Reviewed by Francis Clarke] #13994: Christian Stump: Implementation of EL labellings of posets [Reviewed by Frédéric Chapoton] #14082: Jeroen Demeyer: PARI stack overflow crashes Sage [Reviewed by David Roe] #14090: Franco Saliola, Florent Hivert, Nicolas M. Thiéry, et al.: Thematic tutorials: using the notebook, programming python, comprehensions [Reviewed by Samuel Lelièvre, Sébastien Labbé, Karl-Dieter Crisman, Darij Grinberg] #14111: Sara Billey: Tutorial for quasisymmetric functions (QSYM) [Reviewed by Travis Scrimshaw] #14130: Lucas David-Roesler, Ben Salisbury: Implement Crystals of Generalized Young Walls [Reviewed by Travis Scrimshaw, Anne Schilling] #14155: David Roe: gcd for IntegerMod [Reviewed by Simon Spicer] #14168: Jeroen Demeyer: Fix race condition rebuilding MPIR,... with GCC spkg [Reviewed by Karl-Dieter Crisman, Leif Leonhardy] #14180: Martin Albrecht: SatSolver.clauses [Reviewed by Nathann Cohen] #14184: Jeroen Demeyer: Fix # optional tags [Reviewed by Karl-Dieter Crisman] #14188: John Palmieri, Volker Braun: IPython 0.13: merge user configuration with Sage configuration [Reviewed by Volker Braun, William Stein, John Palmieri] #14193: David Roe: Converting polynomial quotient ring elements to pari yields plain polynomials [Reviewed by Simon Spicer] #14195: Nathann Cohen: Bad error management in the CPLEX interface [Reviewed by David Coudert] #14198: Martin Albrecht: update cryptominisat to most recent upstream release [Reviewed by Nathann Cohen] #14200: Travis Scrimshaw: Add shortcut to add multiple variables with different names [Reviewed by Sara Billey] #14216: Frédéric Chapoton: clean-up of parts of combinat [Reviewed by Nathann Cohen] #14227: R. Andrew Ohana: Cython includes assume rigid directory structure [Reviewed by Jeroen Demeyer] Merged in sage-5.8.beta4: #11410: Paul-Olivier Dehaye: 01 sequence or east-north sequence for partitions [Reviewed by Frédéric Chapoton, Nathann Cohen, Travis Scrimshaw] #14054: Simon King: Cythoned UniqueRepresentation [Reviewed by Travis Scrimshaw] #14189: Simon Spicer: Extend modular degree and congruence modulus of elliptic curves over QQ to arbitrary level. [Reviewed by Aly Deines] #14199: John Palmieri: Docbuilder changes sagetex.rst [Reviewed by Jeroen Demeyer] #14204: Jeroen Demeyer: Building unchanged documentation takes very long [Reviewed by John Palmieri] #14225: Simon King: Remove redundant classcall_private from partitions [Reviewed by Travis Scrimshaw] #14228: Travis Scrimshaw: Caching of data needed for computations in k_dual [Reviewed by Simon King] #14230: Travis Scrimshaw: Update developer conventions page for multiline equations [Reviewed by John Palmieri] #14233: Frédéric Chapoton: small cleanup of sage/homology [Reviewed by John Palmieri] #14236: Jeroen Demeyer: Use "tar", not "cp -pPRL", to copy files in sage-bdist [Reviewed by John Palmieri] Merged in sage-5.8.rc0: #14121: Chris Berg: Fixing bug in shuffle product [Reviewed by Franco Saliola, Frédéric Chapoton, Nathann Cohen] #14245: John Palmieri: Cloning doesn't properly copy the _static doc directory [Reviewed by Florent Hivert] #14254: Jeroen Demeyer: OverflowErrors in TripleDictEraser [Reviewed by Simon King] February 21, 2013 ----------------- Sage 5.7 was released on 19 February 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 78 people contributed to this release. Of those, 7 made their first contribution to Sage: - Alexander Dreyer - Alexandre Blondin Massé - Andrew Mathas - Andrey Novoseltsev - André Apitzsch - Anne Schilling - Beni Keller [first contribution] - Benjamin Jones - Burcin Erocal - Charles Bouillaguet - Chris Berg - Christian Nassau - Christian Stump - Daniel Krenn - David Coudert - David Kirkby - David Loeffler - David Roe - Dmitrii Pasechnik - Dorota Mazur [first contribution] - Emmanuel Charpentier [first contribution] - Eviatar Bach - Florent Hivert - Franco Saliola - François Bissey - Frédéric Chapoton - Geoff Tims [first contribution] - Hugh Thomas - Ivan Andrus - Jaap Spies - Jason Bandlow - Jason Grout - Jean-Pierre Flori - Jernej Azarija - Jeroen Demeyer - John Cremona - John Palmieri - Jonathan Bober - Julian Rueth - Julien Puydt - Kannappan Sampath [first contribution] - Karl-Dieter Crisman - Keshav Kini - Leif Leonhardy - Luis Felipe Tabera Alonso - Luis Serrano - Maarten Derickx - Marc Mezzarobba - Marco Streng - Martin Albrecht - Martin Raum - Michael Orlitzky - Miguel Marco - Mike Hansen - Mike Zabrocki - Moritz Minzlaff - Nathann Cohen - Nicolas Borie - Nicolas M. Thiéry - Nils Bruin - Paul Zimmermann - Punarbasu Purkayastha - R. Andrew Ohana - Radoslav Kirov - Rob Beezer - Robert Bradshaw - Robert Miller - Simon King - Stephan Ehlen [first contribution] - Stephen Montgomery-Smith - Sébastien Labbé - Thomas Feulner - Tom Boothby - Travis Scrimshaw - Uros Slana [first contribution] - Viviane Pons - Volker Braun - William Stein * Release manager: Jeroen Demeyer. * We closed 182 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.7/tickets.html Closed tickets: #8027: change the wiki(...) command to store data in $HOME/.sage [Reviewed by Jeroen Demeyer] #11737: "integrate" fails to integrate a convergent integral (sin(x^2)/x^2). [Reviewed by Dmitrii Pasechnik, Karl-Dieter Crisman] #12115: New MPIR won't build on Cygwin [Reviewed by Volker Braun, Karl-Dieter Crisman, Jean-Pierre Flori] #13974: MathJax and Documentation in sagenb [Reviewed by John Palmieri] #4413: '?' in docstring gets interpreted immediately by the parser [Reviewed by Keshav Kini] #12167: Move SAGE_ROOT/ipython to extcode [Reviewed by Jeroen Demeyer] #12926: `sage -ipython` doesn't use the sage directory for ipython. [Reviewed by Jason Grout] #13313: Sébastien Labbé: Fix gcc error in pyzmq-2.1.11.p0.spkg [Reviewed by Volker Braun] #13950: Robert Bradshaw: Sage-patchbot improvements [Reviewed by Volker Braun] #128: possible clash for EllipticCurve(j-invariant) signature [Reviewed by Paul Zimmermann, Nils Bruin, John Cremona] #4105: multiplication of permutations in distinct subgroups sometimes doesn't work [Reviewed by Punarbasu Purkayastha] #8005: powers of elements in a QuotientRing [Reviewed by Christian Nassau] #8918: Strange behavior for Permutation() [Reviewed by Luis Felipe Tabera Alonso] #9165: cygwin: lcalc does not work for elliptic curves on cygwin [Reviewed by Karl-Dieter Crisman, Jean-Pierre Flori] #9171: cygwin: Documentation not built, which causes test failures [Reviewed by Karl-Dieter Crisman, Jean-Pierre Flori] #10461: Raising doctest coverage to 100% for sage/combinat/partition.py [Reviewed by John Cremona, Alexandre Blondin Massé] #11122: Implementation of the Demazure product in Coxeter groups [Reviewed by Christian Stump] #12350: ValueError when computing palindrome factors of a finite word [Reviewed by Sébastien Labbé] #13430: log plots blank with points, but fine with lines [Reviewed by Punarbasu Purkayastha] #13547: John Cremona: Update Cremona's table of elliptic curves to 300000 [Reviewed by Jonathan Bober] #13554: Documentation of random_matrix insists zero is never used, when it is. [Reviewed by Rob Beezer] #589: improve doctesting of sage-sage script [Reviewed by Jeroen Demeyer] #838: doctest runner should share SAGE initialization using fork() [Reviewed by David Roe] #1446: make check needs to error out on build failure instead of running doctests [Reviewed by Jeroen Demeyer] #6026: python.spkg: ctypes fails to build on 64 bit OSX [Reviewed by Jeroen Demeyer] #6028: get_memory_usage() sucks performance wise on Solaris [Reviewed by William Stein] #6589: bring doctest coverage for ring/laurent_series_ring.py to 100% [Reviewed by David Roe] #7630: Require email confirmation before account activation [Reviewed by Jeroen Demeyer] #7782: Cliquer build fails on HP-UX [Reviewed by Jeroen Demeyer] #7818: Update sage-env [Reviewed by David Kirkby, Jaap Spies] #9169: cygwin: a cachefunc.py doctest hangs seemingly forever [Reviewed by Jean-Pierre Flori] #9172: cygwin: numerical noise in sage/rings/integer.pyx [Reviewed by Jean-Pierre Flori] #9173: cygwin: BSD.py tests behave differently on cygwin, so need to be written to reflect that [Reviewed by Jean-Pierre Flori] #9174: cygwin: robert miller's 2-descent is completely broken on cygwin [Reviewed by Karl-Dieter Crisman] #9276: sage notebook: jsmath image fonts -- optional package -- breakage [Reviewed by Andrey Novoseltsev] #10458: Doctest framework fails to parse multiline input pasted from sage interactive prompt [Reviewed by Keshav Kini] #10524: add emails to the user management list in the notebook [Reviewed by Jason Grout] #11009: Notebook keybindings should be configurable [Reviewed by Ivan Andrus] #11929: Implement quasi-symmetric functions [Reviewed by Jason Bandlow, Chris Berg, Franco Saliola, Nicolas M. Thiéry] #12028: Matchpoly.pyx test sometimes hangs [Reviewed by Jeroen Demeyer] #12458: remove references to deprecated RQDF [Reviewed by Paul Zimmermann] #12856: multiline doctests starting with '....:' [Reviewed by Daniel Krenn] #13864: Configure Python with pydebug when SAGE_DEBUG is set [Reviewed by Volker Braun, Simon King, Jean-Pierre Flori] #13986: doctest creates tmp_f.sobj in cwd [Reviewed by Jeroen Demeyer] #14057: 'environ' is not really available with shared libraries on OSX [Reviewed by Jean-Pierre Flori] Merged in sage-5.7.beta0: #5155: Mike Hansen, Jeroen Demeyer, John Palmieri: Fix doctests that want write access to $SAGE_ROOT [Reviewed by François Bissey] #7557: Burcin Erocal: conversion of complex numbers in symbolic expressions to maxima broken [Reviewed by Volker Braun, Karl-Dieter Crisman] #9559: Robert Miller: *generalized* canonical generation in Cython [Reviewed by Tom Boothby] #12205: R. Andrew Ohana: rewrite conway polynomial spkg and code in Sage library to not use ZODB [Reviewed by François Bissey] #12815: Jeroen Demeyer: bugs in doctesting script for examples with tolerance [Reviewed by Robert Bradshaw] #13137: John Palmieri, Jean-Pierre Flori, Karl-Dieter Crisman: Upgrade MPIR to 2.6.0 [Reviewed by Jeroen Demeyer, Leif Leonhardy, John Palmieri, R. Andrew Ohana, Karl-Dieter Crisman] #13324: Jean-Pierre Flori: Upgrade ECL to 12.12.1 and let it build on (recent) Cygwins [Reviewed by François Bissey, Karl-Dieter Crisman, Dmitrii Pasechnik] #13350: Jean-Pierre Flori: Cannot import rpy2.rinterface.rinterface on Cygwin [Reviewed by Karl-Dieter Crisman] #13364: Jean-Pierre Flori, Dmitrii Pasechnik: Upgrade Maxima to 5.29.1 [Reviewed by Karl-Dieter Crisman, François Bissey, Leif Leonhardy, Paul Zimmermann] #13378: Simon King: Do not cache the non-existence of coerce/convert map too often, and do not pretend that there is a conversion where it doesn't make sense at all [Reviewed by Nils Bruin] #13393: Chris Berg, Eviatar Bach: Vector normalization [Reviewed by Luis Serrano, Benjamin Jones] #13504: John Palmieri: latex_macros: don't evaluate anything on startup [Reviewed by Volker Braun] #13658: Frédéric Chapoton: Typo in Graph.girth() [Reviewed by Nathann Cohen] #13672: Jeroen Demeyer: resultant over GF(q)[t][x] is plain wrong!!! [Reviewed by Paul Zimmermann] #13678: Robert Bradshaw, Volker Braun: Allow tab completion of matrix constructor [Reviewed by Volker Braun] #13717: Jason Grout, Keshav Kini: Upgrade to sagenb 0.10.4 [Reviewed by Volker Braun] #13847: Martin Albrecht: remove sage.crypto.mq.mpolynomialsystem [Reviewed by Alexander Dreyer] #13861: Volker Braun: Segmentation fault in prime_phi [Reviewed by Jeroen Demeyer] #13876: Volker Braun: Singular and SAGE_DEBUG fixes [Reviewed by Simon King] #13889: Volker Braun: Better automatic backtrace [Reviewed by Jeroen Demeyer] #13912: Jean-Pierre Flori: Let iconv build on Cygwin without installing Cygwin libiconv package [Reviewed by Jeroen Demeyer] #13946: Jeroen Demeyer: Some cleanup of signal handling code [Reviewed by Volker Braun] #13963: Jeroen Demeyer: Fix checking for and resetting GAP workspaces [Reviewed by Volker Braun] #13964: Charles Bouillaguet: Missing conversion from PolynomialBooleanRing to (univariate) PolynomialRing over GF(2) via NTL [Reviewed by Alexander Dreyer] #13970: David Coudert: Fix memory allocation in distances all pairs [Reviewed by Nathann Cohen] #13971: Jeroen Demeyer: Remove duplicate fraction_field() method [Reviewed by André Apitzsch] #13977: Charles Bouillaguet: variety() of full ideals fails, whereas it should just be empty [Reviewed by Martin Albrecht] #13983: Jeroen Demeyer: Make crash_logs configurable [Reviewed by Volker Braun] Merged in sage-5.7.beta1: #3103: Charles Bouillaguet: Coercion errors of vectors from ZZ^2 and QQ^2 into CDF^2 [Reviewed by Robert Bradshaw] #5294: Andrew Mathas: Pickle Jar documentation [Reviewed by Julian Rueth] #5917: Charles Bouillaguet: Failing conversions for multipolynomial rings over fraction fields [Reviewed by Simon King] #9167: Jean-Pierre Flori: Resolve ecl.dll conflict on Cygwin [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] #10353: François Bissey: Remove zodb from sage [Reviewed by Jeroen Demeyer] #11641: Christian Stump: Implementation of decorator for combinatorial maps [Reviewed by Mike Zabrocki] #12215: Simon King: Memleak in UniqueRepresentation, @cached_method [Reviewed by Nils Bruin] #12510: Florent Hivert: Add consistency tests for __nonzero__ in TestSuite. [Reviewed by Nathann Cohen] #12615: Robert Bradshaw: sign(integer) is horribly slow [Reviewed by Paul Zimmermann] #12719: Mike Hansen, Volker Braun, Jason Grout, Jeroen Demeyer: Upgrade to IPython 0.13 [Reviewed by Volker Braun, Mike Hansen, Jason Grout, Jeroen Demeyer] #13115: Rob Beezer: "groups" object for organizing examples of groups [Reviewed by Nathann Cohen, Nicolas Borie] #13162: Charles Bouillaguet: add experimental libFES package [Reviewed by Martin Albrecht] #13451: Volker Braun: Classical invariant theory [Reviewed by Dmitrii Pasechnik] #13510: Nathann Cohen, Geoff Tims: Small change to graph_is_strongly_regular (return the number of vertices) [Reviewed by Nathann Cohen] #13588: Volker Braun: libGAP! -- create a Cython library interface to gap [Reviewed by Dmitrii Pasechnik] #13657: Punarbasu Purkayastha, Dmitrii Pasechnik, Volker Braun: Mention RDF, CDF in linear algebra tutorial [Reviewed by Dmitrii Pasechnik] #13721: Jernej Azarija: Additional tests for graph symmetries [Reviewed by Nathann Cohen, Tom Boothby] #13824: Travis Scrimshaw: ZeroDivisionError in finite field __contains__ [Reviewed by Volker Braun, Sébastien Labbé] #13906: Jernej Azarija: Segmentation fault in subgraph_search [Reviewed by Nathann Cohen] #13919: Nathann Cohen: Bug in Graph() when input is a weighted matrix [Reviewed by Frédéric Chapoton] #13943: Frédéric Chapoton: Automorphisms of simplicial complexes [Reviewed by Nathann Cohen] #13955: Christian Stump: LaTeX output for Weyl group elements with prefix [Reviewed by Frédéric Chapoton] #13965: Charles Bouillaguet: BooleanPolynomialRing.remove_var(...) does not return a BooleanPolynomialRing [Reviewed by Alexander Dreyer] #13968: Charles Bouillaguet: BooleanPolynomialSequence.eliminate_linear_variables leaves some linear equations in corner cases [Reviewed by Martin Albrecht] #13972: Mike Zabrocki: Implement the inverse of the method area_dinv_to_bounce_area_map in dyck_word.py [Reviewed by Christian Stump, Dorota Mazur] #13976: Charles Bouillaguet: Problem in the return type of BooleanIdeal.variety() [Reviewed by Martin Albrecht] #13985: Jeroen Demeyer: Fix doctests that want write access to $HOME [Reviewed by François Bissey] #13992: Jeroen Demeyer: Set Fortran compiler variables [Reviewed by François Bissey] #13997: Christian Stump: Fixing a bug in the cyclic sieving phenomenon [Reviewed by Frédéric Chapoton] #14002: Christian Stump: Fixing a type error for Kazhdan-Lusztig polynomials [Reviewed by Anne Schilling] Merged in sage-5.7.beta2: #5562: Christian Nassau: coercion error with vectors and polynomial rings with 1 variable [Reviewed by Travis Scrimshaw] #9921: John Palmieri: nose testing suite as an optional spkg [Reviewed by Karl-Dieter Crisman, Martin Raum] #11672: Marc Mezzarobba: Some more doctests from the book "Calcul mathématique avec Sage" [Reviewed by Martin Albrecht, Charles Bouillaguet] #12014: Radoslav Kirov, Punarbasu Purkayastha: Make linearcode.__iter__ and linearcode.list() faster [Reviewed by Dmitrii Pasechnik] #13077: Frédéric Chapoton: generalised Tamari lattices [Reviewed by Christian Stump, Hugh Thomas] #13204: Travis Scrimshaw: Element construction for CrystalOfTableaux should be robust versus int's [Reviewed by Anne Schilling] #13667: Dmitrii Pasechnik, Punarbasu Purkayastha: fix docs in sage/coding/code_bounds.py [Reviewed by Punarbasu Purkayastha, Dmitrii Pasechnik] #13687: Volker Braun: Parents for groups [Reviewed by David Roe] #13763: Volker Braun: Minkowski subtraction [Reviewed by Dmitrii Pasechnik] #13765: Robert Bradshaw: Cyclotomic embeddings should respect coercions. [Reviewed by Frédéric Chapoton, Stephan Ehlen] #13844: Jean-Pierre Flori: Let patch build on Cygwin on Windows 7 [Reviewed by Dmitrii Pasechnik] #13888: Frédéric Chapoton: Barnette Sphere [Reviewed by Nathann Cohen] #13908: Jeroen Demeyer: Exit Sage gracefully upon SIGHUP [Reviewed by Volker Braun] #13929: Thomas Feulner: Wrong comparison of sparse vectors [Reviewed by Christian Nassau] #13954: Jean-Pierre Flori: New Gap spkg (>=4.5) does not build with shared only GMP/MPIR [Reviewed by Dmitrii Pasechnik] #13958: Maarten Derickx: number of generators of number field ideal blows up under multiplication [Reviewed by Marco Streng] #13984: Nathann Cohen: Improve the is_vertex_transitive test [Reviewed by Jernej Azarija] #13988: Jeroen Demeyer: Run _write_started_file() only from sage-starts [Reviewed by Volker Braun] #13996: Jeroen Demeyer: Clean up spkg/bin/sage [Reviewed by Volker Braun] #13998: Sébastien Labbé: hash of a pickled Sequence is broken [Reviewed by Stephan Ehlen] #14006: Viviane Pons: Bug with dumps() of Hasse diagrams [Reviewed by Frédéric Chapoton] #14008: Emmanuel Charpentier: Some R packages no longer can be installed [Reviewed by Dmitrii Pasechnik] #14022: François Bissey: Get scipy fortran objects be built with -fPIC again [Reviewed by Jeroen Demeyer, Stephen Montgomery-Smith] #14024: Volker Braun: More IPython 0.13 fixes [Reviewed by Keshav Kini] #14027: Jeroen Demeyer: Disable sage-make_relative when upgrading [Reviewed by Volker Braun] #14028: Jeroen Demeyer: Fix "except:" statements [Reviewed by Volker Braun] #14032: Jeroen Demeyer: determinant() of integer matrices of size in [51,63] broken [Reviewed by Volker Braun] Merged in sage-5.7.beta3: #8327: Christian Stump, Simon King: Implement the universal cyclotomic field, using Zumbroich basis [Reviewed by Frédéric Chapoton] #8359: Nicolas M. Thiéry: Coxeter groups as permutation groups [Reviewed by Anne Schilling, Mike Hansen] #9220: Nils Bruin, Robert Bradshaw: Unpredictable parent for polynomial evaluation [Reviewed by Tom Boothby] #10445: Frédéric Chapoton: A Polyhedron should have a "is_simplicial" method. [Reviewed by Andrey Novoseltsev] #12339: Miguel Marco, Volker Braun: Free Groups [Reviewed by Volker Braun] #12725: Jeroen Demeyer: termcap: symlink libtermcap.a to libncurses.a [Reviewed by Volker Braun] #12842: Punarbasu Purkayastha: Incorrect sign in exponential integral via Maxima [Reviewed by Michael Orlitzky] #13531: Martin Raum: short_vector_list_up_to_length is slow and wrong [Reviewed by Volker Braun] #13694: Punarbasu Purkayastha: Implement __getitem__ for LinearCode [Reviewed by Dmitrii Pasechnik] #13764: Volker Braun: CartesianProduct with generators -> silent wrong answer [Reviewed by Nathann Cohen] #13820: Uros Slana: Add the Johnson graph to Sage's constructors [Reviewed by Nathann Cohen] #13823: Kannappan Sampath: Broken link in tutorial [Reviewed by Karl-Dieter Crisman] #13840: Travis Scrimshaw: IntegerListsLex speedup [Reviewed by Mike Hansen] #13891: Nathann Cohen: Default parameters for Graph.plot() and Graph.show() [Reviewed by Punarbasu Purkayastha, Sébastien Labbé] #13922: Simon King: Avoid a regression in the creation of homsets [Reviewed by Volker Braun] #13923: Frédéric Chapoton: Bruckner-Grunbaum 3-Sphere [Reviewed by Nathann Cohen] #13944: Frédéric Chapoton: quaternionic projective plane [Reviewed by Nathann Cohen] #13949: Nils Bruin: Make mutability on matrices a simple bint flag [Reviewed by David Loeffler] #14007: Jeroen Demeyer: Better heuristics for determinant over ZZ and GF(p) [Reviewed by Charles Bouillaguet] #14035: Beni Keller: Typo in German tutorial, programming section [Reviewed by Karl-Dieter Crisman] #14042: John Palmieri: Failure in "R --version" test in sage/misc/interpreter.py [Reviewed by Jeroen Demeyer] #14045: Travis Scrimshaw: Comparison of float('inf') and infinity [Reviewed by Robert Bradshaw] #14048: Hugh Thomas: Fix a bug in class_size for QuiverMutationType (in types F and G) [Reviewed by Christian Stump] #14049: Jason Grout: Matrix slices don't deal with zero rows or columns well [Reviewed by Karl-Dieter Crisman] Merged in sage-5.7.beta4: #5761: Travis Scrimshaw: Bring doctests of sage/misc/latex.py to 100% [Reviewed by André Apitzsch] #9170: Dmitrii Pasechnik: cygwin: get_memory_usage isn't implemented [Reviewed by Jean-Pierre Flori] #12092: Moritz Minzlaff: get doctest coverage of databases/stein_watkins.py to 100% [Reviewed by Karl-Dieter Crisman, David Loeffler, Frédéric Chapoton, Jeroen Demeyer] #12448: Punarbasu Purkayastha: The binomial implementation does a quotient of gamma values, which is wrong [Reviewed by Julien Puydt] #13064: John Palmieri, Travis Scrimshaw: The documentation should search methods in classes [Reviewed by Punarbasu Purkayastha] #13463: Jeroen Demeyer: "/bin/bash" error in fflas_ffpack-1.6.0 [Reviewed by Stephen Montgomery-Smith] #13546: Nathann Cohen: Bug in is_perfect [Reviewed by Jernej Azarija, Sébastien Labbé] #13701: André Apitzsch: Replace some python2 functions with python3 compatible ones in sage/databases [Reviewed by Karl-Dieter Crisman] #13709: Nathann Cohen: Schlafli graph constructor [Reviewed by Volker Braun] #13714: Charles Bouillaguet: multi_polynomial.lift(...) affects libsingular internal state; makes ideal.complete_primary_decomposition() fail [Reviewed by Martin Albrecht, Marco Streng] #13769: John Palmieri: CHomP interface: fix usage of CombinatorialFreeModule [Reviewed by Christian Nassau] #13867: Volker Braun: Remove debugging output from Python command line [Reviewed by Jean-Pierre Flori] #13878: Nils Bruin: Fix failing assertion in linbox/matrix/permutation-matrix.h [Reviewed by Simon King] #13914: Jean-Pierre Flori: Install zlib shared objects on Cygwin [Reviewed by Dmitrii Pasechnik] #13990: Jernej Azarija: Bug fix and small improvement of spanning_trees_count [Reviewed by Nathann Cohen] #14009: Anne Schilling: Fix typos in the crystal category [Reviewed by Nicolas M. Thiery] #14010: Volker Braun: Add `__call__` method to FreeGroupElement [Reviewed by Punarbasu Purkayastha] #14017: Simon King: Determine the correct argspec for python functions defined in cython files [Reviewed by Travis Scrimshaw] #14021: Punarbasu Purkayastha: add ref to ymin/ymax to top of plotting page [Reviewed by Karl-Dieter Crisman] #14034: Kannappan Sampath: Incredibly trivial typo in programming part of tutorial [Reviewed by Karl-Dieter Crisman] #14046: Keshav Kini: Document `sage --sync-build` in `sage --advanced` [Reviewed by Jeroen Demeyer] #14059: Simon King: Fix refcount/deallocation of integers [Reviewed by Jean-Pierre Flori] #14061: Jeroen Demeyer: Fix sage-coverage [Reviewed by Travis Scrimshaw] #14067: Jeroen Demeyer: generic_graph_pyx.pyx invalid free() with MALLOC_CHECK_=3 [Reviewed by Jean-Pierre Flori] #14078: Jean-Pierre Flori: Let r-2.15.2 build on Cygwin [Reviewed by Dmitrii Pasechnik] Merged in sage-5.7.rc0: #14052: Anne Schilling: Enabling plotting of top graded piece of infinite dimensional crystals [Reviewed by Nicolas M. Thiery, Travis Scrimshaw] #14066: Jason Grout: FIx IPython 0.13 issues [Reviewed by Volker Braun, Jeroen Demeyer] #14083: Karl-Dieter Crisman: Fix a few more formatting things in plot.py [Reviewed by Punarbasu Purkayastha] January 24, 2013 ---------------- Sage 5.6 was released on 21 January 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 65 people contributed to this release. Of those, 9 made their first contribution to Sage: - Alexander Dreyer - Andrew Mathas - Andrey Novoseltsev - Andrzej Giniewicz - André Apitzsch - Anne Schilling - Burcin Erocal - Charles Bouillaguet - Chris Berg - Christian Kuper [first contribution] - Christian Nassau [first contribution] - Christian Stump - David Coudert - David Loeffler - Dmitrii Pasechnik - Dylan Rupel [first contribution] - Emil Widmann - François Bissey - Frédéric Chapoton - Gregg Musiker [first contribution] - Guillaume Moroz - Ivan Andrus - Jan Medlock - Jason Grout - Jean-Pierre Flori - Jernej Azarija [first contribution] - Jeroen Demeyer - John Cremona - John Palmieri - John Perry - Julian Rueth - Karl-Dieter Crisman - Keshav Kini - Kevin Halasz - Leif Leonhardy - Marco Streng - Marshall Hampton - Martin Albrecht - Michael Orlitzky - Mike Hansen - Mike Zabrocki - Nathann Cohen - Nicolas M. Thiéry - Nils Bruin - Noud Aldenhoven [first contribution] - Paul Zimmermann - Peter Jeremy - Pierre Cagne [first contribution] - Punarbasu Purkayastha - R. Andrew Ohana - Rob Beezer - Robert Bradshaw - Simon King - Stephen Montgomery-Smith - Steven Trogdon - Taylor Dupuy - Thomas Feulner - Thomas Rehn [first contribution] - Timo Kluck - Travis Scrimshaw - Vincent Delecroix - Volker Braun - William Stein - Xavier Caruso - Yoora Yi Tenen [first contribution] * Release manager: Jeroen Demeyer. * We closed 156 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.6/tickets.html Closed tickets: #13234: Andrey Novoseltsev: Add Normaliz optional package [Reviewed by Dmitrii Pasechnik] #13557: Jeroen Demeyer: Make the autotools spkg an optional spkg [Reviewed by Volker Braun] #7712: error with polynomial with interval coefficients [Reviewed by Travis Scrimshaw] #11231: Sparse and dense polynomials hash differently, but are equal. [Reviewed by Christian Nassau] #11551: Pari segfault on Sage startup in Cygwin [Reviewed by Karl-Dieter Crisman, Jean-Pierre Flori] #11678: sage-4.7 gives error on relocating the root directory [Reviewed by Punarbasu Purkayastha] #12296: Developer Conventions: 'NOTES' inaccuracy [Reviewed by Travis Scrimshaw] #12931: evaluation of coefficients of polynomials [Reviewed by Travis Scrimshaw] #13779: Crash in graph_generators with MALLOC_CHECK_=3 [Reviewed by Nils Bruin] #13790: Allow SR.symbol() to return a tuple. [Reviewed by Nils Bruin] #6391: libGAP! -- create a Cython library interface to gap [Reviewed by Dmitrii Pasechnik, Ivan Andrus, Volker Braun, William Stein] #12463: Polyhedron intersection and equality inconsistencies [Reviewed by Andrey Novoseltsev, Volker Braun] #13877: Metaticket: Make SAGE_DEBUG work [Reviewed by Volker Braun] #13913: Jeroen Demeyer: Provide a "stripped" gcc 4.7.2 spkg [Reviewed by Jean-Pierre Flori] #9298: Memory leak in libsingular polynomial evaluation [Reviewed by Charles Bouillaguet] #10960: Better product error messages when can't multiply [Reviewed by Michael Orlitzky] #13863: Segfault in pari galoisconj0 [Reviewed by Volker Braun] #13939: Fix the "SyntaxError: Non-ASCII character '\xe2'" [Reviewed by Volker Braun] #7773: Test failures with Fedora 12 on intel i7 860 processor [Reviewed by Paul Zimmermann] #9168: cygwin: ratpoints does not work correctly [Reviewed by Karl-Dieter Crisman] #9606: local/bin/sage-sage assumes 'sh' is bash [Reviewed by Leif Leonhardy, John Palmieri, Stephen Montgomery-Smith] #12401: Get Pynac functions to work on FreeBSD [Reviewed by Stephen Montgomery-Smith] #12411: pre-compiled Sage 4.8 binary fails some doctests on Ubuntu [Reviewed by Paul Zimmermann] #13866: Volker Braun: Experimental gdb spkg [Reviewed by Jeroen Demeyer] Merged in sage-5.6.beta0: #1920: Karl-Dieter Crisman: 3d graphics -- constant plot3d's [Reviewed by Punarbasu Purkayastha] #8952: Jernej Azarija: Odd Girth [Reviewed by Rob Beezer, Nathann Cohen] #8992: Simon King: Coercion of univariate quotient polynomial rings [Reviewed by Mike Hansen, Travis Scrimshaw] #11453: Taylor Dupuy: residue function for laurent series ring elements [Reviewed by Frédéric Chapoton, Travis Scrimshaw] #11839: Michael Orlitzky: sage.symbolic.expression.Expression.collect has no documentation [Reviewed by Karl-Dieter Crisman, Travis Scrimshaw] #12021: Emil Widmann: Doctest failure in sage_object.pyx when test run as root [Reviewed by Volker Braun] #12113: Yoora Yi Tenen: Add minor clarification about logs with bases other than e [Reviewed by Travis Scrimshaw] #12780: Michael Orlitzky: Be more careful about setting the Maxima 'domain' [Reviewed by Burcin Erocal] #12930: Pierre Cagne: Poset of Alternating sign matrices [Reviewed by Frédéric Chapoton, Anne Schilling] #13181: Burcin Erocal: _limit_latex_ cannot handle direction argument [Reviewed by Karl-Dieter Crisman] #13303: Xavier Caruso: is_unit and __invert__ for Polynomial Quotient Rings [Reviewed by Travis Scrimshaw] #13319: Jean-Pierre Flori: Python 2.7.3.px spkg does not build on Cygwin. [Reviewed by Dmitrii Pasechnik] #13322: Marco Streng: Precision loss when converting between Magma and Sage [Reviewed by Volker Braun] #13325: Jean-Pierre Flori: eclib does not build on Cygwin [Reviewed by John Cremona] #13417: Thomas Feulner, Punarbasu Purkayastha: Improved iteration on finite \ZZ-submodules and vector spaces over finite fields [Reviewed by Punarbasu Purkayastha, Thomas Feulner] #13446: Michael Orlitzky: Revert fix (but not doctests) from #11919 [Reviewed by Burcin Erocal, Karl-Dieter Crisman] #13719: Jean-Pierre Flori: Illegal free in graph_generators [Reviewed by Nathann Cohen] #13723: Thomas Feulner: Moving hamming_weight from sage.coding to sage.modules [Reviewed by Punarbasu Purkayastha, Travis Scrimshaw] #13728: Christian Stump: Implements some standard methods for fields [Reviewed by Frédéric Chapoton] #13731: Nils Bruin, Simon King: Fix libsingular memory management [Reviewed by Nils Bruin] #13737: Volker Braun: fix cython warning in pynac.pyx [Reviewed by Burcin Erocal] #13740: Volker Braun: Upgrade Cython to 0.17.2 [Reviewed by Robert Bradshaw] #13756: Volker Braun: fix developer manual docstrings [Reviewed by Keshav Kini] #13777: Karl-Dieter Crisman: Fix TimeSeries histogram plotting [Reviewed by Punarbasu Purkayastha] #13782: Michael Orlitzky: Dead code cleanup in rings/polynomial/polynomial_modn_dense_ntl.pyx [Reviewed by André Apitzsch] #13784: Nathann Cohen: Move methods from GenericGraph to Graph [Reviewed by David Coudert] #13791: Travis Scrimshaw: Fixes to the conventions doc [Reviewed by Charles Bouillaguet] #13802: Karl-Dieter Crisman: Extra includes needed for letterplace for Cygwin on XP [Reviewed by Alexander Dreyer] #13813: David Coudert: Fix bug in chessboard graphs generator [Reviewed by Nathann Cohen] #13816: Karl-Dieter Crisman: Fix very minor doc issue for generic graphs [Reviewed by Nathann Cohen] Merged in sage-5.6.beta1: #9016: Burcin Erocal: make morphisms hashable [Reviewed by Robert Bradshaw, Travis Scrimshaw] #11366: Travis Scrimshaw: Incorrect documentation for set difference [Reviewed by Julian Rueth] #11763: Volker Braun: Parents for polyhedra [Reviewed by Dmitrii Pasechnik] #11768: Simon King: Get source code for parent/element classes of categories [Reviewed by Volker Braun] #11795: John Palmieri: Easily customize different viewers for PNG, DVI, PDF [Reviewed by Nathann Cohen] #12407: Thomas Rehn: Add the set of PrimitiveGroups [Reviewed by Vincent Delecroix, Volker Braun] #12587: Travis Scrimshaw: simplicial complexes lack hash function [Reviewed by Christian Stump, John Palmieri] #13211: Volker Braun, Jeroen Demeyer: Upgrade GAP to 4.5.7 [Reviewed by Dmitrii Pasechnik] #13375: Thomas Rehn: MIP set_problem_name crashes with GLPK backend if name is too long [Reviewed by Christian Kuper] #13423: Michael Orlitzky, Punarbasu Purkayastha: arrow2d missing 'linestyle' parameter docs [Reviewed by Punarbasu Purkayastha, Karl-Dieter Crisman] #13503: Jernej Azarija, David Coudert: Enhancement of `is_triangle_free' addition of `triangles_count' and a minor change in `spanning_trees_count' [Reviewed by Jernej Azarija] #13516: Kevin Halasz: prime_powers doesn't work with start very well [Reviewed by Dmitrii Pasechnik, Punarbasu Purkayastha, Karl-Dieter Crisman] #13518: Christian Kuper: Additions for sensitivity analysis in glpk_backend [Reviewed by Nathann Cohen] #13625: Punarbasu Purkayastha: matrix_plot and title don't mix well (yet) [Reviewed by Karl-Dieter Crisman] #13708: Noud Aldenhoven, Burcin Erocal: Get assumptions by variables [Reviewed by Burcin Erocal, Noud Aldenhoven] #13727: Christian Stump: Minor improvements for dict_addition [Reviewed by Frédéric Chapoton] #13734: Christian Stump: Implementation of latex method for ElementWrapper [Reviewed by Nicolas M. Thiéry] #13742: Nathann Cohen: No Permutation should be created that its method cannot handle [Reviewed by Dmitrii Pasechnik] #13755: Jean-Pierre Flori: Let LinBox build with MPIR > 2.5.0 [Reviewed by John Palmieri, Volker Braun] #13760: Guillaume Moroz: Wrong basic interval arithmetic in PolynomialRing [Reviewed by Paul Zimmermann] #13778: Vincent Delecroix: lazy list [Reviewed by Travis Scrimshaw] #13785: Nathann Cohen: Export a graph to a dictionary [Reviewed by David Coudert] #13789: Xavier Caruso: Opposite of sparse polynomials [Reviewed by Charles Bouillaguet] #13796: John Palmieri: fix small bug in Steenrod algebra multiplication [Reviewed by André Apitzsch] #13829: Martin Albrecht: sage.misc.messaging [Reviewed by Volker Braun] #13852: John Palmieri: fix "SEVERE" warning during docbuilding for matrix/benchmark.py [Reviewed by Jeroen Demeyer] Merged in sage-5.6.beta2: #3955: Andrzej Giniewicz: make find_minimum_on_interval use _fast_float_ [Reviewed by Timo Kluck] #4411: Marshall Hampton: phc breaks on one-variable problems [Reviewed by Volker Braun] #11523: Christian Stump: Implementation of Cohen-Macaulay test for simplicial complexes [Reviewed by Travis Scrimshaw] #12518: Vincent Delecroix: Enumerated set from iterator [Reviewed by Travis Scrimshaw] #13032: R. Andrew Ohana: Add ccache as an optional spkg [Reviewed by Punarbasu Purkayastha] #13074: Andrew Mathas: Implementation of TableauTuples [Reviewed by Travis Scrimshaw] #13119: Mike Zabrocki: ._apply_module_morphism() in combinat/free_module.py doesn't handle zero element properly [Reviewed by Travis Scrimshaw] #13366: Kevin Halasz: Add Semidihedral Groups and Split Metacyclic Groups as Permutation Groups [Reviewed by Volker Braun] #13403: Travis Scrimshaw: Implementation of bijection between KirillovReshetikhinCrystals and KirillovReshetikhinTableaux [Reviewed by Anne Schilling] #13638: Volker Braun: fix adjacency of rays [Reviewed by Dmitrii Pasechnik] #13669: Volker Braun: sage -gdb ImportError [Reviewed by Simon King] #13691: Nathann Cohen: Graph.has_homomorphism_to [Reviewed by Volker Braun] #13725: John Palmieri: sum complexes: another example of simplicial complexes [Reviewed by Travis Scrimshaw] #13739: Burcin Erocal: more informative error message from multiplication of symbolic expressions [Reviewed by Nils Bruin, Karl-Dieter Crisman, Michael Orlitzky] #13747: Nathann Cohen: Change default behaviour of Poset to facade = True [Reviewed by Christian Kuper] #13750: Nathann Cohen: List of functions in the Permutations file [Reviewed by Dmitrii Pasechnik] #13762: Chris Berg, Mike Zabrocki: Implement k-bounded quotient space [Reviewed by Anne Schilling] #13775: Ivan Andrus, Nathann Cohen: Bug in the Graph constructor in the presence of loops AND multiple edges [Reviewed by Ivan Andrus, Nathann Cohen] #13799: Jean-Pierre Flori: cvxopt needs to link against gmp/mpir on 32-bit Windows XP Cygwin [Reviewed by Karl-Dieter Crisman] #13800: Christian Nassau: sign error in Steenrod algebra multiplication [Reviewed by John Palmieri] #13809: Nathann Cohen: A constructor for folded cube graphs [Reviewed by David Coudert] #13815: André Apitzsch: Fix type + code cleanup in numerical.optimize [Reviewed by Volker Braun] #13832: Volker Braun: Upgrade Cython to 0.17.3 [Reviewed by Jean-Pierre Flori] #13845: Martin Albrecht: BooleanPolynomialRing.random_element chokes on terms parameter of type rational [Reviewed by Alexander Dreyer] #13859: Steven Trogdon: Failure in gp pexpect interface when $COLUMNS is exported to Sage [Reviewed by Jeroen Demeyer, Steven Trogdon] #13860: Dmitrii Pasechnik: Maxima 5.26.0 update to make it install with also the new ASDF (ECL 12.x) [Reviewed by Leif Leonhardy] #13862: Nathann Cohen: Split graph_generators into several files [Reviewed by David Coudert] #13865: Volker Braun: Document that SAGE_DEBUG is three-state [Reviewed by Jeroen Demeyer] #13873: Jason Grout: Color and get_cmap should accept unicode [Reviewed by Keshav Kini] Merged in sage-5.6.beta3: #5402: Charles Bouillaguet: Sparse determinants are slow [Reviewed by Karl-Dieter Crisman] #10352: William Stein, Nils Bruin, Volker Braun: upgrade ZODB to version 3.10.5 [Reviewed by Jeroen Demeyer] #10538: Christian Stump, Gregg Musiker: Implementation of the class ClusterQuiver [Reviewed by Dylan Rupel] #11635: Jean-Pierre Flori: Ensure that libraries link to the shared version of NTL by default [Reviewed by Karl-Dieter Crisman] #12193: Volker Braun: Dimension of Polyhedron is not well defined [Reviewed by David Loeffler] #12907: André Apitzsch: Replace some deprecated python functions in sage/calculus [Reviewed by Karl-Dieter Crisman] #13203: Frédéric Chapoton: Promotion on Tableaux should force its argument to be an Integer. [Reviewed by Nicolas M. Thiéry] #13460: Travis Scrimshaw: Type D_n spinor bijection [Reviewed by Anne Schilling] #13748: Jeroen Demeyer: Fix sig_block() doctest [Reviewed by Volker Braun] #13806: Jean-Pierre Flori: Building complex_double.pyx fails on Cygwin [Reviewed by Karl-Dieter Crisman] #13821: Punarbasu Purkayastha: Change sage.combinat.combinat.combinations() to use Combinations [Reviewed by Travis Scrimshaw] #13854: Thomas Feulner: Fix of _matrix_times_vector_ [Reviewed by Travis Scrimshaw] #13868: Volker Braun: Deal with hooked tp_* functions when using a debug build of Python [Reviewed by Jean-Pierre Flori] #13880: Volker Braun: Respect ulimit -v for GAP memory pool size [Reviewed by Dmitrii Pasechnik] #13881: Volker Braun: Enhanced debugging: cygdb and better backtraces [Reviewed by Jeroen Demeyer] #13882: Simon King: Deal with a trivial case in dlx_solver [Reviewed by François Bissey] #13883: Alexander Dreyer: Fix an assertion in polybori [Reviewed by Jean-Pierre Flori] #13887: Jeroen Demeyer: Use a temporary directory for inline_fortran [Reviewed by Volker Braun] #13893: Jason Grout: stabilizer doesn't work with custom domain [Reviewed by Mike Hansen] #13896: Robert Bradshaw: Fix cython's gc_track and gc_untrack [Reviewed by Jeroen Demeyer] #13899: Jeroen Demeyer: Don't use TAB characters for indentation [Reviewed by Leif Leonhardy, Karl-Dieter Crisman] #13900: Alexander Dreyer: Remove unused _change_ordering from `BooleanPolynomialRing` [Reviewed by Martin Albrecht] #13902: Jeroen Demeyer: Slowdown for PARI integer determinant [Reviewed by Volker Braun] #13903: John Perry: polynomial .reduce returns type int over p-adic field [Reviewed by Karl-Dieter Crisman] #13909: Marshall Hampton: Add Kirkman's icosahedron to polytope library [Reviewed by Volker Braun] #13910: Karl-Dieter Crisman: Remove databases/conv.py [Reviewed by André Apitzsch] #13911: Anne Schilling, Mike Zabrocki: Updated doc tests for k-Schur function and affine Schubert calculus book [Reviewed by Mike Zabrocki, Anne Schilling] #13920: Jeroen Demeyer: Non-ASCII character in smallgraphs.py [Reviewed by Nathann Cohen] #13924: Jeroen Demeyer: A few more long times [Reviewed by Volker Braun] Merged in sage-5.6.rc0: #7560: Jan Medlock: len(t_span) > 2 case creates len(t_span) - 1 solutions [Reviewed by Timo Kluck] #9543: Peter Jeremy, Jean-Pierre Flori: Enable cephes on FreeBSD and disable it on Cygwin [Reviewed by Stephen Montgomery-Smith, Karl-Dieter Crisman] #12792: Charles Bouillaguet: polybori / gb computation / set error [Reviewed by Alexander Dreyer] #13804: Jean-Pierre Flori: libfplll fails to build in parallel on Cygwin [Reviewed by Karl-Dieter Crisman] #13808: David Coudert: Gromov hyperbolicity of graphs [Reviewed by Nathann Cohen] #13851: Martin Albrecht: Add SAT Solver Interface to Reference Manual [Reviewed by Nathann Cohen, John Palmieri, Nicolas M. Thiéry] #13875: David Coudert: Test memory allocation in distances_all_pairs [Reviewed by Nathann Cohen] #13921: Jeroen Demeyer: Make the GP executable work with SAGE_DEBUG on Darwin [Reviewed by Volker Braun] #13926: Jeroen Demeyer: Undo #13014 [Reviewed by Burcin Erocal, Punarbasu Purkayastha] #13927: Jeroen Demeyer: Disable startuptime test [Reviewed by Volker Braun] #13930: Nils Bruin: remove bad is_subcategory implementation [Reviewed by Simon King] #13936: Nathann Cohen: Add encoding to smallgraphs.py [Reviewed by Jeroen Demeyer] #13937: Jeroen Demeyer: Properly detect GCC-4.3 [Reviewed by John Cremona] #13938: Jeroen Demeyer: Don't set CCACHE_DIR [Reviewed by R. Andrew Ohana, Punarbasu Purkayastha] Merged in sage-5.6.rc1: #13561: Keshav Kini, Jeroen Demeyer: Supply nice error message when starting $SAGE_ROOT/sage without compiling Sage first [Reviewed by Jeroen Demeyer, Punarbasu Purkayastha] #13945: John Palmieri: testcflags.sh leaves a directory in spkg/build [Reviewed by Jeroen Demeyer] #13952: Punarbasu Purkayastha: Add documentation about importing cython function from cells [Reviewed by André Apitzsch] #13959: Volker Braun: Parse wonky "top" output on OSX PPC [Reviewed by Karl-Dieter Crisman] December 25, 2012 ----------------- Sage 5.5 was released on 21 December 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 59 people contributed to this release. Of those, 4 made their first contribution to Sage: - Alexander Dreyer - Aly Deines - Andrew Mathas - André Apitzsch - Anne Schilling - Ben Hutz [first contribution] - Benjamin Jones - Burcin Erocal - Charles Bouillaguet - Chris Berg - Christian Stump - Daniel Bump - David Coudert - David Eklund - David Roe - Dmitrii Pasechnik - Franco Saliola - François Bissey - Frédéric Chapoton - Hugh Thomas - Jan Groenewald - Jason Bandlow - Jason Grout - Jean-Pierre Flori - Jeroen Demeyer - John Cremona - John Palmieri - Joris Vankerschaver - Julian Rueth - Julien Puydt - Karl-Dieter Crisman - Kevin Halasz - Luis Serrano [first contribution] - Marco Streng - Marshall Hampton - Martin Albrecht - Mathieu Guay-Paquet - Michael Brickenstein - Mike Hansen - Mike Zabrocki - Moritz Minzlaff - Nathann Cohen - Nicolas M. Thiéry - Nils Bruin - Philipp Jovanovic [first contribution] - Punarbasu Purkayastha - R. Andrew Ohana - Risan [first contribution] - Robert Bradshaw - Sarah Chisholm - Sebastian Luther - Simon King - Sébastien Labbé - Timo Jolivet - Timo Kluck - Travis Scrimshaw - Volker Braun - William Stein - Xavier Caruso * Release manager: Jeroen Demeyer. * We closed 92 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.5/tickets.html Closed tickets: #11708: maxima doesn't build on Linux ppc64 (silius on skynet) [Reviewed by Jeroen Demeyer] #13210: ATLAS: flush output before os.system() [Reviewed by Jeroen Demeyer] #13333: Copy libpari.dll.a on Cygwin [Reviewed by Dmitrii Pasechnik, Jean-Pierre Flori] #13408: atlas-3.8.4 package does not compile on rhel 5 systems, upgrade to atlas-3.10.0 [Reviewed by Karl-Dieter Crisman] #13450: Fix refcounting of libsingular rings [Reviewed by Nils Bruin] Merged in sage-5.5.beta0: #715: Simon King, Jean-Pierre Flori: Parents probably not reclaimed due to too much caching [Reviewed by Jean-Pierre Flori, Simon King, Nils Bruin] #9265: Jason Bandlow, Andrew Mathas: Remove `CombinatorialClass` from sage.combinat.tableau [Reviewed by Andrew Mathas, Anne Schilling] #10527: Christian Stump: Implementation of quiver mutation type [Reviewed by Hugh Thomas] #11521: Simon King, Nils Bruin: Use weak references to cache homsets [Reviewed by Jean-Pierre Flori, Nils Bruin, Simon King] #12995: Moritz Minzlaff: A first step towards linear systems of hypersurfaces in Sage [Reviewed by David Eklund] #13188: Nathann Cohen: Boring paperwork in the graph/ files [Reviewed by Travis Scrimshaw] #13244: John Palmieri: make some simplicial complexes faster [Reviewed by Travis Scrimshaw] #13306: David Coudert: Generators for chessboard graphs: King, Queen, Knight, Bishop, Rooks [Reviewed by Sebastian Luther, Nathann Cohen] #13406: Nicolas M. Thiéry: Optimize CombinatorialFreeModule.Element._vector_ [Reviewed by Mathieu Guay-Paquet, Franco Saliola,] #13411: Frédéric Chapoton: implement the Holt Graph [Reviewed by Nathann Cohen] #13461: Daniel Bump: Another WeylCharacterRing speedup [Reviewed by Anne Schilling] #13519: Joris Vankerschaver: Spline is not recomputed when interpolation points change [Reviewed by Travis Scrimshaw] #13534: Jean-Pierre Flori, Jeroen Demeyer: Upgrade to PARI-2.5.3 [Reviewed by Dmitrii Pasechnik, François Bissey] #13562: Robert Bradshaw: lazily import graph_generators [Reviewed by David Coudert] #13575: Philipp Jovanovic: Add flexibility when creating exclusion-clauses using 'solve' from boolean_polynomials.py [Reviewed by Martin Albrecht] #13586: Burcin Erocal: BuiltinFunction expects to be instantiated only once [Reviewed by Karl-Dieter Crisman] #13590: John Palmieri: Fix random simplicial complexes [Reviewed by Travis Scrimshaw] #13592: Julian Rueth: padics should not be iterable [Reviewed by David Roe] Merged in sage-5.5.beta1: #4453: William Stein: elliptic curves -- heegner_index command gives nonsense when rank > 1 [Reviewed by John Cremona, Robert Bradshaw] #6822: John Palmieri: "empty" .spkg files in binary builds confusing [Reviewed by Jeroen Demeyer] #9191: Karl-Dieter Crisman, Jeroen Demeyer: Running .spyx files from the command line doesn't work anymore [Reviewed by Jeroen Demeyer, Karl-Dieter Crisman] #11353: David Coudert: bitset complement [Reviewed by Nathann Cohen] #11395: Marshall Hampton, François Bissey: Upgrade Gfan to latest release (version 0.5) [Reviewed by François Bissey, Volker Braun] #11403: Jeroen Demeyer, David Roe: NTL error while inverting q-adic number with fixed modulus precision [Reviewed by Julian Rueth] #12341: R. Andrew Ohana: Empty (full) cremona database in Sage 4.8 causes tests to fail [Reviewed by John Cremona] #12513: Robert Bradshaw: Slow CDF fast_callable powers [Reviewed by Timo Kluck, Jeroen Demeyer] #12584: David Roe: coercing large numbers into elements of GF fails [Reviewed by Travis Scrimshaw] #12586: Julien Puydt: [ARM] Maxima has a strange numerical precision issue [Reviewed by Dmitrii Pasechnik] #12905: Nathann Cohen: Memory leaks with Cliquer [Reviewed by David Coudert] #12943: Hugh Thomas: Tableau_class.__div__, Partition_class.__div__ are checking domination when they should check inclusion [Reviewed by Mike Hansen, Andrew Mathas] #13072: Andrew Mathas: Implementation of PartitionTuple + some minor fixes to partition.py [Reviewed by Travis Scrimshaw] #13082: Robert Bradshaw: Powering rings to a 2-tuple should create matrix spaces. [Reviewed by Jason Grout] #13147: David Roe, Mike Hansen: Delay the evaluation of SAGE_TMP in order to facilitate forking in doctesting [Reviewed by John Palmieri] #13159: Simon King: Cache the number of arguments of a cached method [Reviewed by David Roe] #13365: Kevin Halasz: Add Semidirect Product Method for Permutation Groups [Reviewed by Benjamin Jones] #13412: Simon King: PowerSeriesRing should call Ring.__init__ [Reviewed by Travis Scrimshaw] #13501: Nicolas M. Thiéry, Simon King: Fix two bugs in sage.misc.c3's implementation of the algorithm C3 [Reviewed by Simon King] #13506: Chris Berg: Monomial basis of NCSF [Reviewed by Luis Serrano, Mike Zabrocki] #13520: Joris Vankerschaver: Derivative/integral of cubic splines in sage/gsl/interpolation.pyx [Reviewed by Travis Scrimshaw] #13563: Anne Schilling: KR crystals for spinors in type D [Reviewed by Daniel Bump, Nicolas M. Thiéry] #13574: Jeroen Demeyer: sage-spkg: check much earlier whether package is already installed [Reviewed by John Palmieri] #13578: David Coudert: Generator for Ringed-Tree graphs [Reviewed by Nathann Cohen] #13599: Nathann Cohen: Bugfix in is_cartesian_product [Reviewed by David Coudert] #13634: Travis Scrimshaw: Fix to output of scientific notation for real interval field [Reviewed by Robert Bradshaw] #13639: Jeroen Demeyer: Inverting 0 mod 1 [Reviewed by Robert Bradshaw] #13643: Jason Grout: default norm for RDF/CDF matrices is inconsistent with other types of matrices [Reviewed by Punarbasu Purkayastha] #13646: Nathann Cohen, Volker Braun: Bug in p.add_constraint (when input is True/False) [Reviewed by Dmitrii Pasechnik] #13653: Volker Braun: Missing Exception type in element.pyx [Reviewed by Robert Bradshaw] Merged in sage-5.5.beta2: #7797: Simon King, Michael Brickenstein, Burcin Erocal: Full interface to letterplace from singular [Reviewed by Alexander Dreyer] #11476: Andrew Mathas: PartitionTuples.cardinality has problems [Reviewed by Travis Scrimshaw] #12533: Risan: arbitrary precision LP solver backend [Reviewed by David Coudert, Nathann Cohen, Dmitrii Pasechnik] #12565: R. Andrew Ohana: E = EllipticCurve('10a1') gives a stupid traceback (rather than a smart one) [Reviewed by John Cremona] #13143: John Palmieri: Use MathJax by default when building docs from Makefile [Reviewed by Dmitrii Pasechnik] #13180: Martin Albrecht: Compare elements of finite fields somehow consistently [Reviewed by André Apitzsch] #13419: Frédéric Chapoton: 100% doc for quartic curves [Reviewed by André Apitzsch] #13530: Joris Vankerschaver: Hide sage/gsl/interpolation/Spline internals [Reviewed by Travis Scrimshaw] #13550: Mike Zabrocki: improvements and additions to dyck_words.py [Reviewed by Christian Stump] #13572: Chris Berg: Implement the immaculate basis of NCSF [Reviewed by Luis Serrano, Mike Zabrocki] #13635: Nathann Cohen: sage.isgci.update_db is broken [Reviewed by David Coudert] #13640: Xavier Caruso: q-numbers coutings flags stable under a nilpotent endomorphism [Reviewed by Frédéric Chapoton] #13641: Xavier Caruso: Short representation of morphisms [Reviewed by Travis Scrimshaw] #13663: Punarbasu Purkayastha: Implement __len__ in LinearCode [Reviewed by Dmitrii Pasechnik] #13665: David Coudert: New implementation of the blocks_and_cut_vertices method [Reviewed by Nathann Cohen] #13670: Charles Bouillaguet: Inversion in polynomial quotient rings could give clearer error message when element is non-invertible [Reviewed by Marco Streng] #13671: Charles Bouillaguet: p.lift(...) results are non-deterministic and incoherent for multivariate polynomials [Reviewed by Marco Streng] #13675: Charles Bouillaguet: multivariate polynomials lack the inverse_mod(...) method [Reviewed by Marco Streng] #13676: Sébastien Labbé: Add _latex_ method for WordMorphism [Reviewed by Timo Jolivet] #13692: Nils Bruin: factor_trial_division returns Python longs as exponents [Reviewed by Dmitrii Pasechnik] #13704: Punarbasu Purkayastha: Fix _div_ in multivariate rings [Reviewed by Ben Hutz] Merged in sage-5.5.rc0: #12091: Volker Braun: chained inequalities bug in add_constraint to MixedIntegerLinearProgram [Reviewed by Dmitrii Pasechnik] #13075: Nathann Cohen: Toroidal6RegularGrid2dGraph [Reviewed by David Coudert] #13226: John Palmieri: pseudomanifold test for simplicial complexes [Reviewed by Volker Braun] #13513: Sarah Chisholm: Has standard involution function for algebras. [Reviewed by Aly Deines] #13573: Chris Berg: Implement the dual immaculate basis of QSym [Reviewed by Luis Serrano, Mike Zabrocki] #13650: Volker Braun, Dmitrii Pasechnik: Base rings for MIP backends [Reviewed by Dmitrii Pasechnik, Volker Braun] #13664: Nathann Cohen: Another bug in add_edge [Reviewed by David Coudert] #13668: Sébastien Labbé: MemoryError raised by WordMorphism.fixed_points method [Reviewed by Timo Jolivet] #13677: Sébastien Labbé: Improve __repr__ and __str__ methods of WordMorphism [Reviewed by Timo Jolivet] #13699: Nathann Cohen, David Coudert: Another bug in graph products.... [Reviewed by David Coudert] Merged in sage-5.5.rc1: #13616: David Roe: SIGABRT in unit_part() for padic extension elements [Reviewed by Volker Braun] #13702: Jan Groenewald: Fix path in SAGE_ROOT/spkg/README.txt [Reviewed by Karl-Dieter Crisman] #13741: Simon King: Proper deallocation of the (unique) pari instance [Reviewed by Volker Braun] #13745: Jean-Pierre Flori: Typo in lcalc.py [Reviewed by Volker Braun] #13746: Jean-Pierre Flori, Simon King: Do not delete a borrowed reference to reduction strategies in pbori [Reviewed by Alexander Dreyer] #13794: Jeroen Demeyer, John Palmieri: sage -n is broken in 5.5rc0 [Reviewed by Punarbasu Purkayastha] #13797: Volker Braun: LinearFunction.__hash__ overflow [Reviewed by Dmitrii Pasechnik] #13807: John Palmieri: Fix remaining temporary filename issues (like in animate.py) [Reviewed by Karl-Dieter Crisman] November 22, 2012 ----------------- Sage 5.4.1 was released on 15 November 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 15 people contributed to this release. Of those, 2 made their first contribution to Sage: - Aly Deines - Benjamin Hutz [first contribution] - Burcin Erocal - David Loeffler - Dmitrii Pasechnik - Jeroen Demeyer - John Palmieri - Karl-Dieter Crisman - Kenneth Smith - Paul Zimmermann - Punarbasu Purkayastha - Sarah Chisholm - Sebastien Gouezel [first contribution] - Travis Scrimshaw - Volker Braun * Release manager: Jeroen Demeyer. * We closed 13 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.4.1/tickets.html Closed tickets: #13309: Build Sage on OS X Mountain Lion [Reviewed by Dmitrii Pasechnik] Merged in sage-5.4.1.rc0: #6367: Karl-Dieter Crisman, Kenneth Smith: polygon2d -- several issues: typo in docs, shouldn't have been renamed [Reviewed by Volker Braun] #10803: Paul Zimmermann: critical bug in real_roots [Reviewed by Jeroen Demeyer] #12753: Benjamin Hutz: is_PrimeField import error [Reviewed by David Loeffler] #12859: Aly Deines: quaternion algebra 'ramified at one prime' [Reviewed by Sarah Chisholm] #13382: Dmitrii Pasechnik: build docs for SymmetricGroupRepresentation(s) [Reviewed by Volker Braun, Travis Scrimshaw] #13533: Jeroen Demeyer: Remove "optional - gcc" from doctests [Reviewed by Karl-Dieter Crisman, John Palmieri] #13541: John Palmieri: update scipy to 0.11.0 [Reviewed by Dmitrii Pasechnik] #13598: John Palmieri: 'x' should be defined when using 'sage -c' [Reviewed by Punarbasu Purkayastha] #13632: Sebastien Gouezel: Fix latex display of arguments of symbolic functions [Reviewed by Burcin Erocal] Merged in sage-5.4.1.rc1: #13407: Jeroen Demeyer: Move sage-make_relative to sage-location [Reviewed by Dmitrii Pasechnik] #13452: Jeroen Demeyer: Refactor sage-location [Reviewed by Dmitrii Pasechnik] #13689: Jeroen Demeyer: Fix upgrading from relocated Sage with GCC [Reviewed by John Palmieri] November 11, 2012 ----------------- Sage 5.4 was released on 08 November 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 82 people contributed to this release. Of those, 12 made their first contribution to Sage: - Alejandro Morales [first contribution] - Alex Csar [first contribution] - Alexander Dreyer - Aly Deines - Andrew Mathas - Andrey Novoseltsev - André Apitzsch - Anne Schilling - Armin Straub - Benjamin Jones - Bjarke Hammersholt Roune - Burcin Erocal - Charles Bouillaguet - Chris Berg - Dan Bump - Dan Drake - Daniel Bump - David Coudert - David Kirkby - David Roe - Davide Cervone [first contribution] - Dmitrii Pasechnik - Francis Clarke - Franco Saliola - François Bissey - Frédéric Chapoton - Hugh Thomas - Jason Bandlow - Jason Grout - Jean-Philippe Labbé [first contribution] - Jean-Pierre Flori - Jeroen Demeyer - John Cremona - John Palmieri - John Perry - Jonathan Gutow - Julian Rueth - Karl-Dieter Crisman - Kelvin Li - Keshav Kini - Keshav kini [first contribution] - Kevin Halasz - Kiran Kedlaya - Leif Leonhardy - Luis Felipe Tabera Alonso - Luiz Aquino [first contribution] - Maarten Derickx - Marco Streng - Mariah Lenox - Marshall Hampton - Martin Albrecht - Michael Welsh [first contribution] - Mike Hansen - Mike Zabrocki - Nathan Carter - Nathann Cohen - Nicolas M. Thiéry - Nicolas Thiery - Nils Bruin - Paul Zimmermann - Paul-Olivier Dehaye - Paulo César Pereira de Andrade - Punarbasu Purkayastha - R. Andrew Ohana - Rob Beezer - Robert Bradshaw - Robert Harron - Samuel Lelievre [first contribution] - Sarah Chisholm [first contribution] - Sebastian Luther [first contribution] - Simon King - Stefano Leucci [first contribution] - Stepan Starosta - Stephen Montgomery-Smith - Steven Trogdon - Thomas Feulner [first contribution] - Tim Dumol - Titus Nicolae - Travis Scrimshaw - Valentin Féray - Volker Braun - William Stein * Release manager: Jeroen Demeyer. * We closed 127 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.4/tickets.html Closed tickets: #9238: J. Gutow's update to Jmol in the notebook... [Reviewed by Jason Grout, Karl-Dieter Crisman, William Stein, Jonathan Gutow] #9428: Internationalize the Sage Notebook [Reviewed by Keshav Kini, Luiz Aquino, Dan Drake, Tim Dumol] #11471: Add i18n capabilities to the Flask notebook [Reviewed by Keshav kini, Luiz Aquino, Dan Drake, Tim Dumol, Mike Hansen] #11789: compile python with ssl-support if possible [Reviewed by Jeroen Demeyer] #11805: Update optional MPC spkg to version 0.9 [Reviewed by Jean-Pierre Flori] #12089: Dmitrii Pasechnik, Karl-Dieter Crisman, Jean-Pierre Flori: Singular does not build on Cygwin - static libs problem [Reviewed by Karl-Dieter Crisman, Dmitrii Pasechnik, Jean-Pierre Flori] #12846: Multivariate Factorisation can be randomly slow (over extension fields) [Reviewed by Jeroen Demeyer] #12918: segmentation fault with multivariate polynomial factorization [Reviewed by Jeroen Demeyer] #12928: critical bug in multivariate polynomial factorization over GF(2) [Reviewed by Jeroen Demeyer] #13129: libSingular segmentation fault in factor [Reviewed by Jeroen Demeyer] #13344: Jean-Pierre Flori, Alexander Dreyer, Jeroen Demeyer: on CYGWIN, Singular LIB files get copied to SAGELOCAL/lib [Reviewed by Dmitrii Pasechnik, Jean-Pierre Flori] #13384: Keshav Kini: pyOpenSSL SPKG [Reviewed by John Palmieri] #13410: Robert Bradshaw: Patchbot timeouts [Reviewed by Volker Braun] #6003: Additions to Cholesky decomposition [Reviewed by Rob Beezer] #9511: Upgrade Givaro to version 3.7.0 [Reviewed by Volker Braun] #10153: Canonical generator matrices for linear codes and their automorphism groups [Reviewed by Thomas Feulner] #11718: Upgrade LinBox to version 1.1.7 [Reviewed by Volker Braun, Martin Albrecht] #13340: log scale plot fails if xmin > xmax [Reviewed by Punarbasu Purkayastha] #4319: Update Italian tutorial for #4285 [Reviewed by Jeroen Demeyer] #7832: singular-3-1-0-4-20090818.p2 - fix compilation on FreeBSD [Reviewed by Stephen Montgomery-Smith] #13499: Volker Braun: Update TOPCOM to 0.17.4 [Reviewed by Marshall Hampton] #9965: Make SYMPOW not write to files under global Sage installations [Reviewed by Jeroen Demeyer] #3302: python_gnutls fails to upgrade on OSX in case Sage was moved [Reviewed by Jeroen Demeyer] #4797: Run sage -ba instead of sage -b after upgrading Cython [Reviewed by Jeroen Demeyer] #7511: gnutls-2.2.1 fails to build on HP-UX [Reviewed by Jeroen Demeyer] #7542: Security issues in gnutls-2.2.1 [Reviewed by Jeroen Demeyer] #8437: wrong unix rights/permissions of some files after make dist [Reviewed by Jeroen Demeyer] #9308: Add an spkg-check file for GnuTLS [Reviewed by David Kirkby, Jeroen Demeyer] #9974: The current (rather old) version of GnuTLS fails to install on AIX 5.3 [Reviewed by Jeroen Demeyer] #9975: Update GnuTLS and clean up the package [Reviewed by Mariah Lenox, Jeroen Demeyer] #10624: Slashes disappear in docstrings [Reviewed by John Palmieri] #12331: updating an spkg may render Sage non-relocatable [Reviewed by Jeroen Demeyer] #12785: update the faq: no need for gfortran... [Reviewed by Jeroen Demeyer] #13545: Can't create a symbolic variable named 'lambda' [Reviewed by Nils Bruin, Burcin Erocal] #13551: Autotools spkg does not build correctly on systems without autotools installed [Reviewed by Jeroen Demeyer] #12707: Keshav Kini, John Palmieri, Jeroen Demeyer: Update the git spkg [Reviewed by Leif Leonhardy, Volker Braun] #13150: Jeroen Demeyer: Create an optional GCC-4.7.2 package [Reviewed by Volker Braun] #13292: Jeroen Demeyer: Bad symlink SAGE_DATA/graphs/graphs.db in binary distributions [Reviewed by Leif Leonhardy] #13295: Simon King: p_group_cohomology 2.1.3 [Reviewed by John Palmieri] #13302: Matrix constructor does not return over padic field [Reviewed by Julian Rueth] #13602: partition distinct parts max part error [Reviewed by Alejandro Morales] Merged in sage-5.4.beta0: #5457: Mike Zabrocki, Anne Schilling, Jason Bandlow: Refactor symmetric functions and k-bounded subspace [Reviewed by Dan Bump, Nicolas M. Thiéry, Jeroen Demeyer] #5489: Mike Hansen, Bjarke Hammersholt Roune: Add an interface for 4ti2 to Sage [Reviewed by Martin Albrecht, John Palmieri, Marshall Hampton, Frédéric Chapoton] #9774: Rob Beezer, Davide Cervone, John Palmieri, Jason Grout, Nathan Carter: Use MathJax instead of jsMath [Reviewed by Jason Grout, John Palmieri, Punarbasu Purkayastha, Keshav Kini] #11021: Leif Leonhardy, Kelvin Li, Jeroen Demeyer: Fix install_package() library function [Reviewed by Kelvin Li, Leif Leonhardy, John Palmieri] #11305: Travis Scrimshaw: Bijection between Rigged Configurations and Crystal Paths [Reviewed by Anne Schilling] #11440: Paul-Olivier Dehaye: compute the dimension of partition [Reviewed by Frédéric Chapoton] #11913: John Palmieri: Notebook hang in ?? source display Trackback [Reviewed by Keshav Kini] #12299: Jonathan Gutow: Upgrade Jmol to 12.3.27, Advance Jmol Interactive Features in Flask Notebook [Reviewed by Karl-Dieter Crisman, Steven Trogdon, Punarbasu Purkayastha, John Palmieri, Dan Drake] #12606: Jeroen Demeyer: Fix sage --info [Reviewed by John Palmieri] #12946: Mike Hansen: Bug in Compositions [Reviewed by Andrew Mathas] #13121: Keshav Kini: Upgrade sagenb to 0.10.x [Reviewed by John Palmieri, Jonathan Gutow] #13157: Jeroen Demeyer: inline_fortran is STILL broken on OS X [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #13231: Alex Csar: Check if a lattice is atomic [Reviewed by Frédéric Chapoton] #13237: Jeroen Demeyer, Alexander Dreyer, Dmitrii Pasechnik, Karl-Dieter Crisman, Jean-Pierre Flori: Upgrade Singular [Reviewed by Alexander Dreyer, François Bissey] #13253: Maarten Derickx: galois_action on cusps has a bug and incorrect documentation [Reviewed by Marco Streng] #13259: Andrew Mathas: Correcting implementation of "negative" quantum integers [Reviewed by Armin Straub, Nicolas Thiery] #13294: Stefano Leucci: Add test for not necessarily induced subgraphs to Graph.is_subgraph() method [Reviewed by David Coudert] #13314: Paul Zimmermann, Jeroen Demeyer: segmentation fault with roots over ComplexField [Reviewed by John Cremona] #13385: John Palmieri, Keshav Kini: Remove OpenSSL dependency from Sage [Reviewed by Keshav Kini, John Palmieri] #13389: Keshav Kini: Minor fix to LiE optional SPKG [Reviewed by John Palmieri] #13390: Stepan Starosta: Non Negative Integers: fix contains method [Reviewed by Mike Hansen] Merged in sage-5.4.beta1: #6654: Valentin Féray: New features in group algebra category [Reviewed by Frédéric Chapoton] #8899: Jason Bandlow, Chris Berg, Franco Saliola, Nicolas M. Thiéry: Implement non commutative symmetric functions [Reviewed by Mike Zabrocki, Franco Saliola, Mike Hansen] #9906: Leif Leonhardy, Jeroen Demeyer: Move the RPy package outside of the R package [Reviewed by Karl-Dieter Crisman, John Palmieri] #12883: Paulo César Pereira de Andrade, Martin Albrecht: Update LinBox to most recent upstream release [Reviewed by Volker Braun, Jeroen Demeyer] #12972: John Cremona: Fix small bug in elliptic curve saturation [Reviewed by Volker Braun] #12994: R. Andrew Ohana: Serialization of setuptools targets in spkg/standard/deps [Reviewed by Jeroen Demeyer] #13145: David Roe: Sage's noncommutative rings don't always increment a refcount [Reviewed by Martin Albrecht] #13164: Paulo César Pereira de Andrade, Martin Albrecht, Jean-Pierre Flori: Update Givaro to 3.7.1 [Reviewed by Volker Braun] #13284: Alexander Dreyer: Some conversion between BooleanPolynomialRing and QQ[.....] are missing [Reviewed by Charles Bouillaguet] #13298: John Cremona: Update Cremona's table of elliptic curves to 270000 [Reviewed by R. Andrew Ohana] #13327: Andrey Novoseltsev: Allow conversion of strings to iterated polynomial rings [Reviewed by Frédéric Chapoton] #13391: Daniel Bump: WeylCharacterRing improvement [Reviewed by Anne Schilling] #13395: Jeroen Demeyer: Fix upgrading with GCC [Reviewed by John Palmieri] #13404: Nicolas M. Thiéry, Mike Zabrocki: Improved printing for symmetric function bases and misc refactoring [Reviewed by Anne Schilling] #13416: Jeroen Demeyer: Fix GAP dependencies [Reviewed by Volker Braun] #13427: David Kirkby: Numerical noise causing sage/numerical/optimize.py to fail on SPARC [Reviewed by Volker Braun] #13428: Jeroen Demeyer: Race condition in R installation [Reviewed by John Palmieri] Merged in sage-5.4.beta2: #8908: Jean-Philippe Labbé: Add the Young subgroup method to symmetric groups [Reviewed by Mike Hansen, Frédéric Chapoton] #11442: Paul-Olivier Dehaye: Computes the Plancherel measure of an individual partition [Reviewed by Frédéric Chapoton] #13065: Francis Clarke: simon_two_descent not working [Reviewed by John Cremona] #13107: Titus Nicolae, Burcin Erocal: python long division causing infinite loop [Reviewed by Burcin Erocal, Jean-Pierre Flori] #13123: R. Andrew Ohana, Jeroen Demeyer: Move SAGE_DATA to SAGE_LOCAL/share [Reviewed by François Bissey, Jeroen Demeyer] #13316: Jean-Pierre Flori: Update pynac to version 0.2.5 [Reviewed by Burcin Erocal] #13348: Jeroen Demeyer: Set CPATH in sage-env [Reviewed by Volker Braun] #13361: Volker Braun: Report startuptime exclusive children [Reviewed by John Palmieri] #13362: David Coudert: Fix bug in build_flow_graph [Reviewed by Keshav Kini, Nathann Cohen] #13397: Jeroen Demeyer: sage-location: handle lib64 also [Reviewed by John Palmieri] #13399: Anne Schilling, Mike Zabrocki: Fixes to symmetric functions [Reviewed by Mike Zabrocki, Anne Schilling] #13415: Jeroen Demeyer: Prevent unneeded rebuilding when upgrading [Reviewed by John Palmieri] #13420: Jeroen Demeyer: The usual #long time additions [Reviewed by Volker Braun] #13431: Kevin Halasz: Add sign as an alias for signature for permutations [Reviewed by Rob Beezer, John Cremona] #13443: Jeroen Demeyer: Some clean up of R spkg [Reviewed by Karl-Dieter Crisman, John Palmieri] #13449: Jonathan Gutow: Problem with testjava.sh in jmol package finding bash [Reviewed by Dmitrii Pasechnik] #13454: Jeroen Demeyer: Fix odlyzko database doctests [Reviewed by Volker Braun] #13455: Andrey Novoseltsev: Remove jsMath <> workaround [Reviewed by John Palmieri] #13457: Jeroen Demeyer: Various small fixes to sage-bdist [Reviewed by John Palmieri] #13462: Aly Deines: quaternion algebra discriminant generalized to number fields [Reviewed by Sarah Chisholm] #13497: Jeroen Demeyer, John Palmieri: Disable sage --info test for bdists [Reviewed by John Palmieri] #13502: Jason Grout: vector norm doesn't work with python integers [Reviewed by Rob Beezer] #13508: John Palmieri: deprecate jsmath_avoid_list etc. [Reviewed by Nicolas M. Thiéry] Merged in sage-5.4.rc0: #3979: Francis Clarke: Power series composition messes up precision [Reviewed by Kiran Kedlaya, Luis Felipe Tabera Alonso, Frédéric Chapoton] #5160: Jeroen Demeyer: Change name of misc/sagex_ds.pyx [Reviewed by Karl-Dieter Crisman] #11446: Paul-Olivier Dehaye: compute the outline of a partition [Reviewed by Frédéric Chapoton] #11770: Robert Harron: Add ability to detect CM number fields and take complex conjugate of their elements [Reviewed by Francis Clarke, Jeroen Demeyer] #12496: Samuel Lelievre, Hugh Thomas: Improve doctest coverage for integer_ring.pyx [Reviewed by Hugh Thomas, Jeroen Demeyer] #12802: John Perry: test containment of ideals in class MPolynomialIdeal [Reviewed by Andrey Novoseltsev, Simon King] #13289: David Coudert: Determine if a vertex is a cut vertex [Reviewed by Sebastian Luther] #13444: Anne Schilling, Mike Zabrocki: Doc Tests for book "k-Schur Primer" [Reviewed by Anne Schilling, Mike Zabrocki] #13459: Jeroen Demeyer: spkg/bin/sage: do not change directory [Reviewed by John Palmieri] #13509: Aly Deines: Pari nfhnf - hnf over number fields [Reviewed by Jeroen Demeyer] #13515: Jeroen Demeyer: Support the GCC spkg on Ubuntu 12.04 [Reviewed by Volker Braun] #13524: Michael Welsh: Error in Linear Algebra constructions [Reviewed by Dmitrii Pasechnik] #13527: Franco Saliola: modify repr of SubsetAlgebra (example of with realizations) to conform to standards set out in #13404 [Reviewed by Mike Hansen] Merged in sage-5.4.rc1: #13512: Francis Clarke: Docstring formatting in misc_c.pyx [Reviewed by Jeroen Demeyer] #13537: Julian Rueth: Stopgap for 13439 [Reviewed by Volker Braun] #13544: John Palmieri: Omit .DS_Store when building 'all' documentation [Reviewed by Michael Welsh] Merged in sage-5.4.rc2: #7688: Jeroen Demeyer: Remove byte-compiled files from extcode [Reviewed by R. Andrew Ohana] #9697: Paul-Olivier Dehaye: DS_Store garbage in flint spkg [Reviewed by Karl-Dieter Crisman] #10738: Volker Braun: insecure temp file in testcc.sh, testcxx.sh [Reviewed by Jeroen Demeyer] #13579: Jeroen Demeyer, Volker Braun: Python sys.path security risk [Reviewed by Volker Braun, Jeroen Demeyer, David Roe] #13582: John Palmieri: Add (brief) info about SAGE_TESTDIR to other pieces of doc [Reviewed by Karl-Dieter Crisman] #13595: Jeroen Demeyer: LD_LIBRARY_PATH potential security risk [Reviewed by Volker Braun] Merged in sage-5.4.rc3: #13258: André Apitzsch: Replace some deprecated functions in the documentation [Reviewed by Robert Bradshaw] #13631: Jeroen Demeyer: Sage refuses to run despite safe directory [Reviewed by Volker Braun] Merged in sage-5.4.rc4: #13681: Jeroen Demeyer: fix issues with SAGE_TMP [Reviewed by Volker Braun] September 10, 2012 ------------------ Sage 5.3 was released on 08 September 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 72 people contributed to this release. Of those, 10 made their first contribution to Sage: - Adrien Brochard [first contribution] - Alan Lauder [first contribution] - Alexander Dreyer - Aly Deines - Andrey Novoseltsev - Andrzej Giniewicz - André Apitzsch - Anne Schilling - Benjamin Jones - Birk Eisermann - Burcin Erocal - Charles Bouillaguet - Chris Berg - Dan Drake - Daniel Smertnig [first contribution] - David Coudert - David Eklund - David Kirkby - David Loeffler - David Roe - Dmitrii Pasechnik - Douglas McNeil - Eviatar Bach - Florent Hivert - Florian Bouyer [first contribution] - Franco Saliola - François Bissey - Frédéric Chapoton - Guy Achard - Ivan Andrus - J Beier [first contribution] - Jan Vonk - Jason Grout - Jean-Pierre Flori - Jeremy Martin [first contribution] - Jeroen Demeyer - Jessica Striker [first contribution] - John Cremona - John Palmieri - Julian Rueth - Julien Puydt - Karl-Dieter Crisman - Keshav Kini - Kevin Halasz - Kwankyu Lee - Lauren Keough [first contribution] - Laurent Pierron - Leif Leonhardy - Luis Felipe Tabera Alonso - Maarten Derickx - Marc Masdeu - Marco Streng - Mark Shimozono - Martin Albrecht - Martin Cross [first contribution] - Michael Orlitzky - Mike Hansen - Mike Zabrocki - Nathann Cohen - Nicolas M. Thiéry - Punarbasu Purkayastha - Robert Bradshaw - Simon King - Sébastien Labbé - Timo Jolivet - Timo Kluck - Travis Scrimshaw - Vincent Delecroix - Viviane Pons - Volker Braun - William Stein - 王瑞期 [first contribution] * Release manager: Jeroen Demeyer. * We closed 108 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.3/tickets.html Closed tickets: #480: Make Sage work with SELinux on Linux [Reviewed by Mike Hansen] #1760: on osx make a symlink sage.command --> sage [Reviewed by Karl-Dieter Crisman] #8668: Sage 6.0 press release [Reviewed by Karl-Dieter Crisman, Jason Grout] #10509: cvxopt: undefined symbol: ilaenv_ [Reviewed by Volker Braun] #11647: Numerical approximation to one digit [Reviewed by Karl-Dieter Crisman, Julian Rueth, Eviatar Bach] #12201: The new R spkg breaks building from source on at least one OS X system. [Reviewed by Maarten Derickx] #418: Martin Albrecht: Add SAT Solvers [Reviewed by Alexander Dreyer] #3358: [with patch, needs review] Improve the building of eclib (shared/static objects) [Reviewed by François Bissey] #10234: Notebook does not remove files for deleted plots [Reviewed by Andrey Novoseltsev] #12623: PIL package doesn't know about debian multiarch [Reviewed by Julien Puydt] #12624: gdmodule package doesn't know about debian multiarch [Reviewed by Julien Puydt] #13003: numerical evaluation of `erf` crashes PARI at large numbers [Reviewed by Benjamin Jones] #5814: Timo Kluck: %prun doesn't work in the notebook [Reviewed by Keshav Kini] #11510: Do not sdist the SAGE_ROOT hg repository [Reviewed by Jeroen Demeyer] #11717: sage.schemes.generic.scheme initialization [Reviewed by Volker Braun] #13357: Jeroen Demeyer: Create an experimental autotools spkg [Reviewed by François Bissey] #9904: ATLAS fails to build on OpenSolaris if SAGE_FAT_BINARY=yes [Reviewed by Jeroen Demeyer] #10303: clean up sage-check-64 and use of SAGE64 [Reviewed by John Palmieri, David Kirkby, Leif Leonhardy] #10437: f2py and sage : impossible to create a .so lib ? [Reviewed by Jeroen Demeyer] #11077: revise the script sage-check-64 [Reviewed by Jeroen Demeyer] #13405: Jeroen Demeyer, Keshav Kini: Remove old docs when upgrading sagenb [Reviewed by John Palmieri] Merged in sage-5.3.beta0: #2607: Dan Drake, Andrey Novoseltsev, Andrzej Giniewicz, Volker Braun: find_minimum_on_interval() uses the wrong scipy function [Reviewed by Karl-Dieter Crisman, Mike Hansen, Andrey Novoseltsev] #5612: Adrien Brochard: example of solving a system of linear equations symbolically using symbolic matrices [Reviewed by Marc Masdeu, Benjamin Jones] #10444: Karl-Dieter Crisman: Make solve documentation better [Reviewed by Benjamin Jones] #12043: Alan Lauder: Hecke series for overconvergent modular forms [Reviewed by David Loeffler, Jan Vonk] #12120: Julian Rueth: Improve documentation of numerical_approx() [Reviewed by Eviatar Bach, Karl-Dieter Crisman] #12140: Mike Zabrocki: Symmetric functions uses lrcalc in symmetrica and bug fix in skew Schur function indexed by [[], []] [Reviewed by Anne Schilling] #12503: Kwankyu Lee: Convenient history fetch commands [Reviewed by Dmitrii Pasechnik] #12612: Marc Masdeu: Fix is_unit() in padics so that it is mathematically correct [Reviewed by David Roe, Robert Bradshaw, Kwankyu Lee] #12643: Vincent Delecroix: irreducibility of generalized permutation [Reviewed by Frédéric Chapoton] #12768: David Roe, John Palmieri: Better plotting for isogeny graphs of elliptic curves, and handling of LMFDB labels [Reviewed by John Cremona, Volker Braun] #12840: Martin Albrecht, John Palmieri: update M4RI to newest upstream release [Reviewed by Simon King, Volker Braun] #12841: Martin Albrecht: update M4RIE to newest upstream release [Reviewed by Simon King, Jeroen Demeyer, Volker Braun] #12860: Daniel Smertnig: Incorrect computation of maximal orders in quaternion algebras [Reviewed by Aly Deines] #12923: Florent Hivert: Comparison of vectors is O(n) even in the simple cases [Reviewed by Travis Scrimshaw] #12959: Nicolas M. Thiéry, Franco Saliola: Improvements to Sets.WithRealizations [Reviewed by Mike Zabrocki] #12969: Simon King: Coercion failures in symmetric functions [Reviewed by Anne Schilling] #13089: David Eklund: Implement weighted projective spaces. [Reviewed by Andrey Novoseltsev] #13100: John Cremona: EllipticCurve_from_j (over QQ) should not always compute minimal twist [Reviewed by David Roe] #13218: David Roe: Laurent series ring doesn't carry over default prec [Reviewed by Robert Bradshaw] #13224: Anne Schilling: Implementation of test method for slender posets [Reviewed by Chris Berg] #13229: Alexander Dreyer: Adding `DegNegLex` to TermOrder [Reviewed by Martin Albrecht] #13233: J Beier: Add simple SST poset to the posets examples [Reviewed by Jessica Striker, Anne Schilling] #13238: Franco Saliola: add functionality for counting, generating, and manipulating non-negative integer matrices [Reviewed by Chris Berg] #13243: Franco Saliola, Nicolas M. Thiéry, Florent Hivert, Chris Berg: new methods for compositions [Reviewed by Chris Berg, Mike Zabrocki] #13265: Alexander Dreyer: Missing attributes of `pbori.pyx`'s `BooleConstant` [Reviewed by Martin Albrecht] Merged in sage-5.3.beta1: #5512: Mike Hansen: CombinatorialSpeciesStructures with different labels are equal [Reviewed by Laurent Pierron, Guy Achard] #11310: Jeroen Demeyer, Volker Braun: Monkey-patch catchall `except:` statements so they at least don't catch `KeyboardInterrupt` errors [Reviewed by Keshav Kini] #12251: Mark Shimozono, Anne Schilling: Implementation of Littelmann path model for crystals [Reviewed by Anne Schilling, Mark Shimozono] #12454: Timo Jolivet: A draw_rauzy_fractal method for WordMorphism [Reviewed by Vincent Delecroix, Sébastien Labbé] #12549: Julian Rueth: p-adic is_zero doesn't normalize at the beginning [Reviewed by David Roe] #12811: Daniel Smertnig: (reduced) norm of quaternion ideals is broken [Reviewed by Aly Deines] #12861: Daniel Smertnig: maximal_order of quaternion algebras should be more general [Reviewed by Aly Deines] #12924: Viviane Pons: SchubertPolynomialRing causes symmetrica and Sage to crash on bad input [Reviewed by Mike Hansen] #13067: Nathann Cohen: is_strongly_regular [Reviewed by Frédéric Chapoton] #13160: François Bissey: upgrade cvxopt to 1.1.5 [Reviewed by Volker Braun] #13192: Birk Eisermann: some code clean up for sage/graphs/graph.py [Reviewed by Nathann Cohen, Karl-Dieter Crisman] #13202: Alexander Dreyer, Charles Bouillaguet: conversion problems in BooleanPolynomialRing with degrevlex order [Reviewed by Martin Albrecht, Charles Bouillaguet] #13242: Jeremy Martin, Lauren Keough: Determine if an edge in a graph is a cut-edge (bridge) [Reviewed by David Coudert] #13293: Julian Rueth: Change add_big_oh to add_bigoh in padic factorization code [Reviewed by David Roe] #13310: John Palmieri: `:trac:` links are broken [Reviewed by Punarbasu Purkayastha] #13315: Jeroen Demeyer: Clean up MANIFEST.in, spkg-delauto and spkg-dist [Reviewed by John Palmieri] #13328: Volker Braun: Remove wrong and outdated SELinux advice from installation guide. [Reviewed by Mike Hansen] #13329: Jeroen Demeyer, Volker Braun: Add OpenSSL prereq check [Reviewed by Volker Braun, Jeroen Demeyer] #13330: Jean-Pierre Flori: flint-1.5.2.p0.spkg installation fails on Cygwin [Reviewed by Dmitrii Pasechnik] #13334: Jean-Pierre Flori: ecl.pyx won't build on Cygwin [Reviewed by Dmitrii Pasechnik] #13335: Jean-Pierre Flori: matrix_*.pyx do not compile on Cygwin [Reviewed by Dmitrii Pasechnik] #13336: Jean-Pierre Flori: farey_symbol.pyx fails to build on Cygwin [Reviewed by Dmitrii Pasechnik] #13337: Jean-Pierre Flori: expression.pyx fails to build on Cygwin [Reviewed by Dmitrii Pasechnik] #13338: Jean-Pierre Flori: stl_vector.pyx fails on Cygwin [Reviewed by Volker Braun] Merged in sage-5.3.beta2: #6538: Travis Scrimshaw: bug in Partitions [Reviewed by Benjamin Jones] #7956: Michael Orlitzky: constructing a scheme morphism to an affine curve [Reviewed by Marco Streng] #10512: Jason Grout, Punarbasu Purkayastha, Sébastien Labbé: wrap matplotlib's title functionality [Reviewed by Sébastien Labbé, Punarbasu Purkayastha] #11143: Benjamin Jones, Volker Braun: define symbolic functions for exponential integrals [Reviewed by Burcin Erocal, Karl-Dieter Crisman, William Stein] #11455: Marco Streng: Add algorithm Magma to Conic methods [Reviewed by Florian Bouyer] #12181: Douglas McNeil, Frédéric Chapoton: random_DAG does not terminate on it's default inputs [Reviewed by David Coudert] #12310: Ivan Andrus: Don't specify a port number in sage-notebook [Reviewed by John Palmieri] #12346: Jeroen Demeyer: Re-enable Pari hermite form with flag=4 and include_zero_rows=False once it is fixed upstream [Reviewed by Volker Braun] #12380: Sébastien Labbé: Move methods from Word_nfactor_enumerable to FiniteWord_class [Reviewed by André Apitzsch] #12990: Simon King, Luis Felipe Tabera Alonso: Add another doctest to connecting conversion maps [Reviewed by Keshav Kini, Marco Streng] #13061: Michael Orlitzky: Add a symbolic expression interface to Maxima's rectform() [Reviewed by Timo Kluck] #13114: Nathann Cohen: Bug in is_isomorphic for multigraphs ! [Reviewed by David Coudert] #13132: David Coudert: Small string formatting bug in Graph.delete_vertex [Reviewed by Timo Jolivet] #13189: Volker Braun: fan isomorphism check [Reviewed by Andrey Novoseltsev] #13271: Karl-Dieter Crisman: wrong sign with function Ei and limit [Reviewed by Benjamin Jones] #13286: Punarbasu Purkayastha: inconsistent behaviour of solve [Reviewed by Frédéric Chapoton] #13287: Leif Leonhardy: Override more compiler-related environment variables if Sage's GCC is used [Reviewed by Jeroen Demeyer] #13290: Jeroen Demeyer: Upgrade MPC to version 1.0 [Reviewed by Leif Leonhardy, Volker Braun] #13308: Daniel Smertnig: eigenspaces_left() sometimes raises an error concerning variable names [Reviewed by Maarten Derickx] #13320: Jeroen Demeyer: Upgrade to PARI-2.5.2 [Reviewed by Marco Streng] #13353: Jeroen Demeyer: In sage-spkg, export SAGE_KEEP_BUILT_SPKGS [Reviewed by John Palmieri] #13359: Timo Kluck: [Performance] Expression::__nonzero__ shouldn't call variables() unless it is necessary [Reviewed by Mike Hansen] #13363: Mike Hansen: Move sage/graphs/planarity/ to sage/graphs/planarity_c/ [Reviewed by John Palmieri] Merged in sage-5.3.rc0: #3401: Martin Cross: Make Li symbolic and work with complex input [Reviewed by Mike Hansen, Karl-Dieter Crisman, Burcin Erocal, Benjamin Jones] #10742: Marco Streng: Local solubility of conics over number fields [Reviewed by Florian Bouyer] #11425: Travis Scrimshaw: to_standard modifies the original permutation [Reviewed by Mike Hansen] #13161: Dan Drake, 王瑞期: Fix unicode issue in axes labels [Reviewed by Sébastien Labbé] #13251: Kevin Halasz: Add General Dihedral Groups as Permutation Groups [Reviewed by Benjamin Jones] #13260: Karl-Dieter Crisman: Add tutorials from PREP workshops to standard documentation [Reviewed by André Apitzsch, Andrey Novoseltsev, John Palmieri, Benjamin Jones] #13339: Jean-Pierre Flori: wrapper_*.pyx fail to build on Cygwin [Reviewed by Dmitrii Pasechnik] #13349: Jeroen Demeyer: Deprecate SAGE_FORTRAN, support FC [Reviewed by Leif Leonhardy, John Palmieri] #13373: Leif Leonhardy, Jeroen Demeyer: Make sage -i http://.../foo.spkg work immediately [Reviewed by John Palmieri] Merged in sage-5.3.rc1: #12324: Jeroen Demeyer: Fix upgrading of root repository [Reviewed by John Palmieri] #12486: Robert Bradshaw, Dan Drake: Make the Sage patchbot an optional spkg [Reviewed by Volker Braun] #13341: Jean-Pierre Flori, Leif Leonhardy: GAP's spkg-install fails on recent Cygwin [Reviewed by Dmitrii Pasechnik] #13392: Keshav Kini: Remove GNUTLS-related packages [Reviewed by John Palmieri] #13402: Dmitrii Pasechnik: a bug in matching() [Reviewed by David Coudert] #13421: Jeroen Demeyer: polynomial_real_mpfr_dense.pyx: remove signal handling around list(x) [Reviewed by Volker Braun] July 30, 2012 ------------- Sage 5.2 was released on 25 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 54 people contributed to this release. Of those, 5 made their first contribution to Sage: - Alexander Dreyer - Andrey Novoseltsev - André Apitzsch - Anne Schilling - Armin Straub - Benjamin Jones - Birk Eisermann [first contribution] - Burcin Erocal - Charles Bouillaguet - Chris Berg - Dan Drake - Daniel Krenn - David Coudert - David Roe - Dima Pasechnik - Dmitrii Pasechnik - Douglas McNeil - Franco Saliola - François Bissey - Frédéric Chapoton - Hugh Thomas - Ivan Andrus - Jason Grout - Javier López Peña - Jeroen Demeyer - Johan Bosman - John Palmieri - Jonathan Gutow - Karl-Dieter Crisman - Keshav Kini - Leif Leonhardy - Luis Felipe Tabera Alonso - Marshall Hampton - Martin Albrecht - Martin Raum - Mike Hansen - Nathann Cohen - Nicolas M. Thiéry - Niels Ranosch - Paul Ivanov [first contribution] - Paulo César Pereira de Andrade - Punarbasu Purkayastha - R. Andrew Ohana - Rado Kirov [first contribution] - Rob Beezer - Robert Bradshaw - Samuel Gonshaw [first contribution] - Simon King - Stephen Montgomery-Smith - Timothy Walsh [first contribution] - Titus Nicolae - Volker Braun - Wai Yan Pong - William Stein * Release manager: Jeroen Demeyer. * We closed 87 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.2/tickets.html Closed tickets: #1861: Ivan Andrus: better document sage.el [Reviewed by Karl-Dieter Crisman] #5873: Fix matplotlib build on FreeBSD [Reviewed by Stephen Montgomery-Smith, Paul Ivanov] #6582: Potential issue in polybori - 0.5rc.p8 and/or 0.5rc.p9 [Reviewed by Alexander Dreyer] #6880: docstrings and @cached_method -- if you used cached_method then docstring displays wrong file, etc. [Reviewed by Simon King] #7003: Update jmol [Reviewed by Jason Grout] #7831: numpy-1.5.0 fixes for FreeBSD [Reviewed by Stephen Montgomery-Smith] #9547: x * Infinity assumes that x is positive [Reviewed by Burcin Erocal, Volker Braun] #10340: Strange error in groebner_basis() [Reviewed by Alexander Dreyer] #11423: Make atan2(0,0) consistent [Reviewed by Volker Braun, Titus Nicolae, Burcin Erocal] #12059: Make R work on FreeBSD [Reviewed by Stephen Montgomery-Smith] #12303: leave beta symbolic for exact complex inputs [Reviewed by Burcin Erocal] #12654: polybori crash (Linux) [Reviewed by Alexander Dreyer] #12984: Possible future issues with ECL build with unicode enabled [Reviewed by Karl-Dieter Crisman, Paulo César Pereira de Andrade] #13126: John Palmieri, Jeroen Demeyer: Update and clean up openssl [Reviewed by Jeroen Demeyer, John Palmieri, Karl-Dieter Crisman, Benjamin Jones] #13144: Fix Sympow on FreeBSD [Reviewed by Stephen Montgomery-Smith] #3766: move sage_fortran from fortran spkg to sage_scripts spkg [Reviewed by Karl-Dieter Crisman] #12818: Building polybori under FreeBSD [Reviewed by Stephen Montgomery-Smith, Alexander Dreyer, Karl-Dieter Crisman] #13040: Polybori spkg: allow CC to contain multiple words [Reviewed by R. Andrew Ohana] #876: Implement or wrap Braid Groups [Reviewed by Karl-Dieter Crisman] #8393: bring plot3d.py to 100% coverage [Reviewed by Karl-Dieter Crisman] #10144: Update plot.py to 100% coverage [Reviewed by Karl-Dieter Crisman] #10694: bug with plot [Reviewed by Karl-Dieter Crisman] #11953: Marshall Hampton, John Palmieri: Upgrade optional package biopython to version 1.60 [Reviewed by Marshall Hampton, John Palmieri] #13205: make LP return bounds on variables [Reviewed by Dmitrii Pasechnik] #13207: Please consider updating to gfan 0.5 [Reviewed by Marshall Hampton] #13270: Jason Grout, Keshav Kini: Restarted notebook server allows user registration [Reviewed by Punarbasu Purkayastha] Merged in sage-5.2.beta0: #10764: François Bissey, André Apitzsch: Cleanup a few Cython warnings [Reviewed by François Bissey, André Apitzsch] #11078: William Stein, Jonathan Gutow: jmol in the flask notebook [Reviewed by Jason Grout] #11080: Mike Hansen, Rado Kirov, William Stein, Jason Grout, Jeroen Demeyer: move notebook to flask/wsgi-based notebook [Reviewed by Rado Kirov, Dan Drake, Jason Grout, Simon King, Dmitrii Pasechnik, John Palmieri, Punarbasu Purkayastha] #11503: Jonathan Gutow: Make new spkg to install Jmol in SAGE_LOCAL/share [Reviewed by Dan Drake, Jason Grout, Punarbasu Purkayastha] #11528: Wai Yan Pong: Allow deleting row or column from matrix [Reviewed by Rob Beezer] #11851: Niels Ranosch, Burcin Erocal: make pybtex an optional spkg [Reviewed by John Palmieri] #11874: Rado Kirov, Jason Grout: Remove twisted spkg [Reviewed by Dmitrii Pasechnik, Jason Grout] #12229: Jason Grout, Karl-Dieter Crisman: Add section in the developers manual about sagenb development [Reviewed by William Stein, Jeroen Demeyer, Punarbasu Purkayastha, Karl-Dieter Crisman, Keshav Kini] #12327: Ivan Andrus: Improve loading page of Mac App [Reviewed by Karl-Dieter Crisman] #12917: Nathann Cohen: is_cartesian_product [Reviewed by David Coudert] #12974: Punarbasu Purkayastha: make Graphics class inheritable and some clean ups [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] #12989: Nathann Cohen: Ellingham–Horton graphs [Reviewed by Keshav Kini] #13014: Douglas McNeil: lcm for SR rationals [Reviewed by Dan Drake, William Stein] #13038: Nathann Cohen: ClebschGraph, CoxeterGraph, HoffmanGraph [Reviewed by Keshav Kini] #13052: Rob Beezer: Positive definite check for matrices over RDF/CDF [Reviewed by Dan Drake, Andrey Novoseltsev] #13090: Punarbasu Purkayastha: Make LinearCode take minimum distance as a parameter [Reviewed by Dmitrii Pasechnik] #13103: Charles Bouillaguet: Makes BooleanPolynomial more compatible with MPolynomial [Reviewed by Martin Albrecht] #13113: Keshav Kini: sage -pkg can't handle its own options [Reviewed by John Palmieri] #13139: André Apitzsch: Bug in IntegerFactorization [Reviewed by R. Andrew Ohana] #13148: Dima Pasechnik: make LP return the number of variables [Reviewed by Nathann Cohen] #13167: Jeroen Demeyer: Clarify some comments concerning the matplotlib Delaunay code in list_plot3d.py [Reviewed by Karl-Dieter Crisman] #13168: Anne Schilling: Fixing typos in latex options documentation [Reviewed by Nicolas M. Thiéry] #13172: David Roe: Bug in mod(a, p^k).nth_root() for p>62, k>1 [Reviewed by Robert Bradshaw] Merged in sage-5.2.beta1: #4529: Punarbasu Purkayastha, Karl-Dieter Crisman: Implement plots with logarithmic scale [Reviewed by Karl-Dieter Crisman, Punarbasu Purkayastha] #5043: Ivan Andrus: gap_console help broken [Reviewed by Karl-Dieter Crisman] #10795: Rob Beezer: Fix and upgrade double dense matrix QR decomposition [Reviewed by Martin Raum, Dan Drake] #12433: R. Andrew Ohana, Leif Leonhardy: Make zn_poly respect the CC environment variable, work around GCC 4.7.0 bug on ia64 (and clean up the spkg) [Reviewed by Leif Leonhardy, Jeroen Demeyer] #12544: Andrey Novoseltsev: Switch cones to `PointCollection` [Reviewed by Volker Braun] #12706: Frédéric Chapoton: monomials of 0 [Reviewed by Keshav Kini] #12751: Jeroen Demeyer: Allow building Sage with GCC-4.7.x [Reviewed by Volker Braun] #12806: Daniel Krenn, Javier López Peña: upgrade of spkg networkx-1.2.p2 to 1.6 [Reviewed by Keshav Kini, Karl-Dieter Crisman] #12965: Andrey Novoseltsev: X.Kaehler_cone().lattice() is not a lattice [Reviewed by Volker Braun] #13029: Robert Bradshaw: Upgrade Cython to 0.17 [Reviewed by R. Andrew Ohana] #13058: Nathann Cohen, Dima Pasechnik: Hall-Janko Graph [Reviewed by Keshav Kini, Dima Pasechnik] #13124: Alexander Dreyer: Updating PolyBoRi to release 0.8.2 [Reviewed by Martin Albrecht] #13140: John Palmieri, Rob Beezer: OS X Lion doctest failures for double dense QR decomposition [Reviewed by Rob Beezer, John Palmieri] #13155: Charles Bouillaguet: Boolean Multivariate Ideals should not have negative dimension.... [Reviewed by Martin Albrecht] #13166: Armin Straub: Compute q-binomial coefficients more efficiently [Reviewed by Javier López Peña] #13169: Nicolas M. Thiéry: Little doctest improvements in permutation groups [Reviewed by Frédéric Chapoton] #13170: Simon King: Speedup the default nonzero test for matrices [Reviewed by Javier López Peña] #13175: Jeroen Demeyer: Upgrade Mercurial [Reviewed by Volker Braun] #13187: André Apitzsch: Minpoly and charpoly don't check their arguments correctly [Reviewed by Robert Bradshaw] #13191: Volker Braun: Construct a 2-d fan from rays only [Reviewed by Andrey Novoseltsev] #13196: Charles Bouillaguet, Javier López Peña: GL(n, GF(q)).random_element() is way too slow for what it does [Reviewed by Dima Pasechnik, Charles Bouillaguet] #13206: André Apitzsch: Remove from __future__ import with_statement [Reviewed by Volker Braun] #13208: Franco Saliola: Move the basis method from CombinatorialFreeModule to ModulesWithBasis.ParentMethods [Reviewed by Chris Berg] #13216: Frédéric Chapoton: one test in lattice polytope should be tagged # random [Reviewed by Volker Braun] #13217: Armin Straub: Expand the Dedekind eta function more efficiently [Reviewed by Frédéric Chapoton] #13219: John Palmieri: Document 'make' targets [Reviewed by Keshav Kini] #13222: Franco Saliola: Fix is_graded for Posets to use appropriate definition [Reviewed by Anne Schilling] Merged in sage-5.2.rc0: #10607: Marshall Hampton, John Palmieri: Update phcpack to latest verson [Reviewed by Marshall Hampton, John Palmieri] #11563: Nicolas M. Thiéry: Make lrcalc a standard package [Reviewed by Anne Schilling, Jeroen Demeyer, John Palmieri] #11996: Johan Bosman: Bug in LaTeX representation of subgroups of permutation groups [Reviewed by Samuel Gonshaw] #12343: Luis Felipe Tabera Alonso: Cleanup unexisting methods after #10263 [Reviewed by André Apitzsch] #12925: Nicolas M. Thiéry, Hugh Thomas: Thematic tutorial on combinatorics [Reviewed by Hugh Thomas, Nicolas M. Thiéry, Timothy Walsh] #13073: Birk Eisermann: recognition of weakly chordal graphs [Reviewed by Nathann Cohen,Birk Eisermann] #13088: Frédéric Chapoton: implement the Paley graphs [Reviewed by Nathann Cohen] #13109: Volker Braun: Rewrite deprecation to use trac ticket numbers [Reviewed by John Palmieri, Karl-Dieter Crisman] #13146: David Roe: Removing tabs in .rst, .tex and .pxi files [Reviewed by Keshav Kini, André Apitzsch, Jeroen Demeyer] #13193: Benjamin Jones: erf evaluation is wrong along imaginary axis [Reviewed by Karl-Dieter Crisman] #13220: John Palmieri: bug in morphisms of chain complexes [Reviewed by Marshall Hampton] July 10, 2012 ------------- 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] June 11, 2012 ------------- Sage 5.0.1 was released on 09 June 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 26 people contributed to this release. Of those, 1 made their first contribution to Sage: - Alexander Dreyer - Andrey Novoseltsev - Dan Drake - David Kirkby - David Roe - Frithjof Schulze - Ivan Andrus - Jason Grout - Javier Mora [first contribution] - Jeroen Demeyer - John Palmieri - John Perry - Karl-Dieter Crisman - Keshav Kini - Leif Leonhardy - Mariah Lenox - Mike Hansen - Minh Van Nguyen - Moritz Minzlaff - Nils Bruin - Paul Zimmermann - Peter Jeremy - Punarbasu Purkayastha - Robert Miller - Volker Braun - William Stein * Release manager: Jeroen Demeyer. * We closed 35 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.0.1/tickets.html Closed tickets: #2801: add a get_page function which supports https via GNUTLS [Reviewed by Mike Hansen] #3349: OSX: make sure LDFLAGS are set for linking purposes [Reviewed by Karl-Dieter Crisman] #3565: worksheet.py -- increase doctest coverage to 50%. [Reviewed by David Roe] #3730: Sage scripts ending with .py [Reviewed by Karl-Dieter Crisman] #4636: improve polynomial_modn_dense_ntl.Polynomial_dense_mod_p [Reviewed by Mike Hansen] #4852: graph plotting using @option and @suboption [Reviewed by Robert Miller, Karl-Dieter Crisman] #6058: [with patch, needs comments] Add basic statistics functionality at the top level [Reviewed by Karl-Dieter Crisman] #6580: ratpoints -- this must be fixed to build with gcc-3.4.x [Reviewed by Minh Van Nguyen, Karl-Dieter Crisman] #7459: sage virtualbox -- install imagemagick [Reviewed by Volker Braun] #8035: make SageTeX able to detect version mismatches [Reviewed by Dan Drake] #8860: incoherent types for real numbers [Reviewed by Paul Zimmermann, Mike Hansen] #9568: Update IML to the newest upstream release, and improve spkg-install [Reviewed by Keshav Kini] #9601: Fix cvxopt on FreeBSD [Reviewed by David Kirkby, Mike Hansen, Peter Jeremy] #9759: Addition of SI prefixes capabilities to the units module [Reviewed by Javier Mora, Karl-Dieter Crisman] #10717: Prime typeset badly on plots [Reviewed by Andrey Novoseltsev] #10893: problem parsing integers starting with 0 [Reviewed by Volker Braun, Mike Hansen] #11034: bug in the way vectors are created for submodules of free modules [Reviewed by William Stein, Moritz Minzlaff] #11438: optional package libtheora-1.1.1.spkg does not build on sage-4.7.1.alpha1 [Reviewed by Dan Drake, Karl-Dieter Crisman] #11444: optional package cbc-2.3.p2.spkg does not build on some platforms on sage-4.7.1.alpha1 [Reviewed by Karl-Dieter Crisman, Dan Drake, John Perry] #12007: creation of extension field of finite field needs more parameter checking [Reviewed by David Roe] #12127: fix comparison R == Z [Reviewed by Andrey Novoseltsev, Frithjof Schulze] #12556: optional package database_cremona_ellcurve-20120113.spkg causes test failure [Reviewed by Mariah Lenox] #12723: Update python spkg to add a feature to python's doctest module [Reviewed by Volker Braun, David Roe] #12735: doctest framework bug that was somehow observed via -- "optional magma doctest fails on sage-5.0.beta9" [Reviewed by William Stein, Mike Hansen] #12752: resulant of two polynomials returns incorrect value [Reviewed by Nils Bruin] #13027: Upgrade and clean up IML [Reviewed by Keshav Kini] Merged in sage-5.0.1.rc0: #12954: Jeroen Demeyer: Make MPIR support SAGE_FAT_BINARY on all systems [Reviewed by William Stein, Karl-Dieter Crisman] #12963: Jeroen Demeyer: PolyBoRi links against system -lboost_unit_test_framework [Reviewed by Alexander Dreyer] #12970: Jeroen Demeyer: MPIR fails to build when CPU's architecture name doesn't match its actual capabilities [Reviewed by Volker Braun, William Stein] Merged in sage-5.0.1.rc1: #10822: John Palmieri, Jason Grout: sage -sh doesn't set the path right if default shell is zsh on OSX [Reviewed by Ivan Andrus, Jeroen Demeyer, Punarbasu Purkayastha] #12760: Leif Leonhardy: gfan 0.4plus [p1] fails to build with GCC 4.7.0 [Reviewed by Jeroen Demeyer] #12761: Leif Leonhardy, Jeroen Demeyer: Givaro's (3.2.13.rc1) C++ headers don't conform to C++11 [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] #12762: Leif Leonhardy: LinBox (1.1.6) fails to build with GCC 4.7.0, and lacks an `spkg-check` [Reviewed by Jeroen Demeyer, Karl-Dieter Crisman] #13013: Volker Braun: Update to python-2.7.3 [Reviewed by Jeroen Demeyer] #13024: Volker Braun, Jeroen Demeyer: Remove sage-libdist [Reviewed by Dan Drake] May 15, 2012 ------------ Sage 5.0 was released on 14 May 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 126 people contributed to this release. Of those, 22 made their first contribution to Sage: - Alex Ghitza - Alexander Dreyer - Aly Deines - Anders Buch [first contribution] - Andrey Novoseltsev - André Apitzsch - Anne Schilling - Aran Carmon [first contribution] - Benjamin Jones - Benjamin Lundell [first contribution] - Burcin Erocal - Cassie Williams [first contribution] - Chris Wuthrich - Christian Stump - Christopher Swenson [first contribution] - Craig Citro - Dan Drake - Daniel Krenn - David Coudert - David Eklund - David Kirkby - David Kohel - David Loeffler - David Roe - Dmitrii Pasechnik - Douglas McNeil - Ege Sertçetin [first contribution] - Emil Widmann - Fidel Barrera-Cruz - Florent Hivert - Francis Clarke - Franco Saliola - François Bissey - Frederic Han [first contribution] - Fredrik Johansson - Fredrik Stromberg [first contribution] - Frithjof Schulze - Frédéric Chapoton - Georg S. Weber - Harald Schilly - Hartmut Monien [first contribution] - Hugh Thomas - Itai Bar-Natan [first contribution] - Ivan Andrus - Ivo Hedtke - Jaap Spies - Jan Vonk [first contribution] - Jason Grout - Javier López Peña - Jean-Pierre Flori - Jennifer Balakrishnan - Jeroen Demeyer - Jim Stark [first contribution] - Joal Heagney [first contribution] - Johan Bosman - Johannes Klaus Fichte [first contribution] - John Cremona - John Palmieri - John Perry - Jonathan Bober - Julian Rueth - Julien Puydt - Justin Walker - Karen T. Kohl [first contribution] - Karl-Dieter Crisman - Kelvin Li - Kenneth Smith - Keshav Kini - Kiran Kedlaya - Kwankyu Lee - Leif Leonhardy - Luca De Feo - Luis Felipe Tabera Alonso - Lukáš Lánský - Maarten Derickx - Marc Masdeu [first contribution] - Marc Mezzarobba - Marco Streng - Mariah Lenox - Mario Pernici - Mark Shimozono [first contribution] - Marshall Hampton - Martin Albrecht - Martin Raum - Michael Boratko [first contribution] - Michael Brickenstein - Michael Orlitzky - Michiel Kosters - Mike Hansen - Minh Van Nguyen - Moritz Minzlaff - Nathan Carter - Nathann Cohen - Nicolas Borie - Nicolas M. Thiéry - Niels Ranosch - Niles Johnson - Nils Bruin - Oleksandr Motsak - Paul Zimmermann - Peter Story - Punarbasu Purkayastha - R. Andrew Ohana - Rob Beezer - Robert Bradshaw - Robert Miller - Ron Evans - Ryan Grout - Sebastian Pancratz - Simon King - Sonseeahray Rucker [first contribution] - Stepan Starosta - Steven Trogdon - Sébastien Labbé - Thierry Monteil - Timo Jolivet - Tom Boothby - Travis Scrimshaw [first contribution] - Valentin Féray - Vincent Delecroix - Viviane Pons - Volker Braun - Wilfried Huss - William Stein - Xavier Caruso [first contribution] - Özge Çelik [first contribution] * Release manager: Jeroen Demeyer. * We closed 506 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-5.0/tickets.html Closed tickets: #1159: [reported upstream] Bug in python range [Reviewed by Jason Grout] #10139: Problem found in graphs.is_planar() when the graph has no edges. [Reviewed by Nathann Cohen] #10970: Do not generate pipestatus from spkg/install [Reviewed by Jeroen Demeyer] #11470: Re-enable at symbol in notebook username [Reviewed by Karl-Dieter Crisman] #12001: performance of dimension of cusp forms for Gamma(N) is insanely slow [Reviewed by David Loeffler] #12219: Dan Drake: loading a worksheet from a https url gives poor error message when SSL not available [Reviewed by Keshav Kini] #12237: erf of complex arguments [Reviewed by Jeroen Demeyer] #12238: a bug in taking n() of a definite integral [Reviewed by Volker Braun] #12277: Warnings in `plot_slope_field` [Reviewed by Karl-Dieter Crisman, Andrey Novoseltsev] #9630: Python ints should have a conversion to Maxima [Reviewed by Michael Orlitzky, Burcin Erocal] #1158: mathematical functions should remain symbolic [Reviewed by Karl-Dieter Crisman] #8148: looking at the dual of a poset: IndexError [Reviewed by Lukáš Lánský] #8175: update installation guide for SPARC Solaris 10 [Reviewed by Karl-Dieter Crisman] #9819: Add a default gcd and lcm methods for fields [Reviewed by Marco Streng] #11694: Unlabelled edges are doubled when creating multiedge graph [Reviewed by Ivan Andrus, Nathann Cohen] #12256: if x=var('x') and n is an integer then n.binomial(x) should return binomial(SR(n),x) [Reviewed by Burcin Erocal] #10459: serious troubles with gcd [Reviewed by Luis Felipe Tabera Alonso, Douglas McNeil] #10808: atlas-3.8.3.p16 doesn't build on ARM [Reviewed by Julien Puydt, Dmitrii Pasechnik] #11594: Symbolic integration of abs() failure [Reviewed by Karl-Dieter Crisman, Michael Orlitzky] #12042: Emil Widmann: Update the documentation how to use the VM image, especially to avoid confusion about Virtualbox and VM Player [Reviewed by Marco Streng] #12320: install cephes on the ARM platform [Reviewed by Julien Puydt, Dmitrii Pasechnik] #9162: cygwin/ARM:pynac.pyx use double precision special functions instead of long double (REVISITED) [Reviewed by Burcin Erocal] #10111: random_prime is badly documented. [Reviewed by Francis Clarke] #11656: Imaginary part of symbolic variable disappears in simplify_full() [Reviewed by Burcin Erocal] #11842: substitute_function doesn't work as expected in many cases [Reviewed by Burcin Erocal] #6810: improve doctest coverage in schemes/homset.py [Reviewed by Volker Braun, Andrey Novoseltsev] #10289: Convenient history fetch facilities [Reviewed by Kwankyu Lee] #12154: broken doctests in magma.py for integers in QQ and conversion of number field elements [Reviewed by Marco Streng] #12294: Failures in sage0 pexpect interface with specific length of $DOT_SAGE using a "screen" terminal [Reviewed by Jeroen Demeyer] #12301: Conventions for Coding SEEALSO format [Reviewed by Florent Hivert] #12546: Inequalities in MixedIntegerLinearProgram are not properly handled [Reviewed by Dmitrii Pasechnik, Punarbasu Purkayastha] #4258: switch multiplication of dense matrices over finite prime fields to LinBox [Reviewed by Martin Albrecht] #5397: [with patch, needs work] SmallGroups library can't be used in Sage-3.3 [Reviewed by Simon King] #7766: Jaap Spies, Ivan Andrus: Upgrade optional spkg valgrind to valgrind-3.7.0 [Reviewed by Jean-Pierre Flori] #11326: make ATLAS respect CC environment variable [Reviewed by Volker Braun] #12422: CFBundle.h on OS X 10.6 uses __attribute__((format_arg)) improperly [Reviewed by Jeroen Demeyer] #12457: Problems with C++ exception handling on OS X with custom GCC [Reviewed by Jeroen Demeyer] #12578: sage-list-packages script needs write permissions to SAGE_ROOT/tmp [Reviewed by John Palmieri, R. Andrew Ohana] #12593: Bring algebras/free_algebra_quotient.py to 100% coverage [Reviewed by Javier López Peña] #2999: Some packages don't respect the CC environment variable [Reviewed by Michael Orlitzky, R. Andrew Ohana] #3000: Some packages don't respect the CXX environment variable [Reviewed by Michael Orlitzky, R. Andrew Ohana] #3631: Delete *.pyc files when building Sage specific spkgs like extcode [Reviewed by Jeroen Demeyer] #7626: delete PBUILD code in local/bin/sage-sage script [Reviewed by Jeroen Demeyer] #11303: Fix the documentation of attach [Reviewed by Florent Hivert] #3306: Shared library for symmetrica [Reviewed by François Bissey] #12427: make f2c respect global CC flag [Reviewed by R. Andrew Ohana] #12429: make flint respect global CC and CXX flags [Reviewed by R. Andrew Ohana] #12431: make palp respect global CC flag [Reviewed by R. Andrew Ohana] #1386: Implement splitting fields [Reviewed by Jeroen Demeyer] #3517: "sage -upgrade" does not upgrade $SAGE_ROOT/sage [Reviewed by Jeroen Demeyer] #3898: [with spkg, needs work] Make an optional, self contained gcc 4.3.4 spkg [Reviewed by Jonathan Bober, David Roe] #6365: bug in constructing extensions of finite fields [Reviewed by Jennifer Balakrishnan] #7066: sympow ignores CC and uses gcc even when CC is set to Sun's compiler [Reviewed by R. Andrew Ohana] #12184: Change example in doc/bordeaux/elliptic_curves.rst [Reviewed by R. Andrew Ohana] #12712: John Palmieri: update optional spkg 'database_gap' [Reviewed by Jeroen Demeyer, Dmitrii Pasechnik] #6375: Run sage once as part of install process to generate sage-flags.txt [Reviewed by Jeroen Demeyer] #6494: sage should *never* ever import numpy by default on startup. Yet again it does! [Reviewed by Mike Hansen] #9894: Simon King: Group cohomology spkg, version 2.1.2 [Reviewed by Karl-Dieter Crisman, John Palmieri] #11329: make f2c spkg respect CC environment variable [Reviewed by R. Andrew Ohana] #11906: PolyBoRi 0.7.1 should obey some standard environment variables [Reviewed by Jeroen Demeyer, Alexander Dreyer] #12621: use bash for prereq install file [Reviewed by Jeroen Demeyer] #12704: Restore doctesting of non-library files [Reviewed by Francis Clarke] #12754: Fix scoping / name look-up issue in PolyBoRi 0.8.1 and support flags from the environment [Reviewed by Alexander Dreyer, Leif Leonhardy, Martin Albrecht, Burcin Erocal] #12758: Jeroen Demeyer: update optional spkg 'gap_packages' [Reviewed by Dmitrii Pasechnik] #2102: add incoming/outgoing wrappers to HG objects (like hg_sage) [Reviewed by Mike Hansen] #4780: relative number field constructor -- error message when given poly of degree < 1 is bad [Reviewed by Mike Hansen, David Loeffler] #7038: ratpoints 2.1.2.p2 ignores CC and uses gcc whatever [Reviewed by Leif Leonhardy] #8125: problem with "text" in matplotlib [Reviewed by John Palmieri] #11702: interfaces/magma.py test fails [Reviewed by Marco Streng, David Loeffler] #11875: Correct general brokenness of Farey symbols [Reviewed by David Loeffler] #12004: copying a linear program using Coin solver consumes enormous amounts of memory [Reviewed by Nathann Cohen] #11909: Merging fixes for PolyBoRi 0.7.1 into 0.8 spkg [Reviewed by Alexander Dreyer, Leif Leonhardy] #12435: lcalc does not respect global CXX flag [Reviewed by Leif Leonhardy] #12441: singular does not respect global cxx flag [Reviewed by Leif Leonhardy] #12700: stopgap for #11832 [Reviewed by John Palmieri] #12710: Stopgap for 11358 [Reviewed by Michael Orlitzky] #2732: cython in Debian build doesn't have the right include paths [Reviewed by Jeroen Demeyer] #5943: Sage 3.4.2.a0: len(prime_range(2^50)) segfaults [Reviewed by Michael Orlitzky, Keshav Kini, Volker Braun] #11844: Race condition in building MPIR/yasm [Reviewed by Leif Leonhardy] #12315: OS X Lion: pari fails self tests [Reviewed by John Palmieri] #12319: OS X Lion: gsl fails self tests [Reviewed by John Palmieri] #12424: OS X Lion: symmetrica doesn't work [Reviewed by John Palmieri] #12765: MPIR doesn't compile with GCC-4.7.0 on ia64 [Reviewed by Jeroen Demeyer] #12782: When building GCC, build MPIR without the C++ interface [Reviewed by Jeroen Demeyer] #10810: singular-3-1-1-4.p3 doesn't build on ARM [Reviewed by Julien Puydt] #11881: Metaticket: build Sage on OS X 10.7 Lion [Reviewed by John Palmieri] #12459: Interrupt test failures on OS X 10.7 [Reviewed by Jeroen Demeyer] Merged in sage-5.0.beta0: #2956: Michael Orlitzky: generic multivariate polynomials are buggy on exponent overflow [Reviewed by Paul Zimmermann] #5048: David Loeffler: congruence subgroups are not integrated into the coercion model [Reviewed by Johan Bosman, Georg S. Weber] #6777: Michael Orlitzky: segfault with univariate polynomial, realfield, complexfield [Reviewed by Mike Hansen] #9138: Simon King: Categories for all rings [Reviewed by Volker Braun] #9361: Jeroen Demeyer: Maxima timeout on Mac OS X 10.4 (Tiger) [Reviewed by Karl-Dieter Crisman] #9958: François Bissey, Steven Trogdon, Jeroen Demeyer: Upgrade python to 2.7.x [Reviewed by John Palmieri, Karl-Dieter Crisman, Jason Grout, Jeroen Demeyer, Steven Trogdon, Leif Leonhardy, Sébastien Labbé, François Bissey] #10596: Sebastian Pancratz, André Apitzsch: Misc improvements to integer.pyx [Reviewed by Aly Deines, John Cremona] #10757: Nathan Carter: normalized laplacian throws an error if the graph has an isolated vertex [Reviewed by Karl-Dieter Crisman] #10785: Nathann Cohen: Setting solver-specific options [Reviewed by Johannes Klaus Fichte] #11073: Volker Braun, Jeroen Demeyer: remove the spkg/base repo! [Reviewed by John Palmieri, William Stein] #11115: Simon King: Rewrite cached_method in Cython [Reviewed by Nicolas M. Thiéry, Andrey Novoseltsev, Volker Braun] #11513: Burcin Erocal: add is_trivial_zero() method to symbolic expressions [Reviewed by Benjamin Jones, Paul Zimmermann] #11900: Simon King: Serious regression caused by #9138 [Reviewed by Jeroen Demeyer, Nicolas M. Thiéry, Simon King, Jason Grout] #11915: Jason Grout: upgrade matplotlib to 1.1.0 [Reviewed by François Bissey, Jeroen Demeyer, Karl-Dieter Crisman] #11942: Nathann Cohen, Keshav Kini, Jeroen Demeyer: segfault on Graph().connected_component_containing_vertex('') [Reviewed by Keshav Kini, David Coudert, Nathann Cohen] #11986: Jeroen Demeyer: inconsistent integer hashing on 64bit systems with python 2.7 [Reviewed by François Bissey] #12084: David Roe: Restores a test in sage/tests/french_book/number_theory.py [Reviewed by David Loeffler] #12153: William Stein: Make series of data available on sage_timeit return objects [Reviewed by Nils Bruin] #12155: Nathann Cohen: Bug when taking complement of bipartite graph. [Reviewed by Rob Beezer] #12182: Michiel Kosters: Calculate the trace dual of an order in a number field [Reviewed by Johan Bosman] #12218: Michiel Kosters: Content of general polynomial not defined. [Reviewed by David Loeffler] #12221: Jeroen Demeyer: Failures in gp pexpect interface with specific length of $DOT_SAGE using a "screen" terminal [Reviewed by Georg S. Weber] #12243: Rob Beezer: Girth of a graph fails for non-integer vertices [Reviewed by Nathann Cohen] #12244: Nathann Cohen: Empty graphs and new distance computations [Reviewed by David Coudert] #12247: Volker Braun: var(['x','y']) should work but doesn't [Reviewed by Burcin Erocal] #12286: Peter Story: docstring for factorial function mentions unsupported algorithm keyword [Reviewed by Karl-Dieter Crisman] #12304: Jeroen Demeyer: Singular build failure on OS X 10.4 when directory name is long [Reviewed by Karl-Dieter Crisman] #12305: Martin Albrecht: interreduced basis shouldn't crash on all zero ideal [Reviewed by Burcin Erocal] #12307: William Stein: fix typo in docstring in cm.py (cm elliptic curves) [Reviewed by John Cremona] Merged in sage-5.0.beta1: #4539: Michael Brickenstein, Burcin Erocal, Oleksandr Motsak, Alexander Dreyer, Simon King: plural wrapper [Reviewed by Simon King, Alexander Dreyer] #5014: Michael Orlitzky: matrix rank should call echelon_form over *fraction field* [Reviewed by Andrey Novoseltsev] #7965: Michael Orlitzky: quo_rem attribute error (probably easy to fix?) [Reviewed by Marco Streng, Michael Orlitzky] #8046: Kenneth Smith, John Palmieri: Add matrix/matrix_double_dense.py to documentation [Reviewed by John Palmieri, Karl-Dieter Crisman] #9393: Michael Orlitzky: symbolic sum cannot handle python ints [Reviewed by Burcin Erocal] #10489: Ryan Grout, Jason Grout, Nathan Carter: plot_slope_field broken [Reviewed by Aly Deines, Ryan Grout, Benjamin Jones] #10546: Ron Evans, David Loeffler: implement a custom cusps() method for principal congruence subgroups Gamma(N) [Reviewed by Jan Vonk] #10658: David Loeffler: Compute local components of modular forms [Reviewed by Martin Raum] #10953: Lukáš Lánský, Jeroen Demeyer: is_regular yields StopIterator error on empty graph [Reviewed by Michael Orlitzky] #11068: Simon King: Basic implementation of one- and twosided ideals of non-commutative rings, and quotients by twosided ideals [Reviewed by John Perry] #11313: Keshav Kini: Animated GIF plots should repaint bgcolor after each frame [Reviewed by John Palmieri] #11375: William Stein, Craig Citro: speed up computation of level one eisenstein series [Reviewed by Craig Citro, William Stein] #11461: Mike Hansen: make @parallel work with class/instance methods [Reviewed by Karl-Dieter Crisman, Niles Johnson] #11462: Nathan Carter: Improve @parallel documentation to give examples of functions with multiple arguments [Reviewed by Karl-Dieter Crisman] #11487: Peter Story, John Palmieri: Add graph plotting to reference manual [Reviewed by Karl-Dieter Crisman] #11575: Alexander Dreyer: Update PolyBoRi to release 0.8.0 [Reviewed by Martin Albrecht] #11601: David Loeffler: Generic congruence subgroups [Reviewed by Johan Bosman] #11606: John Perry: simplify constraints in linear programs [Reviewed by Nathann Cohen] #11673: Johan Bosman: is_unit not properly implemented for algebraic integers [Reviewed by David Loeffler] #11780: Simon King: Creating a polynomial ring over a number field results in a non-unique polynomial ring over the rationals [Reviewed by Martin Albrecht, David Loeffler] #11819: John Palmieri: don't use the deprecated 'new' module [Reviewed by Julian Rueth] #11822: Aly Deines: Wraps E.reduction(p)(P) so you can call P.reduction(p) [Reviewed by William Stein, Cassie Williams, Jeroen Demeyer] #11879: Niels Ranosch: Intersection for more than two ideals [Reviewed by Julian Rueth] #12044: William Stein: improve doctest coverage of algebras/free_algebra_quotient*: (add about 30 tests) [Reviewed by Mike Hansen] #12045: Peter Story: Add gsl/interpolation.pyx to the reference manual [Reviewed by Karl-Dieter Crisman] #12210: Jeroen Demeyer: GF(p) constructor should check primality of p only once [Reviewed by Marco Streng] #12239: Nils Bruin: Better conversion to/from ECL bignums [Reviewed by Burcin Erocal] #12246: David Coudert: Wiener index without dictionary [Reviewed by Nathann Cohen] #12265: William Stein: massively optimize f.change_ring(QQ) for f in ZZ['x'] [Reviewed by Sebastian Pancratz] #12323: William Stein, John Palmieri: make docbuild cache corruption error message usable [Reviewed by John Palmieri, William Stein] #12330: Jeroen Demeyer: Increase eval_using_file_cutoff for gp interface [Reviewed by Georg S. Weber] Merged in sage-5.0.beta2: #6442: Sebastian Pancratz, Michael Orlitzky: Random(?) index error with determinant method [Reviewed by Paul Zimmermann] #6569: Michael Orlitzky: sparse integer matrix doesn't raise an error on non-integer index [Reviewed by William Stein] #6804: Michael Orlitzky: Permutation.weak_excedences inconsistency [Reviewed by Nathann Cohen] #7952: Michael Orlitzky: broken binomial sum (fixed in maxima) [Reviewed by Karl-Dieter Crisman] #9054: William Stein, Robert Bradshaw, Maarten Derickx, Moritz Minzlaff, Julian Rueth: create a class for basic function_field arithmetic for Sage [Reviewed by Maarten Derickx, Julian Rueth] #10135: Lukáš Lánský: eulerian_circuit() of Graph can't handle multiple edges [Reviewed by Nathann Cohen] #10333: Mike Hansen, Anders Buch, Nicolas M. Thiéry, Anne Schilling: An interface to Anders Buch's Littlewood-Richardson Calculator ``lrcalc`` [Reviewed by Nicolas M. Thiéry, Anne Schilling] #10899: Lukáš Lánský: is_chordal can raise TypeError [Reviewed by Paul Zimmermann] #10959: Lukáš Lánský: BipartiteGraph adding edges between new nodes ignores partition [Reviewed by Nathann Cohen] #11235: Maarten Derickx: Make the ipython edit magic command edit the right file and show both files when doing ?? [Reviewed by Marco Streng] #11429: Volker Braun: Count integral points without PALP [Reviewed by Andrey Novoseltsev, Jeroen Demeyer] #11485: Ege Sertçetin, Ivo Hedtke, Jeroen Demeyer: Turkish Translation of "A Tour of Sage" [Reviewed by Jan Vonk, Julian Rueth, Özge Çelik, Michael Orlitzky] #11614: Volker Braun: Make Cython libcpp usable [Reviewed by Jeroen Demeyer, John Perry] #11677: Karl-Dieter Crisman, Kenneth Smith, Peter Story: Polygon fill doesn't work [Reviewed by Peter Story, Kenneth Smith, Karl-Dieter Crisman] #11977: Jason Grout: matrix plots are missing tick marks on one of top or bottom [Reviewed by Karl-Dieter Crisman] #12068: Florent Hivert, Burcin Erocal: Numerator for symbolic expression shouldn't use maxima [Reviewed by Burcin Erocal, Florent Hivert, Karl-Dieter Crisman] #12094: Michael Orlitzky: Upgrade Maxima to 5.24.0 [Reviewed by Karl-Dieter Crisman] #12134: Lukáš Lánský: is_planar(set_pos=True) doesn't work with small graphs [Reviewed by Nathann Cohen] #12150: Stepan Starosta: upgrade defect() of a finite word [Reviewed by Vincent Delecroix] #12172: John Palmieri: R doctest starts X11 on OSX [Reviewed by Karl-Dieter Crisman] #12235: Nathann Cohen: Slow computation of strongly connected components [Reviewed by David Coudert] #12267: Dan Drake: multiply defined labels when using sagetex with multline [Reviewed by Dmitrii Pasechnik] #12309: John Perry: GLPK crashes or hangs on certain inputs [Reviewed by Nathann Cohen] #12314: Travis Scrimshaw: Latex method for partitions and cores [Reviewed by Anne Schilling] #12329: Jeroen Demeyer: Remove unneeded dependencies of the Sage library [Reviewed by François Bissey] #12332: Punarbasu Purkayastha: MixedIntegerLinearProgram().new_variable docs don't mention nonnegativity [Reviewed by Dmitrii Pasechnik] #12390: William Stein: the documentation for number_of_partitions mentions a bug in PARI that was fixed long, long ago. Delete this. [Reviewed by David Roe] #12396: David Roe: A few whitespace changes [Reviewed by Robert Bradshaw] Merged in sage-5.0.beta3: #7509: William Stein, Wilfried Huss: notebook -- make it possible to debug Python code in the notebook, e.g., something like pdb that works in the notebook [Reviewed by David Roe] #8458: Lukáš Lánský: iterator for graphs() doesn't return independent graphs [Reviewed by Nathann Cohen] #8879: Michael Orlitzky: Clean up whitespace in padic hyperelliptic curve file [Reviewed by Karl-Dieter Crisman] #10175: Volker Braun: symmetric and exterior powers of characters [Reviewed by David Roe] #10441: Lukáš Lánský: Error creating an empty multi-edge (di)graph [Reviewed by Nathann Cohen] #10628: Maarten Derickx, Simon King: initialization of matrices from vectors or list of lists can be way faster [Reviewed by Simon King] #10868: Michael Orlitzky: A wrong (easy) limit [Reviewed by Aly Deines] #10916: Lukáš Lánský: Multiple loops and edges are lost upon pickling [Reviewed by Nathann Cohen] #10923: Thierry Monteil, Michael Orlitzky: Bad sign in integral() [Reviewed by Benjamin Jones, Karl-Dieter Crisman] #10940: Frederic Han: giac interface [Reviewed by David Kohel] #11483: Michael Orlitzky, Jason Grout: enable abs_integrate package from maxima [Reviewed by Karl-Dieter Crisman] #11591: Michael Orlitzky: Incorrect results for integrals involving exponential functions [Reviewed by Aly Deines] #11739: Lukáš Lánský: add_vertex w/o params should return the new vertex [Reviewed by Paul Zimmermann] #11920: Jeroen Demeyer: Sympow needs to disable fused-multiply-add and should create datafiles [Reviewed by Leif Leonhardy, Volker Braun] #11981: Daniel Krenn: map_coefficients (of multivariate polynomial ring) cannot change base_ring [Reviewed by Julian Rueth] #12105: Johan Bosman: RuntimeError: Segmentation fault with nth_root [Reviewed by Karl-Dieter Crisman] #12144: William Stein: better document a technical confusing point in the Hidden Markov Model code [Reviewed by Jason Grout] #12261: David Roe: Bring Doctest coverage for element_ext_pari.py to 100% [Reviewed by Karl-Dieter Crisman, Aly Deines] #12317: Francis Clarke: printing factorisations [Reviewed by Robert Bradshaw] #12325: Lukáš Lánský: Eulerian circuits/paths for (di)graphs [Reviewed by Nathann Cohen] #12328: François Bissey: GMP_BITS_PER_MP_LIMB is deprecated in gmp/mpir [Reviewed by Robert Bradshaw] #12370: Javier López Peña: Change is_singular to use rank instead of determinant [Reviewed by Keshav Kini] #12378: Joal Heagney, Nathann Cohen: Graph chromatic_number documentation [Reviewed by Karl-Dieter Crisman] #12386: Julien Puydt: [ARM] pickling issues in the matrix_mod2_dense code [Reviewed by Martin Albrecht] #12389: Nathann Cohen: Rounding error in graph coloring [Reviewed by David Coudert] #12395: David Roe: Change some random variable indexes that cause doctest failures if doctests are run in a different order. [Reviewed by Karl-Dieter Crisman] #12412: Jim Stark: TypeError when creating a zero map from a zero dimensional vector space to a positive dimensional vector space [Reviewed by Aly Deines] Merged in sage-5.0.beta4: #4498: Karen T. Kohl, Burcin Erocal: Implement a symbolic version of the arg function [Reviewed by Karl-Dieter Crisman, Burcin Erocal] #6581: John Perry: Groebner basis not working over symbolic ring [Reviewed by Martin Albrecht] #10807: David Loeffler: Modular Symbols trouble restoring saved objects [Reviewed by Marco Streng] #10998: Frédéric Chapoton, Christian Stump, Nicolas M. Thiéry: Categories for posets [Reviewed by Franco Saliola, Christian Stump, Nicolas M. Thiéry, Florent Hivert] #11003: Mike Hansen: Improve support for lazy_import inside classes [Reviewed by Nicolas M. Thiéry, Florent Hivert] #11118: Florent Hivert: Add a cache for .list() method in FiniteEnumeratedSet [Reviewed by Nicolas M. Thiéry] #11250: Florent Hivert: Fix link in coercion.rst [Reviewed by Nicolas M. Thiéry] #11257: Nicolas Borie: Avoid a coercion when computing an element to the power of 0 [Reviewed by Nathann Cohen] #11967: John Palmieri: os x 10.7 Lion -- Sage segfaults on startup when initializing GiNaC [Reviewed by Jeroen Demeyer] #12006: William Stein: sage-4.8 and magma-2.18 not playing well together [Reviewed by Marco Streng] #12034: William Stein: improve doctest coverage of matrix/benchmark.py from 0% to 100% [Reviewed by Martin Albrecht, Karl-Dieter Crisman] #12135: Lukáš Lánský: Multiple loops handling in c_graph [Reviewed by Nathann Cohen] #12318: Lukáš Lánský: **kwds in the Graph constructor is confusing [Reviewed by Nathann Cohen] #12336: Martin Albrecht: The optional doctests in sage/databases/symbolic_data.py are misformatted so they are never run [Reviewed by Michael Orlitzky] #12344: Martin Albrecht: Interface to GINV [Reviewed by Dmitrii Pasechnik] #12353: David Roe: wrong comparison between RealIntervalField and RealField [Reviewed by Paul Zimmermann] #12363: Jeroen Demeyer: Upgrade PARI to 2.5.1 [Reviewed by John Palmieri] #12366: Jeroen Demeyer: In mpfr, delete old libraries *after* build [Reviewed by Michael Orlitzky] #12367: Jeroen Demeyer: Add a script to check whether the compiler supports a certain flag [Reviewed by R. Andrew Ohana] #12373: Sonseeahray Rucker, William Stein: Possible typo in Units Module Avogadro constant [Reviewed by William Stein] #12385: Keshav Kini: Questionable semantics of DiGraph().all_simple_paths [Reviewed by Nathann Cohen] #12416: Jeroen Demeyer: Mercurial assumes that any system with XCode *installed* will use XCode to *build* Mercurial [Reviewed by R. Andrew Ohana] #12430: R. Andrew Ohana, Jeroen Demeyer: Add -fwrapv cflag when building Python [Reviewed by R. Andrew Ohana] #12464: Florent Hivert, Nicolas M. Thiéry: Improved uniqueness for combinatorial free modules [Reviewed by Nicolas M. Thiéry, Florent Hivert] #12474: Jean-Pierre Flori: Doc fix for UniqueRepresentation class [Reviewed by Nicolas M. Thiéry] #12478: Andrey Novoseltsev: Typo in an error message of Fan constructor [Reviewed by Volker Braun] #12481: Jeroen Demeyer: Fix branch_current_hg() [Reviewed by André Apitzsch] #12483: Nicolas M. Thiéry: Workaround #12482 causing history-dependent behaviour of Family [Reviewed by Viviane Pons] #12490: Florent Hivert: Create a role :trac: to link to trac ticket in sphinx [Reviewed by Nathann Cohen, Jeroen Demeyer] #12492: Keshav Kini: Polyhedron().radius() is nonsensical [Reviewed by Punarbasu Purkayastha] #12500: John Palmieri: sagetex: fix self-tests on OpenSolaris [Reviewed by Jeroen Demeyer] Merged in sage-5.0.beta5: #4949: John Palmieri: Optionally build spkgs in $SAGE_BUILD_DIR [Reviewed by Mariah Lenox, Leif Leonhardy, Maarten Derickx, Jeroen Demeyer] #8983: Benjamin Jones: erf(0) should return 0 [Reviewed by Burcin Erocal, Douglas McNeil] #9362: Lukáš Lánský: Invalidate None as a vertex label. [Reviewed by Paul Zimmermann] #9714: Lukáš Lánský, Robert Miller: Graph(..., format='incidence_matrix') doesn't work with graphs that have loops, but G.incidence_matrix() does. So? [Reviewed by Nathann Cohen] #10347: Christian Stump: Implementation of is_(skew_)symmetrizable for matrices [Reviewed by Hugh Thomas] #10670: Frédéric Chapoton, Florent Hivert: Mobius matrices of posets are integer matrices [Reviewed by Florent Hivert, Nicolas M. Thiéry] #11382: Florent Hivert: Speedup subposet and _vertex_to_element [Reviewed by Nicolas M. Thiéry] #11384: Volker Braun: Construct the complex of a fan [Reviewed by Andrey Novoseltsev] #11603: Rob Beezer: Deprecate eigenspaces for matrices over RDF/CDF [Reviewed by Punarbasu Purkayastha] #12025: William Stein: get doctest coverage of monoids/monoid.py to 100% [Reviewed by Michael Orlitzky, Thierry Monteil, Karl-Dieter Crisman] #12223: Jeroen Demeyer: the 'sage.rings.complex_mpc' optional extension is broken in sage-4.8.alpha3 and over [Reviewed by François Bissey] #12306: Nathann Cohen: Static sparse graphs for fast low-level computations [Reviewed by David Coudert] #12356: John Cremona, William Stein: many missing class number 2 orders in CM j-invariant function over quadratic fields [Reviewed by John Cremona, William Stein] #12368: Jeroen Demeyer: Make "ratpoints" check whether -fnested-functions is supported by the compiler [Reviewed by R. Andrew Ohana] #12423: Jeroen Demeyer: Numpy wrongly assumes that any non-i386 OS X system is PowerPC [Reviewed by William Stein] #12475: Sébastien Labbé: Define WordMorphism.__ne__ [Reviewed by Timo Jolivet] #12477: Nathann Cohen: Graph.relabel modifies the dictionary given as an input [Reviewed by Nicolas M. Thiéry] #12484: Nicolas M. Thiéry: CombinatorialFreeModule's: customizing the order of terms in the output of elements [Reviewed by Florent Hivert] #12488: Jeroen Demeyer: Make sage-make_devel_packages not fail if there is nothing to commit [Reviewed by Volker Braun] #12489: Nicolas M. Thiéry: Fix equality of combinatorial free module on non totally ordered basis [Reviewed by Florent Hivert] #12501: Jeroen Demeyer: Fix packages wanting to run autoconf [Reviewed by Volker Braun] #12506: William Stein: fix typo in debug() docstring [Reviewed by Aran Carmon] #12507: Benjamin Jones: Mark random symbolic expression doctests with #random [Reviewed by Burcin Erocal] #12511: Robert Bradshaw: Unable to take numeric powers of I [Reviewed by Burcin Erocal] #12517: William Stein: EllipticCurve(E.a_invariants()) doesn't work [Reviewed by Robert Bradshaw] #12522: Jeroen Demeyer: Check assignment of SAGE_ROOT in $SAGE_ROOT/sage [Reviewed by Volker Braun] #12530: Nicolas M. Thiéry: Improve the sage-combinat script to support guards for developpers versions of Sage [Reviewed by Florent Hivert] Merged in sage-5.0.beta6: #7027: R. Andrew Ohana: clean up f2c spkg [Reviewed by Michael Orlitzky] #8718: Marc Mezzarobba, Julian Rueth: Polynomial.apply_map() [Reviewed by Daniel Krenn] #9130: Karen T. Kohl, Burcin Erocal, Karl-Dieter Crisman: Access to beta function [Reviewed by Benjamin Jones, Burcin Erocal, Karl-Dieter Crisman] #9469: Nicolas M. Thiéry: Category membership, without arguments [Reviewed by Florent Hivert] #9744: Jason Grout, Michael Boratko, Benjamin Jones: implicit_plot fill option fills entire plot [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #10192: Leif Leonhardy, Punarbasu Purkayastha: SageNB broken when SAGE_PATH contains flavours of '.' during installation [Reviewed by Florent Hivert, Jeroen Demeyer] #10349: Christian Stump: Implementation of mutations for matrices [Reviewed by Hugh Thomas] #10603: Florent Hivert: DisjointUnionEnumeratedSets should not always define Element and _element_constructor_ [Reviewed by Nicolas M. Thiéry] #11256: Mario Pernici: Update big_oh for use with multivariate power series [Reviewed by Niles Johnson] #11400: Andrey Novoseltsev: Add PointCollection [Reviewed by Volker Braun] #11754: Nathann Cohen: Computation of rank-decompositions in Sage [Reviewed by David Coudert, Jeroen Demeyer] #12078: Florent Hivert: Add an example of SEE ALSO section in the dev-guide [Reviewed by Nicolas M. Thiéry] #12107: John Palmieri: animate: a*b, a+b broken some of the time [Reviewed by Kelvin Li] #12161: Ivan Andrus: Make Sage App on Mac work right all the time on OS X 10.7 Lion, and OS X 10.6 Snow Leopard also [Reviewed by Georg S. Weber] #12171: Mike Hansen, Paul Zimmermann, Jean-Pierre Flori: Update MPFI to 1.5.1 [Reviewed by François Bissey] #12241: Volker Braun: exp, log, derivative of multivariate power series [Reviewed by Niles Johnson] #12280: Volker Braun: Incorrect saturation of integer matrix [Reviewed by William Stein] #12333: Francis Clarke: Restore --grep and --grepdoc command line options [Reviewed by William Stein, John Palmieri] #12425: Jeroen Demeyer: Twisted uses non-standard C generated by old Pyrex [Reviewed by Volker Braun] #12456: Jeroen Demeyer: Numerical noise on OS X 10.7 [Reviewed by Robert Bradshaw, John Palmieri] #12476: Florent Hivert, Nathann Cohen: Little fixes for a major speedup of join/meet matrices for FiniteLatticePoset [Reviewed by Florent Hivert, Nicolas M. Thiéry] #12487: Jeroen Demeyer: sdist in /tmp/sage-sdist-$$/sage-VERSION [Reviewed by Volker Braun] #12528: Nicolas M. Thiéry: Little optimizations in CombinatorialFreeModule [Reviewed by Florent Hivert, John Palmieri] #12539: David Coudert: graphs and digraphs distances distribution [Reviewed by Nathann Cohen] #12548: Jeroen Demeyer: In MPFR, don't delete old libraries [Reviewed by John Palmieri] #12558: Volker Braun: Numerical noise in hmm.pyx [Reviewed by Jeroen Demeyer] #12563: Jeroen Demeyer: Don't "import site" in sympy's installer [Reviewed by William Stein] #12574: John Palmieri: python spkg: don't use xcodebuild to check Xcode version [Reviewed by Jeroen Demeyer] Merged in sage-5.0.beta7: #5491: Michael Orlitzky: sylow_subgroup gives syntax error [Reviewed by Daniel Krenn] #7071: R. Andrew Ohana: palp spkg ignores global CC and CFLAGS variables [Reviewed by Volker Braun] #10075: Karen T. Kohl, Karl-Dieter Crisman: Make log gamma symbolic [Reviewed by Karl-Dieter Crisman, Benjamin Jones] #11666: Mike Hansen, Jean-Pierre Flori, Volker Braun: Upgrade MPFR to 3.1.0 [Reviewed by Paul Zimmermann, Jean-Pierre Flori, Volker Braun, Jeroen Demeyer] #11683: Julian Rueth, John Cremona: ell_curve_isogeny initialization [Reviewed by Julian Rueth, Frithjof Schulze] #11910: Nathann Cohen: Connectivity of complete graphs [Reviewed by Jason Grout, David Coudert] #12013: Punarbasu Purkayastha: Fix entropy function in devel/sage/sage/coding [Reviewed by Daniel Krenn] #12055: Volker Braun: Upgrade PALP [Reviewed by Andrey Novoseltsev, Jeroen Demeyer, R. Andrew Ohana] #12413: Martin Albrecht: Sage crashes in matrix/vector multiplication with zero extents [Reviewed by Volker Braun] #12471: Burcin Erocal: real evaluation of symbolic expressions with complex coefficients [Reviewed by Daniel Krenn] #12479: Jeroen Demeyer: Clean up sage-spkg [Reviewed by John Palmieri] #12495: Karl-Dieter Crisman: Bring plot.py to 100% coverage [Reviewed by John Palmieri] #12570: Jeroen Demeyer: remove xcodebuild check from Mercurial [Reviewed by Dmitrii Pasechnik, John Palmieri] #12572: Jeroen Demeyer: Add extra memory to pdflatex to build PDF manuals [Reviewed by Minh Van Nguyen] #12579: John Palmieri: Mechanism to skip self-tests (spkg-check) for certain packages [Reviewed by Jeroen Demeyer] #12594: William Stein: fix some trivial noise issues on some architecture with hidden markov models [Reviewed by John Cremona] #12599: Jeroen Demeyer: setuptools: make spkg-install executable [Reviewed by Jean-Pierre Flori] #12604: Benjamin Lundell: A patch adding .dimensions() to a matrix. [Reviewed by William Stein, Daniel Krenn] #12608: Jeroen Demeyer: Remove "Dependencies check" from ppl [Reviewed by Volker Braun] #12611: Marc Masdeu: Add optional argument 'p' in valuation() and ordp() methods for padics [Reviewed by David Roe] Merged in sage-5.0.beta8: #9128: Florent Hivert: Sphinx should be aware of all.py to find its links [Reviewed by Andrey Novoseltsev, Nicolas M. Thiéry] #10296: Simon King: Singular interface wasting time by waiting for the prompt too often [Reviewed by Martin Albrecht] #10682: Dmitrii Pasechnik: Upgrade maxima to 5.26 [Reviewed by Jean-Pierre Flori, Nils Bruin] #10817: Christian Stump: implementation of the generalized associahedron as a polyhedral complex [Reviewed by Frédéric Chapoton, Nicolas M. Thiéry] #10976: Christopher Swenson: computing order of a certain subgroup of a permutation group is double dog slow (compared to Magma) [Reviewed by William Stein] #12202: Sebastian Pancratz, David Loeffler: Bug in hecke_operator_on_basis [Reviewed by Jan Vonk] #12392: David Roe: Doctest fix in sage/categories/modules_with_basis.py [Reviewed by Jim Stark] #12397: David Roe: Change doctests to remove trailing backslashes [Reviewed by Jim Stark] #12405: Jeroen Demeyer: Add $SAGE_LOCAL/lib64 to LD_LIBRARY_PATH [Reviewed by Volker Braun] #12470: Jeroen Demeyer: Remove scripts related to the Debian distribution [Reviewed by Punarbasu Purkayastha] #12480: David Roe: NTL segfault on OS X 10.7 [Reviewed by William Stein, Jeroen Demeyer] #12519: Jeroen Demeyer: cvxopt should not add -lcblas and -latlas on Darwin [Reviewed by Dmitrii Pasechnik] #12562: Jeroen Demeyer: In Singular spkg-install, disable -pipe on SunOS [Reviewed by John Palmieri] #12564: Daniel Krenn: documentation of SR wildcard: n instead of i [Reviewed by David Loeffler] #12581: Karl-Dieter Crisman: Fix contour and other plot default aspect ratio [Reviewed by Benjamin Jones, David Loeffler] #12585: Hugh Thomas: Bring matrix/matrix0.pyx to 100% coverage [Reviewed by David Loeffler, Karl-Dieter Crisman] #12616: Nathann Cohen: The LP are not deallocated because of cyclic references ! [Reviewed by Simon King] #12618: Jeroen Demeyer: Don't delete dist/sage-rsync directory in sage-rsyncdist script [Reviewed by David Roe] #12625: David Roe: Conversion of pari elements to Sage fails on some negative valuation elements [Reviewed by Xavier Caruso] #12626: David Coudert: Kautz, Imase and Itoh, and Generalized de Bruijn digraph generators [Reviewed by Nathann Cohen] #12629: Jeroen Demeyer: Completely disable the LinBox commentator [Reviewed by Martin Albrecht] #12632: David Loeffler: bug comparing trivial Dirichlet characters [Reviewed by Jonathan Bober] #12633: Nils Bruin: Fix doc of attach [Reviewed by Justin Walker] #12635: Jeroen Demeyer: Remove pbuild files [Reviewed by Punarbasu Purkayastha] #12637: John Palmieri: Follow-up to #4949: don't delete the current working directory [Reviewed by Jeroen Demeyer] #12642: Nils Bruin: magma_free interface is broken [Reviewed by William Stein] #12645: Simon King: Fix rst markup for sage/combinat/sf/sf.py (and add to manual) and sage/structure/dynamic_class.py [Reviewed by Nicolas M. Thiéry] Merged in sage-5.0.beta9: #8096: Tom Boothby, Robert Bradshaw, Simon King: Speed up parent creation for multiplication of square matrices [Reviewed by Simon King, David Loeffler] #8241: David Roe: p-adic fields should have Witt Frobenius [Reviewed by Kiran Kedlaya, David Loeffler] #9367: Michael Orlitzky: S_unit return type is incorrect [Reviewed by David Loeffler] #9770: Douglas McNeil: SphericalDistribution() is not random [Reviewed by Jason Grout, Jeroen Demeyer] #11104: Rob Beezer: Add check for normal matrices [Reviewed by David Loeffler] #11208: Douglas McNeil: Remove numpy warnings in slope field [Reviewed by David Loeffler, Karl-Dieter Crisman] #11306: Rob Beezer: Upgrade unitary check for RDF/CDF matrices [Reviewed by David Loeffler] #11464: Marc Masdeu: Maximal orders in QuaternionAlgebra of prime discriminant has a bug [Reviewed by David Loeffler] #11599: Volker Braun: Wrap fan morphism in toric morphism [Reviewed by Andrey Novoseltsev] #11709: Hartmut Monien: FareySymbol [Reviewed by Martin Raum, Leif Leonhardy, David Loeffler] #11790: John Palmieri, Jeroen Demeyer: `sage --sh -c ...` shouldn't print [that many] messages [Reviewed by Jeroen Demeyer, John Palmieri] #11954: John Palmieri, David Loeffler: improve the documentation of sage/misc/cython.py [Reviewed by David Loeffler, John Palmieri] #12093: André Apitzsch: Replace __getslice__ with functionality in __getitem__ in several files (part 2) [Reviewed by François Bissey, David Loeffler] #12119: André Apitzsch: Replace remaining __getslice__ with functionality in __getitem__ (part 3) [Reviewed by David Loeffler] #12151: Johan Bosman, John Cremona: Bug in global_integral_model for elliptic curves over number fields [Reviewed by David Loeffler] #12159: Volker Braun: Placing triangulation and normal cones [Reviewed by Marshall Hampton] #12290: Simon King: Fix the hash of matrix spaces and improve its performance [Reviewed by David Loeffler] #12351: David Loeffler: AttributeError raised by method __eq__ of poset element [Reviewed by Nicolas M. Thiéry, Simon King] #12362: David Coudert: Improvement of GNP generators for graphs and digraphs [Reviewed by Nathann Cohen] #12384: David Roe: sage.combinat.e_one_star uses MS-DOS style line breaks [Reviewed by David Loeffler] #12491: Karl-Dieter Crisman: Bring three more plot3d files to 100% coverage [Reviewed by David Loeffler, John Palmieri] #12527: Nicolas M. Thiéry: Use cached_method for FractionField.is_exact [Reviewed by David Loeffler] #12538: Andrey Novoseltsev: Remove NEFPartition [Reviewed by David Loeffler] #12647: Jeroen Demeyer: Add support for a "sagerc" script [Reviewed by John Palmieri] #12651: Douglas McNeil, Michael Orlitzky: Don't add each piece of piecewise functions to the legend [Reviewed by Karl-Dieter Crisman] #12656: Alexander Dreyer: Fix inconsistencies in the PolyBoRi interface [Reviewed by Martin Albrecht] #12675: William Stein: bug in is_cyclic for abelian groups [Reviewed by Karl-Dieter Crisman] #12680: Leif Leonhardy: Fix (a single) hardcoded 'g++' in Singular 3-1-3-3 [Reviewed by R. Andrew Ohana] #12681: Leif Leonhardy: Fix hardcoded 'g++' in Lcalc 1.23 [p9] [Reviewed by R. Andrew Ohana] #12682: Leif Leonhardy: Fix "hardcoded" 'gcc' in ratpoints 2.1.3 [p2] [Reviewed by R. Andrew Ohana] Merged in sage-5.0.beta10: #6588: Nicolas M. Thiéry: Categories for root systems and many misc improvements [Reviewed by Anne Schilling, Mark Shimozono, Florent Hivert] #10492: Jeroen Demeyer: Rework spkg/install, spkg/standard/deps, spkg/standard/newest_version [Reviewed by John Palmieri] #11585: Luca De Feo, Florent Hivert: Make deprecated_function_alias print the whole module path when it differs from the original [Reviewed by Rob Beezer] #11586: David Roe: bug in p-adic extension norm method [Reviewed by Jennifer Balakrishnan] #11615: John Palmieri: optional doctests: clean up and document "known bug", "optional: requires PKG" [Reviewed by Karl-Dieter Crisman] #11634: Volker Braun: Base Polyhedron on PPL (by default) [Reviewed by Marshall Hampton, David Loeffler, Andrey Novoseltsev] #11921: Peter Story, Burcin Erocal: Allow Sympy conversion sign/sgn [Reviewed by Karl-Dieter Crisman] #12018: R. Andrew Ohana: sage-list-packages will fail if user can't write to SAGE_ROOT [Reviewed by John Palmieri] #12062: David Roe: FiniteField_ntl_gf2e to Python [Reviewed by David Loeffler] #12355: Nathann Cohen: Bug in Graph.girth [Reviewed by David Coudert, Jeroen Demeyer] #12499: Punarbasu Purkayastha: The density() function of a sparse matrix looks at every matrix entry [Reviewed by Rob Beezer] #12512: Vincent Delecroix: fixed point and periodic point of word morphism [Reviewed by Timo Jolivet] #12541: Andrey Novoseltsev: Remove Sequence test in span [Reviewed by Rob Beezer] #12602: Jeroen Demeyer: Rework download/extract code in sage-spkg [Reviewed by John Palmieri] #12609: John Palmieri, Jeroen Demeyer: Update developer guide for SPKGs [Reviewed by Jeroen Demeyer, John Palmieri] #12617: R. Andrew Ohana: Update Cremona's table of elliptic curves [Reviewed by John Cremona, Jennifer Balakrishnan] #12640: William Stein: some special cases of dimension_new_cusp_forms are broken [Reviewed by Jennifer Balakrishnan] #12644: R. Andrew Ohana: redundant source in elliptic_curves spkg [Reviewed by Jennifer Balakrishnan] #12670: John Palmieri: Store lazy import caches in .sage/cache/ rather than in .sage [Reviewed by Florent Hivert] #12678: Nicolas M. Thiéry: Extract a method to get the name of the .rst file corresponding to a python module, and doctest it. [Reviewed by Mike Hansen] #12689: William Stein: Segfault in solve_left for sparse matrices over ZZ [Reviewed by Douglas McNeil] #12691: David Roe, William Stein: Create a stopgap warning [Reviewed by R. Andrew Ohana] #12694: Keshav Kini: Fix four SPKGs with irregular directory structures [Reviewed by R. Andrew Ohana] #12698: Jeroen Demeyer: Add a warning not to install packages using the Sage shell [Reviewed by John Palmieri] #12701: Jennifer Balakrishnan: Stopgap for 6667 [Reviewed by R. Andrew Ohana] #12702: John Palmieri: document "stopgaps" [Reviewed by R. Andrew Ohana] Merged in sage-5.0.beta11: #1013: Mike Hansen: Matrix_real_double_dense overrides parent numpy() method with less-functional version [Reviewed by David Loeffler] #5646: William Stein: vectors over CDF allow a coercion from scalars [Reviewed by Johan Bosman] #7980: Nicolas M. Thiéry: Implement generic support for parents with (multiple) realizations [Reviewed by Simon King, Florent Hivert] #8791: Fredrik Johansson, Harald Schilly, David Loeffler: improve doctest coverage of libs/mpmath/ext_main.pyx [Reviewed by David Loeffler, Jeroen Demeyer] #11372: William Stein: nasty side effect of a failed simon_two_descent search [Reviewed by Jennifer Balakrishnan] #11445: Michael Orlitzky: symbolic integration fails on a very simple test case [Reviewed by Karl-Dieter Crisman] #11584: Nathann Cohen: DegreeSequences class ! [Reviewed by David Coudert] #11766: Robert Bradshaw: fast_callable always segfaults when input is a polynomial of large degree [Reviewed by Tom Boothby] #11800: David Eklund: Problem with points at infinity in hyperelliptic curves [Reviewed by Marco Streng] #12069: John Palmieri: fix doctesting of .sage files [Reviewed by Francis Clarke] #12102: Jeroen Demeyer: Make bzip2 a standard (instead of base) package [Reviewed by John Palmieri] #12262: David Roe, David Loeffler: Bring Doctest coverage for sage/rings/finite_rings to 100% [Reviewed by David Loeffler] #12311: John Palmieri: In spkgs, run testcc.sh and testcxx.sh without explicit path [Reviewed by Jeroen Demeyer] #12371: Julien Puydt: The graph_decompositions/ code seems to have bounds issues [Reviewed by Nathann Cohen, Jeroen Demeyer] #12382: David Roe: Output of a two functions in sage.plot.plot3d.base is nondeterministic due to use of set [Reviewed by Karl-Dieter Crisman] #12461: André Apitzsch: Replace some deprecated python functions in sage/algebras [Reviewed by David Loeffler] #12497: Punarbasu Purkayastha: GeneralDiscreteDistribution can segv sage [Reviewed by David Loeffler] #12653: Nicolas M. Thiéry: Add support for DiGraph() [Reviewed by David Loeffler] #12658: David Loeffler: Use the matrix displayhook hack for arithmetic subgroup elements [Reviewed by Martin Raum] #12662: David Loeffler: Improve doctest coverage for sage.rings.qqbar [Reviewed by Jim Stark] #12665: Mike Hansen: Coercion problem with QQbar [Reviewed by David Loeffler] #12667: Mark Shimozono: category root lattice realization issue: infinite loop while trying to reflect to the positive chamber [Reviewed by Anne Schilling] #12669: Mike Hansen: Conductor of trivial Dirichlet character has type int [Reviewed by David Loeffler] #12674: Valentin Féray: permutation length and size [Reviewed by Mike Hansen] #12677: Nicolas M. Thiéry: Make the doctests of sage.misc.sageinspect.sage_getargspec independent of ``Poset`` [Reviewed by Anne Schilling] #12684: Mike Hansen: Rename sage/graphs/graph_decompositions/rankwidth/ [Reviewed by David Coudert] #12687: Jeroen Demeyer: Fix Singular doctest error on OpenSolaris [Reviewed by Simon King] #12692: David Roe, Jennifer Balakrishnan: Stopgap for 12509 [Reviewed by R. Andrew Ohana] #12714: Jeroen Demeyer: Remove f2c [Reviewed by François Bissey] #12727: William Stein: AA minpoly bug [Reviewed by David Loeffler] #12742: Jeroen Demeyer: matplotlib must be a dependency of cvxopt [Reviewed by Julien Puydt] Merged in sage-5.0.beta12: #7711: Alex Ghitza: integral() does not reduce coefficients in finite field [Reviewed by Paul Zimmermann] #7926: Robert Bradshaw, Jennifer Balakrishnan, David Loeffler: Bring coverage of monsky_washnitzer up to 50% [Reviewed by Paul Zimmermann, Jeroen Demeyer] #11238: Michael Orlitzky: failing calculation of a symbolic integral [Reviewed by Karl-Dieter Crisman] #11358: William Stein: matrix multiplication over ZZ sometimes gives incorrect results [Reviewed by Douglas McNeil] #11832: John Palmieri: bug fixes for profile functions for the Steenrod algebra [Reviewed by William Stein] #11958: Nathann Cohen, Jason Grout: cplex needs another symbolic link [Reviewed by David Coudert] #11995: Jeroen Demeyer: Length argument for PARI Vec() [Reviewed by Aly Deines] #12080: Chris Wuthrich: manin constant [Reviewed by William Stein] #12136: Johannes Klaus Fichte: FVS function in DiGraph returns [0] instead of [] if already directed acyclic [Reviewed by David Coudert] #12381: David Roe: Typo in sage.combinat.sf.classical [Reviewed by Nathann Cohen, Nicolas M. Thiéry, David Loeffler] #12638: Jeroen Demeyer: Add some patches to the PARI sources [Reviewed by Johan Bosman] #12739: Jeroen Demeyer: Put prereq under revision control [Reviewed by John Palmieri] #12747: Jim Stark: is_R_algebra is useless and wrong and should be deleted [Reviewed by David Loeffler] #12749: Jim Stark: Raise algebras/free_algebra.py coverage to 100% [Reviewed by David Loeffler] #12750: Alexander Dreyer: Fix scoping / name look-up issue in PolyBoRi 0.8.0 and support flags from the environment [Reviewed by Leif Leonhardy] #12755: Jeroen Demeyer: Make coverage remove return types from Cython functions [Reviewed by Mike Hansen] #12757: David Loeffler: Clean up dead links in sage/modular/ documentation [Reviewed by Alex Ghitza] #12763: R. Andrew Ohana: elliptic_curves spkg is broken for system installs [Reviewed by François Bissey] #12764: Rob Beezer: Remove ill-advised doctest for testing normal matrices [Reviewed by John Palmieri] #12771: David Roe: Kodaira symbol latex is wrong [Reviewed by Mike Hansen] #12772: William Stein: bug in compact_system_of_eigenvalues for level 1 modular symbols [Reviewed by Fredrik Stromberg] #12775: David Roe: Small Kodaira symbols typo [Reviewed by David Eklund, Kiran Kedlaya] #12779: William Stein: customization hook for modular symbols spaces [Reviewed by David Loeffler] #12788: Nils Bruin: Provide Integer class with a __format__ method [Reviewed by Mike Hansen] #12793: Jeroen Demeyer: Fix __cmp__ tests in sage/combinat/root_system/type_dual.py [Reviewed by Nicolas M. Thiéry] Merged in sage-5.0.beta13: #9563: Mike Hansen: Remove the English-language tutorial's Makefile [Reviewed by Jeroen Demeyer] #12011: Jeroen Demeyer, John Palmieri: cvxopt: fix illegal BLAS call and fix Solaris build [Reviewed by Jeroen Demeyer, John Palmieri] #12112: John Palmieri, Jeroen Demeyer: Update the prereq script [Reviewed by Jeroen Demeyer, David Kirkby] #12220: John Perry, Nathann Cohen: Updated CBC spkg [Reviewed by John Perry, Nathann Cohen] #12369: Jeroen Demeyer: Add a gcc package [Reviewed by Simon King] #12515: Jeroen Demeyer: Upgrade mpc and make it a standard package [Reviewed by Jean-Pierre Flori, Volker Braun] #12576: John Palmieri: OS X Lion: don't require setting SAGE_PORT [Reviewed by Jeroen Demeyer] #12613: John Palmieri: Add option "-c" to sage-spkg to run the test-suite [Reviewed by Jeroen Demeyer] #12631: Jeroen Demeyer: Get rid of spkg/base/dir-0.1-install [Reviewed by John Palmieri] #12655: Alexander Dreyer: Update PolyBoRi to release 0.8.1 [Reviewed by Martin Albrecht, Jeroen Demeyer, Leif Leonhardy] #12668: David Loeffler: Delete sage/rings/coerce_python.py [Reviewed by Jeroen Demeyer] #12713: John Palmieri: Excise MoinMoin [Reviewed by Jeroen Demeyer] #12784: John Palmieri: Add comment to deps explaining dependency of cvxopt on matplotlib [Reviewed by Karl-Dieter Crisman] #12799: Alexander Dreyer: Fix PolyBoRi's dependencies in `module_list.py` [Reviewed by Leif Leonhardy] #12805: John Palmieri: Do not create SAGE_TESTDIR/tmp [Reviewed by Leif Leonhardy] #12814: Jeroen Demeyer: Add prereq-0.9-install to .hgignore [Reviewed by John Palmieri] Merged in sage-5.0.beta14: #8577: Martin Albrecht: Fix ETuple.eadd_p [Reviewed by Mike Hansen] #8720: Jason Grout, Mike Hansen, Paul Zimmermann: CC and CDF do not display numeric 0 [Reviewed by Paul Zimmermann, Karl-Dieter Crisman] #9826: Johan Bosman, Michael Orlitzky: Memory corruption in polynomial complex_roots() method [Reviewed by Michael Orlitzky, Johan Bosman, Volker Braun] #10281: William Stein: Multimodular echelon form over cyclotomic fields fails [Reviewed by Martin Raum] #10328: Julien Puydt: Flint-1.5.2 with ARM 32-bits [Reviewed by Dmitrii Pasechnik] #10901: Alex Ghitza: segfault in roots() in wrong ring [Reviewed by Michael Orlitzky] #10914: Michael Orlitzky: Integration involving abs gives wrong result [Reviewed by Karl-Dieter Crisman] #11625: John Palmieri: speed up "remove_faces" for simplicial complexes [Reviewed by Mike Hansen] #12169: Fidel Barrera-Cruz: Adding Harary graphs to graph generators. [Reviewed by David Coudert, Nathann Cohen] #12347: Punarbasu Purkayastha: make install broken in Sage 4.8 [Reviewed by Jeroen Demeyer, Paul Zimmermann] #12493: John Palmieri: tol and optional in doctests don't play well together [Reviewed by Marco Streng] #12536: Anne Schilling, Nicolas M. Thiéry: Implementation of class for Linear Extensions of a finite Poset [Reviewed by Nicolas M. Thiéry, Anne Schilling] #12551: Julian Rueth: characteristic() does not work for extensions for function field [Reviewed by Jeroen Demeyer] #12568: Itai Bar-Natan, Jean-Pierre Flori: make doesn't work properly for targets 'test' and 'micro_release' [Reviewed by Jeroen Demeyer] #12596: Benjamin Jones: poor documentation of elliptic integrals in functions/special.py [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] #12597: Mike Hansen: Error in creating a Permutation Group [Reviewed by Daniel Krenn] #12620: Karl-Dieter Crisman: problems with bezier3d command [Reviewed by Michael Orlitzky] #12636: Johan Bosman: 0.is_squarefree() raises a PariError [Reviewed by Jeroen Demeyer] #12717: Florent Hivert: Add \NN to standard latex constant, fixes a few glitches in LaTeX/HTML output [Reviewed by Nicolas M. Thiéry] #12766: David Roe: Better plotting for elliptic curves [Reviewed by Kiran Kedlaya] #12769: David Roe: Better error message when looking up an elliptic curve by nonexistent label [Reviewed by Mike Hansen] #12791: David Coudert: Running time improvements of some (di)graphs products [Reviewed by Nathann Cohen] #12796: Nils Bruin: Allow more general evaluation of FDerivativeOperator [Reviewed by Michael Orlitzky] #12800: Jeroen Demeyer: Upgrade zlib to 1.2.6 [Reviewed by Michael Orlitzky, Julien Puydt, Leif Leonhardy] #12801: Nils Bruin: substitute_function misses some substitutions [Reviewed by Michael Orlitzky] #12820: Jeroen Demeyer: OS X Lion: use "clang" as default C compiler [Reviewed by Leif Leonhardy] #12825: Jeroen Demeyer: Fine-tune auto-detection of whether to install GCC [Reviewed by Dan Drake, Leif Leonhardy] #12829: Paul Zimmermann, Jeroen Demeyer: Remove cast in real_mpfi.pyx [Reviewed by François Bissey] #12849: Florent Hivert, Jeroen Demeyer: The argspecs of extension function/methods is broken in the Sphinx documentation [Reviewed by Mike Hansen] #12853: Andrey Novoseltsev: Severe slow-down in elliptic_curve integral_points() [Reviewed by Jeroen Demeyer] Merged in sage-5.0.rc0: #5859: Michael Orlitzky: sage -coverageall fails on directories with zero tests [Reviewed by André Apitzsch] #8119: Robert Bradshaw: Rename change the hash value of some objects [Reviewed by Florent Hivert, Nicolas M. Thiéry, Nicolas Borie] #11616: Leif Leonhardy, Jeroen Demeyer: Upgrade MPIR to a more recent upstream release [Reviewed by Jeroen Demeyer, Leif Leonhardy, Volker Braun] #12272: Jeroen Demeyer: More # long time additions [Reviewed by Georg S. Weber] #12812: Andrey Novoseltsev: Bug in summation of toric divisors [Reviewed by Volker Braun] #12830: Leif Leonhardy: Work around GCC 4.7.0 bug on ia64 and improve the GMP-ECM spkg [Reviewed by Jeroen Demeyer] #12833: Nathann Cohen: Crashes and doctests problems with Gurobi [Reviewed by John Perry] #12837: Leif Leonhardy: MPFR doesn't compile with GCC-4.7.0 on ia64 [Reviewed by Volker Braun] #12857: Jeroen Demeyer: Split off Graphics class from plot.py [Reviewed by Benjamin Jones, Florent Hivert] #12888: David Coudert: Set new default parameters for RandomGNP [Reviewed by Nathann Cohen] Merged in sage-5.0.rc1: #12898: Jeroen Demeyer: Update top-level README.txt [Reviewed by William Stein, Karl-Dieter Crisman, David Kirkby, Martin Raum] #12899: Jeroen Demeyer: Update the "Install from Source Code" docs for sage-5.0 [Reviewed by Nathann Cohen] #12909: Robert Bradshaw, Jeroen Demeyer: gdmodule: don't use /sw and /usr/local paths [Reviewed by Volker Braun] January 20, 2012 ---------------- Sage 4.8 was released on 20 January 2012. It is available at http://www.sagemath.org/download.html * About Sage (http://www.sagemath.org) Sage is developed by volunteers and combines over 90 open source packages. It is available for download from www.sagemath.org and its mirrors in source or binary form. 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. Please report build and doctest results to the Google group * sage-release: http://groups.google.com/group/sage-release The following 94 people contributed to this release. Of those, 22 made their first contribution to Sage: - Alexander Dreyer - Aly Deines - Andrey Novoseltsev - André Apitzsch - Anne Schilling - Benjamin Jones - Bogdan Banu [first contribution] - Burcin Erocal - Charlie Turner - Christian Stump - Colton Pauderis [first contribution] - Dan Drake - Daniel Krenn [first contribution] - David Coudert [first contribution] - David Eklund [first contribution] - David Joyner - David Kirkby - David Krumm [first contribution] - David Loeffler - David Roe - Dmitrii Pasechnik - Douglas McNeil - Eduardo Dueñez [first contribution] - Emil Widmann - Eviatar Bach - Fidel Barrera-Cruz - Florent Hivert - Francis Clarke - François Bissey - Fredrik Johansson - Frithjof Schulze [first contribution] - Frédéric Chapoton - Georg S. Weber - Hiroto Mulia [first contribution] - Ivo Hedtke - Jan Elffers [first contribution] - Jason Grout - Jeroen Demeyer - Johan Bosman - Johan Sebastian Rosenkilde Nielsen - John Cremona - John Palmieri - John Pang [first contribution] - John Perry - Joris Vankerschaver - Julian Rueth - Julien Puydt - Justin Walker - Karl-Dieter Crisman - Kenneth Smith [first contribution] - Keshav Kini - Kiran Kedlaya - Leif Leonhardy - Leonardo Sampaio - Luis Felipe Tabera Alonso - Lukáš Lánský [first contribution] - Maarten Derickx - Marco Streng - Marshall Hampton - Martin Albrecht - Martin Raum - Michael Orlitzky [first contribution] - Michiel Kosters [first contribution] - Miguel Marco - Mike Hansen - Mike Zabrocki - Minh Van Nguyen - Mitesh Patel - Monique van Beek [first contribution] - Moritz Minzlaff - Nathan Carter [first contribution] - Nathann Cohen - Nicolas Thiery - Niels Ranosch - Nils Bruin - Ondrej Certik - Paul Zimmermann - Peter Müller [first contribution] - Peter Story [first contribution] - Punarbasu Purkayastha - R. Andrew Ohana - Reg Burgess - Rob Beezer - Robert Bradshaw - Robert Campbell [first contribution] - Robert Harron [first contribution] - Robert Miller - Sam Scott [first contribution] - Simon King - Steven Trogdon - Tim Dumol - Tom Boothby - Volker Braun - William Stein * Release manager: Jeroen Demeyer. * We closed 241 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-4.8/tickets.html Closed tickets: #12308: R. Andrew Ohana: Update Cremona's table of elliptic curves for Sage [Reviewed by John Cremona] #1385: Re-organize number field element inheritance hierarchy [Reviewed by Jeroen Demeyer, David Loeffler] #5377: weird output for trivial class group [Reviewed by Jeroen Demeyer] #9389: Bug in polynomials over residue fields (was: sage crashing when computing local_data() for an EC) [Reviewed by Jeroen Demeyer] #10141: bug in printing trivial class groups (trivial to fix) [Reviewed by Jeroen Demeyer] #10200: Catch Sphinx WARNING or ERROR [Reviewed by Minh Van Nguyen, Jeroen Demeyer] #10730: simon_two_descent -- reports points as being independent, but they are not [Reviewed by Robert Miller] #10910: Avoid nfinit while factoring polynomials [Reviewed by Luis Felipe Tabera Alonso] #11119: ECL 11.1.1 fails on Cygwin [Reviewed by Jeroen Demeyer] #10195: Occasional doctest failure in libs/fplll/fplll.pyx [Reviewed by Jeroen Demeyer] #6894: Plot list of functions with different colors by default [Reviewed by Karl-Dieter Crisman] #9408: relativize in number fields is broken [Reviewed by Luis Felipe Tabera Alonso] #9847: Handle a preset R_PROFILE variable [Reviewed by Leif Leonhardy, Karl-Dieter Crisman] #12000: Volker Braun: block_matrix over cyclotomics fails [Reviewed by Johan Bosman] #12031: Jeroen Demeyer: Remove sage-sage.py [Reviewed by John Palmieri] #1236: tate pairings on elliptic curves -- add to sage [Reviewed by David Roe] #6124: Bug in galois_group of a p-adic field extension [Reviewed by David Roe] #7929: Pickling fails for some residue fields [Reviewed by David Roe] #8274: R's spkg-install needs a good overhaul. [Reviewed by Karl-Dieter Crisman] #11414: CartesianProduct should return a list of tuples [Reviewed by David Roe] #11826: coercing to the residue field of p-adic extensions [Reviewed by David Roe] #11916: add numerical integration to reference manual [Reviewed by Jeroen Demeyer] #12017: Adds CoerceKey [Reviewed by David Roe] #879: "sage -testall" should summarize all failures at the end of the run [Reviewed by Michael Orlitzky] #3447: sage -t foo gives wrong path to the file foo in the output [Reviewed by Maarten Derickx, Michael Orlitzky] #10967: R breaks if SAGE_LOCAL undefined [Reviewed by Jeroen Demeyer] #11260: ECL-11.1.1 fails to compile maxima on WIndows 7 / Cygwin 1.7.9 [Reviewed by Dmitrii Pasechnik] #12065: Failing doctest - R installation broken? [Reviewed by Burcin Erocal, Volker Braun] #12104: Cygwin import problem with randstate [Reviewed by Dmitrii Pasechnik, Karl-Dieter Crisman] #1634: update zodb to 3.8.1 [Reviewed by Keshav Kini] #5323: "./sage -t" gives misleading error message when doctesting non-existing file with absolute patch [Reviewed by Michael Orlitzky] #5938: graph plotting -- ploting of graphs (networks) is somehow messed up/scaled wrong/cropped wrong since it doesn't work with graphics_array [Reviewed by Jason Grout] #5970: Weak references in Polynomial Ring cache [Reviewed by Simon King] #6439: doctests beginning with Sage: are silently ignored [Reviewed by Michael Orlitzky] #11325: Multiple line cells generation in live help broken, lots of samples unusable [Reviewed by Jeroen Demeyer, Peter Story] #11497: Twisted won't build on Cygwin - sometimes [Reviewed by Reg Burgess, Karl-Dieter Crisman, Dmitrii Pasechnik] #11502: Maxima fails to build on Cygwin 1.7.3 on XP [Reviewed by Karl-Dieter Crisman] #11724: only print warnings when needed [Reviewed by Maarten Derickx] #12072: Wrap pynac ex.normal method [Reviewed by Jason Grout] #12130: CPLEX acquires maximal number of threads on system [Reviewed by Nathann Cohen] #12163: Missing digits in numerical_approx [Reviewed by Karl-Dieter Crisman] #12185: Bug in norm for orders of relative number fields [Reviewed by David Loeffler] #12252: latex(number field) sometimes looks stupid (though is technically correct) [Reviewed by David Loeffler] #12285: Update darwin_memory_usage.c for Lion header files [Reviewed by Nathan Carter] Merged in sage-4.8.alpha0: #8664: Mike Hansen, Leif Leonhardy: Upgrade Sage's MPIR spkg to version 2.1.3 [Reviewed by Leif Leonhardy, Dmitrii Pasechnik] #9858: Leif Leonhardy: FLINT 1.5.0.p5's test suite fails to build with new GMP/MPIR [Reviewed by Jeroen Demeyer] #9992: Leif Leonhardy: Python scripts try to run before Python is built. [Reviewed by John Palmieri] #10155: Christian Stump: Implementation of the Cyclic Sieving Phenomenon [Reviewed by Frédéric Chapoton] #10275: John Palmieri, Julian Rueth: matrix output strangeness for cached methods [Reviewed by Julian Rueth, John Palmieri] #10505: Nathann Cohen: Round values returned by CPLEX when the variable's type is integer/binary [Reviewed by David Coudert] #10954: Nathann Cohen: Expose weight options in distance method [Reviewed by Leonardo Sampaio] #11099: Nathann Cohen: digraphs.RandomDirectedGNM [Reviewed by David Coudert] #11367: Nathann Cohen: Rounding values, and inconsistencies in graph methods [Reviewed by Leonardo Sampaio] #11560: François Bissey: update sympy to 0.7.1 [Reviewed by David Joyner] #11587: R. Andrew Ohana: update Cremona's tables for Sage [Reviewed by John Cremona, Tom Boothby] #11742: Anne Schilling, Mike Zabrocki: Implementation of class for cores [Reviewed by Nicolas Thiery, Mike Zabrocki] #11812: Marco Streng: traceback with load and attach of .sage files [Reviewed by Johan Bosman] #11846: Nathann Cohen: Independent set through Linear Programming (sometimes, it is faster !) [Reviewed by David Coudert] #11869: Jeroen Demeyer: Horrible bug in number field conversion [Reviewed by Marco Streng] #11882: John Palmieri: update readline to 6.2 [Reviewed by Leif Leonhardy, Alexander Dreyer] #11883: John Palmieri: fix boehm-gc so it builds on OS X Lion [Reviewed by William Stein] #11885: Benjamin Jones: call function in sage.libs.mpmath.utils doesn't handle parent=parent(float) [Reviewed by Burcin Erocal] #11891: Jeroen Demeyer: NumberField(...).pari_polynomial() should return an integral polynomial [Reviewed by Luis Felipe Tabera Alonso] #11896: Leif Leonhardy, Jeroen Demeyer: MPIR 2.x may fail to build on 32-bit operating systems [Reviewed by Steven Trogdon, Jeroen Demeyer, Leif Leonhardy] #11914: Leif Leonhardy: `sage -n` fails when current directory is $SAGE_ROOT/devel/sage [Reviewed by Keshav Kini, John Palmieri] #11917: Nathann Cohen: Memory leaks with LP Solvers [Reviewed by Peter Müller, Paul Zimmermann] #11923: Fidel Barrera-Cruz: Graph Theory: Small fix on show3d for graphs [Reviewed by Nathann Cohen] #11926: Jeroen Demeyer: "make" should run Sage once [Reviewed by John Palmieri, Leif Leonhardy] #11928: Nathann Cohen: Update Graph.clique_number to use MILP [Reviewed by David Coudert] #11944: Nathann Cohen: Update Graph.clique_maximum to use MILP [Reviewed by David Coudert] #11959: John Palmieri: Remove the necessity to set SAGE_PARALLEL_SPKG_BUILD [Reviewed by Leif Leonhardy] #11964: Leif Leonhardy: MPIR: Use proper ABI name on Linux PPC64 [Reviewed by John Palmieri] #11972: John Palmieri: avoid race conditions when creating directories [Reviewed by Jeroen Demeyer] Merged in sage-4.8.alpha1: #8654: R. Andrew Ohana, Jeroen Demeyer: add "sage -sqlite3" command line option [Reviewed by William Stein, Leif Leonhardy, John Palmieri] #9211: Jason Grout: graph vertices cut off [Reviewed by Punarbasu Purkayastha] #9334: Aly Deines, Marco Streng, Jeroen Demeyer: Implement Hilbert symbols over number fields [Reviewed by David Loeffler, John Cremona, Marco Streng, Jeroen Demeyer] #10112: Mike Hansen, Francis Clarke: random_prime does not handle erroneous input gracefully - it hangs [Reviewed by David Kirkby, Johan Bosman] #10767: Jeroen Demeyer: Fractional ideals intersection gives wrong answers in some cases. [Reviewed by John Cremona] #11130: Jeroen Demeyer, John Cremona: Update PARI to version 2.5.0 [Reviewed by John Cremona, Jeroen Demeyer, William Stein] #11321: Jeroen Demeyer, Leif Leonhardy: Make lcalc compatible with the new PARI [Reviewed by Volker Braun, Leif Leonhardy, William Stein] #11555: Rob Beezer: Expand print representation of free module morphisms [Reviewed by Julian Rueth] #11604: Jeroen Demeyer: PARI qfminim bug on 32-bit systems (Sage 4.7 and 4.6.2) [Reviewed by Leif Leonhardy] #11607: John Perry: read constraints from linear program [Reviewed by Nathann Cohen] #11761: Robert Bradshaw: Upgrade Cython to 0.15.1 [Reviewed by Jeroen Demeyer] #11762: Robert Bradshaw: More import cleanup [Reviewed by Maarten Derickx] #11836: Jeroen Demeyer: gens_reduced() does not handle "large" ideals [Reviewed by Marco Streng] #11854: Jeroen Demeyer: Fix conversion QQ -> PARI [Reviewed by William Stein] #11886: John Palmieri: fix scipy so it builds on OS X Lion [Reviewed by Mike Hansen, Leif Leonhardy] #11890: Jeroen Demeyer: Sage cannot factor polynomials over number fields with unfactorable discriminant [Reviewed by Luis Felipe Tabera Alonso] #11911: Simon King: Fix missing uniqueness of parents when unpickling libsingular polynomial rings [Reviewed by Martin Albrecht, Volker Braun] #11946: Jeroen Demeyer: Change iteration order for finite field multiplicative_generator() [Reviewed by Keshav Kini] #11988: Johan Bosman: Bug in LaTeX representation of Dirichlet characters [Reviewed by Andrey Novoseltsev] #11991: John Palmieri: record time, version in sage-starts [Reviewed by Leif Leonhardy] #11993: Leif Leonhardy: Fix output of `sage --version` [Reviewed by John Palmieri] Merged in sage-4.8.alpha2: #8239: David Roe: misleading teichmuller behaviour [Reviewed by Johan Bosman] #10620: John Palmieri: Upgrade Sphinx to version 1.1.2 [Reviewed by Jeroen Demeyer] #11279: Nathann Cohen: Convex Hulls, Hull number in graphs [Reviewed by Leonardo Sampaio] #11721: Rob Beezer: Silent failures in matrix code [Reviewed by Johan Bosman] #11781: Robert Harron: Conversion from Zmod element to padic element raises "not a power of the same prime" incorrectly, add conversion from residue_field [Reviewed by David Roe] #11784: Luis Felipe Tabera Alonso: Add more sanity checks to FiniteField constructor [Reviewed by Johan Bosman] #11927: Hiroto Mulia, John Pang: option degree_sequence for graphs [Reviewed by Dmitrii Pasechnik] #11937: Daniel Krenn: Doctest fails in gap_reps.py when Kash is installed [Reviewed by Johan Bosman] #11949: Nathann Cohen: Gurobi Support ! [Reviewed by Peter Müller] #11952: Jeroen Demeyer: Fix conversion Python -> PARI [Reviewed by Robert Bradshaw] #11965: William Stein: OS X 10.7 Lion: Error building sage.misc.darwin_utilities extension [Reviewed by Jeroen Demeyer] #11966: William Stein: OS X 10.7 Lion: Maxima fails to build [Reviewed by Leif Leonhardy, John Palmieri] #11969: Jeroen Demeyer: Clean up top-level Makefile [Reviewed by John Palmieri, Leif Leonhardy] #11971: Jeroen Demeyer: get_memory_usage() doctest failure [Reviewed by Justin Walker] #11994: Nathann Cohen: Vertex separation and pathwidth in Sage [Reviewed by David Coudert] #12002: Jeroen Demeyer: avoid race conditions when creating directories - scripts [Reviewed by John Palmieri] #12026: William Stein: root finding misses a root over QQbar [Reviewed by Keshav Kini] #12029: Simon King, Florent Hivert: Fast conversion of ClonableIntArray to list [Reviewed by Florent Hivert, Simon King] #12036: William Stein: improve doctest coverage of gsl/interpolation.pyx from 0% to 100% [Reviewed by Karl-Dieter Crisman] #12037: Dan Drake: `search_src` and friends shouldn't look in hidden files [Reviewed by John Palmieri] #12038: David Roe: Complex numbers can segfault if given bad input to the __init__ method [Reviewed by Robert Bradshaw] Merged in sage-4.8.alpha3: #4260: Burcin Erocal, Martin Albrecht, Rob Beezer: use LinBox as native matrix representation for dense matrices over GF(p) [Reviewed by Burcin Erocal, Simon King, Martin Albrecht, Jeroen Demeyer] #5177: Tim Dumol, Mitesh Patel: Notebook keeps directories for deleted cells [Reviewed by Jason Grout] #5852: Jeroen Demeyer: Properly canonicalize $SAGE_ROOT [Reviewed by John Palmieri, Leif Leonhardy] #9562: Martin Albrecht: Add M4RIE to Sage [Reviewed by Paul Zimmermann, Simon King] #9751: Rob Beezer: Documentation for AdditiveMagmas' addition_table [Reviewed by Florent Hivert] #11583: Maarten Derickx, Dan Drake: Sagetex example has some nontrivial dependancy's [Reviewed by John Palmieri] #11650: John Palmieri: Make 'convert' the standard way to produce animated gifs (again) [Reviewed by Dan Drake] #11796: Paul Zimmermann: inconsistency between 0.nbits() and 0.ndigits(base=2) [Reviewed by André Apitzsch] #11847: John Perry: unexpexted behavior of degree() with matrix ordering [Reviewed by Martin Albrecht] #11884: Dmitrii Pasechnik, Mike Hansen, Karl-Dieter Crisman, William Stein, John Palmieri, Jeroen Demeyer: Fix ECL so it builds on OS X Lion [Reviewed by Karl-Dieter Crisman, Reg Burgess, François Bissey, Leif Leonhardy, John Palmieri] #11924: John Palmieri: lazy_import_cache.get_cache_file doesn't work well if DOT_SAGE doesn't end with a slash [Reviewed by Jeroen Demeyer] #11936: Johan Bosman: image_type of galois_representation of EllipticCurve hangs on first call [Reviewed by Daniel Krenn] #11963: Jason Grout: aspect ratio is not handled correctly in combined plots [Reviewed by Dan Drake] #11997: William Stein: fix a mistake in the docstring for lift_to_sl2z (etc.) [Reviewed by Johan Bosman, Jeroen Demeyer] #12012: John Palmieri: 'make distclean' should clean up start.log, spkg/parallel_make.cfg [Reviewed by Michael Orlitzky] #12019: Nathann Cohen: doctest failure in linear_programming.rst (multiple correct solutions) [Reviewed by Emil Widmann] #12020: Martin Albrecht, Volker Braun, Jeroen Demeyer: bug in zero_matrix rewrite in matrix_space.py [Reviewed by William Stein, Jeroen Demeyer, Volker Braun,] #12022: Nathann Cohen: failing doctest in integer_vector.py (gale ryser theorem) / multiple solutions [Reviewed by Emil Widmann] #12041: André Apitzsch: Replace __getslice__ with functionality in __getitem__ in several files [Reviewed by François Bissey] #12047: Jeroen Demeyer: numerical_integral(f, a, a) should always be zero [Reviewed by Michael Orlitzky] #12049: Daniel Krenn: matrix_integer_dense.pyx: 'algorithn' instead of 'algorithm' [Reviewed by Burcin Erocal] #12052: Nathann Cohen: Some distance computations remained *slow* [Reviewed by David Coudert] #12056: Jeroen Demeyer: sage -sdist/-bdist should use the current branch [Reviewed by Volker Braun] #12058: Jeroen Demeyer: Mercurial should not enable pager by default [Reviewed by Volker Braun] #12079: Fredrik Johansson: Two memory leaks in mpmath extension code [Reviewed by Volker Braun] #12081: Jeroen Demeyer: Do not include doc/output in sage spkg [Reviewed by John Palmieri] #12082: Jeroen Demeyer: spkg-install of extcode, sage_scripts should preserve timestamp [Reviewed by John Palmieri] #12085: Jeroen Demeyer, André Apitzsch: Fix docstring in sage/crypto/boolean_function.pyx [Reviewed by Volker Braun] #12086: Jeroen Demeyer: Do not include doc/en/reference/sage in sage spkg [Reviewed by Dmitrii Pasechnik] #12087: Jeroen Demeyer: Clean up devel/sage/.hgignore [Reviewed by Keshav Kini] #12097: Jeroen Demeyer: General clean-up of sage-make_relative [Reviewed by Volker Braun] #12098: Jeroen Demeyer: Readline should depend on termcap [Reviewed by Volker Braun] Merged in sage-4.8.alpha4: #5352: André Apitzsch: the valgrind log files in sage-doctest are written to $HOME/.sage instead of $DOT_SAGE [Reviewed by Burcin Erocal, Michael Orlitzky] #8525: David Roe: mistake in docstring for R=Zp(3)'s R.plot method. [Reviewed by Johan Bosman] #10292: David Roe: padics, precision, list() and printing [Reviewed by Johan Bosman] #11526: Miguel Marco, David Eklund, Frithjof Schulze: count_points() error for generic schemes. (includes patch) [Reviewed by Johan Bosman, Julian Rueth] #11556: Rob Beezer: Linear transformations, built from free module morphisms [Reviewed by Martin Raum, Jason Grout] #11735: Nathann Cohen: Bug in is_chordal [Reviewed by David Coudert] #11782: Johan Bosman: Bug in discriminant of polynomials over Z/nZ with n composite [Reviewed by Julian Rueth] #11933: Jeroen Demeyer: Fix qepcad doctests [Reviewed by Karl-Dieter Crisman] #11987: Nils Bruin, Karl-Dieter Crisman: integrate returns divergent, maxima.integrate the correct result [Reviewed by Karl-Dieter Crisman, Nils Bruin] #12035: Dan Drake: `list_plot` should accept lists of complex numbers [Reviewed by Keshav Kini] #12057: Volker Braun: Upgrade R (r-project.org) [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] #12063: Jeroen Demeyer: EllipticCurve._pari_() should use .pari_curve() [Reviewed by David Roe] #12096: Jeroen Demeyer: Disable parallel "make install" in Python spkg [Reviewed by François Bissey] #12106: Jeroen Demeyer: Implement sage --rsyncdist [Reviewed by Volker Braun] #12111: David Roe: Bug in Integer.is_power_of [Reviewed by André Apitzsch] #12122: Jeroen Demeyer: Add doctest to check sage_make_relative [Reviewed by Volker Braun] #12126: John Palmieri: Fix upgrading of boehm-gc package [Reviewed by Jeroen Demeyer] #12128: Jeroen Demeyer: "hg verify" is not a proper way to check whether there is an hg repo [Reviewed by Michael Orlitzky] #12137: Jeroen Demeyer: Fix parallel building of Singular [Reviewed by Volker Braun] #12138: Jeroen Demeyer: Fix parallel building zlib [Reviewed by John Palmieri] #12139: Jeroen Demeyer: Disable parallel "make install" in MPIR spkg [Reviewed by Volker Braun] Merged in sage-4.8.alpha5: #2220: Michael Orlitzky: irreducibility testing in relative extensions seems to be messed up [Reviewed by Colton Pauderis] #6087: Michael Orlitzky: graph automorphism group segfaults on invalid input (fixed already; add doctest) [Reviewed by Jason Grout] #6424: Ondrej Certik, Douglas McNeil: One can no longer convert I=sqrt(-1) to sympy [Reviewed by Mike Hansen] #8078: Michael Orlitzky: Fix algsys in Maxima [Reviewed by Mike Hansen] #8168: Mitesh Patel: Keyword option to make reset() detach all attached files [Reviewed by Mike Hansen] #9786: Lukáš Lánský: Subsets(list, submultiset=True): wrong output [Reviewed by Mike Hansen] #10172: Moritz Minzlaff: Rational Point algorithm bug [Reviewed by John Cremona] #10621: Marco Streng: Make Conic class able to find points over number fields [Reviewed by John Cremona] #10642: Ivo Hedtke, Julian Rueth: Additional points in a documentation titles [Reviewed by Julian Rueth, Jason Grout] #10791: Rob Beezer: Fix and upgrade Gram-Schmidt [Reviewed by Martin Raum, John Palmieri] #11597: Volker Braun: Dimension of the singular set [Reviewed by Andrey Novoseltsev] #11637: Nathann Cohen: Updated docstring for Graph.cores() [Reviewed by Jason Grout] #11758: David Krumm, Maarten Derickx: Bug in global_height function [Reviewed by Frithjof Schulze] #11799: André Apitzsch: typo in tiny_integrals [Reviewed by Julian Rueth] #11899: Jeroen Demeyer: Add #long time at various places [Reviewed by Julian Rueth] #11904: Jeroen Demeyer: Change default variable name for NumberField and NumberFieldElement -> PARI conversion [Reviewed by John Cremona] #11947: Jeroen Demeyer: Implement cardinality for polynomial quotient rings [Reviewed by John Cremona] #11950: Nathann Cohen: Bug in topological_sort [Reviewed by David Coudert] #11961: Nathann Cohen, Jan Elffers: Fixes a bug in is_chordal -- two algorithms [Reviewed by David Coudert] #11976: Jason Grout: matrix plot colorbars [Reviewed by Rob Beezer] #12003: John Palmieri: improving the list of command-line options in the Sage reference manual [Reviewed by Julian Rueth] #12016: John Palmieri, Jeroen Demeyer: parallelism in Sage: just use value of 'MAKE' [Reviewed by John Palmieri, Jeroen Demeyer] #12108: Lukáš Lánský: is_eulerian doesn't handle disconnected graphs properly [Reviewed by Nathann Cohen] #12118: Jeroen Demeyer, Justin Walker: Fix parallel building of libgpg_error [Reviewed by Justin Walker] #12131: Volker Braun, Simon King: $SAGE_LOCAL/lib and lib64 [Reviewed by Simon King, Volker Braun] #12146: William Stein: hidden markov models: add option to sample/generate to specify the starting state of sequence [Reviewed by Jason Grout] #12157: François Bissey: Segfault in __Pyx_check_binary_version [Reviewed by Volker Braun] #12158: Jeroen Demeyer: Segfault in PARI's err_init() during pari_init_opts() [Reviewed by Volker Braun] #12164: Jason Grout: graph subgraph_search does not return copy of subgraph [Reviewed by Nathann Cohen] #12166: Johan Bosman: Elliptic curves: improve documentation of period_lattice [Reviewed by John Cremona] #12176: Michiel Kosters: Compute Minkowski bound for relative number fields [Reviewed by Monique van Beek] #12213: William Stein: aspect_ratio and figsize for graphics do not work as expected in sage-4.8.alpha5 [Reviewed by Jason Grout] Merged in sage-4.8.alpha6: #8029: Eduardo Dueñez, Michael Orlitzky: Defect: Power series over a polynomial ring with real coefficients [Reviewed by Mike Hansen, Francis Clarke, Robert Campbell] #9419: John Palmieri: Update Developers Guide to state how patches should be made. [Reviewed by Karl-Dieter Crisman] #11245: Karl-Dieter Crisman, Dmitrii Pasechnik: broken tar on cygwin (Windows 7), cddlib and networkx fail to install [Reviewed by Reg Burgess, Dmitrii Pasechnik, Karl-Dieter Crisman] #11319: Johan Bosman: Cannot create homomorphism from prime residue field to finite field [Reviewed by Kiran Kedlaya, Michiel Kosters] #11417: Sam Scott: binomial of polynomial is not polynomial [Reviewed by Johan Bosman] #11704: Jeroen Demeyer: Resolve symbolic links in $HOME/.sage [Reviewed by John Palmieri] #11838: Paul Zimmermann: multivariate factorization over non-prime finite fields hangs [Reviewed by Bogdan Banu] #11877: Niels Ranosch: complete_primary_decomposition should be available as primary_decomposition_complete [Reviewed by Julian Rueth] #11902: Andrey Novoseltsev: Fan subdivision should check rays [Reviewed by Volker Braun] #11948: Jeroen Demeyer: Fix numeric evaluation of error function [Reviewed by Karl-Dieter Crisman] #12066: R. Andrew Ohana: delete databases/gamma0wt2.py [Reviewed by Julian Rueth] #12067: R. Andrew Ohana: delete databases/bz2Pickle.py [Reviewed by Julian Rueth] #12124: Jeroen Demeyer: Fix Eisenstein L-series precision [Reviewed by Frithjof Schulze, David Loeffler] #12147: Johan Sebastian Rosenkilde Nielsen: Binary NTL Finite field elements can't coerce to GF(2) [Reviewed by Julian Rueth] #12156: Jeroen Demeyer, Punarbasu Purkayastha: Pretty print LatexExpr directly [Reviewed by Andrey Novoseltsev, Punarbasu Purkayastha, John Palmieri] #12178: Punarbasu Purkayastha: Error in typeset of polynomials [Reviewed by Andrey Novoseltsev, Jeroen Demeyer] #12187: Charlie Turner: Bug in is_singular for plane projective curves [Reviewed by David Loeffler] #12190: Maarten Derickx: Remove useless scripts from local/bin [Reviewed by Julian Rueth, Jeroen Demeyer] #12191: Michiel Kosters: is_squarefree for integer polynomials [Reviewed by Monique van Beek, David Loeffler] #12196: Colton Pauderis: Improve latex for quadratic fields [Reviewed by Michiel Kosters] #12197: Jeroen Demeyer: Improve LaTeX of differential form elements [Reviewed by Joris Vankerschaver] #12207: William Stein, Jeroen Demeyer: Typing "sage -cython" doesn't work due to bug in wrapper script [Reviewed by Volker Braun] #12208: Rob Beezer: LU decomposition gives wrong results on cyclotomic matrices (MacOSX-specific) [Reviewed by Dmitrii Pasechnik] #12211: David Eklund: bug in equation checking for quasi projective/affine schemes [Reviewed by Volker Braun] Merged in sage-4.8.rc0: #8245: Kenneth Smith: tutorial: typo in section "Euler’s Method for Systems of Differential Equations" [Reviewed by Karl-Dieter Crisman] #10965: Peter Story, Kenneth Smith: Fix trivial problems in plot/polygon [Reviewed by Karl-Dieter Crisman] #11970: Leif Leonhardy: r-2.10.1.p4 may fail to configure with readline (BLOCKS Sage from building on Ubuntu 11.10) [Reviewed by Jeroen Demeyer] #12110: Julien Puydt: [ARM] Singular 3-1-3-3.p1 doesn't compile as-is [Reviewed by Dmitrii Pasechnik] #12149: William Stein: float('nan')>1 crashes Sage. [Reviewed by Simon King, David Loeffler] #12206: William Stein: Put SAGE_SCRIPTS first in spkg/standard/deps [Reviewed by John Palmieri] #12222: Jason Grout: default aspect ratio for geometric objects [Reviewed by Karl-Dieter Crisman] #12245: Martin Albrecht, David Loeffler: M4RIE test suite fails due to missing dependencies [Reviewed by Martin Albrecht, David Loeffler] #12248: Jeroen Demeyer: Do not run "make -q" when upgrading [Reviewed by John Palmieri, Volker Braun] #12249: Jeroen Demeyer: Add doctest for sage-run [Reviewed by Volker Braun] #12258: Keshav Kini: Prune .hgtags files [Reviewed by Punarbasu Purkayastha] #12263: Jeroen Demeyer: Unset TERM when running sage non-interactively [Reviewed by Volker Braun] #12274: Eviatar Bach: Typo in FreeModuleElement.norm [Reviewed by Minh Van Nguyen] #12282: Jeroen Demeyer: Fix strcmp() with NULL argument in termcap library [Reviewed by Georg S. Weber] #12283: Jeroen Demeyer: Numerical noise in chmm.pyx [Reviewed by Marshall Hampton] #12288: John Palmieri: hg_sage and friends should unset HGPLAIN [Reviewed by Karl-Dieter Crisman] #12312: Jeroen Demeyer: Disable parallel building of ATLAS [Reviewed by Volker Braun] November 03, 2011 ----------------- Sage 4.7.2 was released on 29 October 2011. It is available at http://www.sagemath.org/download.html * About Sage (http://www.sagemath.org) Sage is developed by volunteers and combines over 90 open source packages. It is available for download from www.sagemath.org and its mirrors in source or binary form. 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. Please report build and doctest results to the Google group * sage-release: http://groups.google.com/group/sage-release The following 100 people contributed to this release. Of those, 19 made their first contribution to Sage: - Achim Fassbender [first contribution] - Alexander Dreyer - Alex Ghitza - Alex Raichev [first contribution] - Aly Deines - André Apitzsch - Andrey Novoseltsev - Anne Schilling - Benjamin Jones - Bruce Cohen [first contribution] - Burcin Erocal - Christian Stump - Christopher Hall [first contribution] - Chris Wuthrich - Dan Drake - Dan Shumow - David Joyner - David Kirkby - David Loeffler - David Montminy [first contribution] - David Perkinson - David Roe - Diego de Estrada [first contribution] - Dima Pasechnik - Dmitrii Pasechnik - Douglas McNeil - Eviatar Bach - Florent Hivert - Francis Clarke - François Bissey - Franco Saliola - Frédéric Chapoton [first contribution] - Gustavo Rama - Harald Schilly - Ivan Andrus - Ivo Hedtke [first contribution] - Jan Groenewald - Jason Grout - Jason Hill [first contribution] - Jean-Pierre Flori - Jeroen Demeyer - Johan Bosman - John Cremona - John Palmieri - John Perry - Jonathan Bober - Joris Vankerschaver - Julian Rueth [first contribution] - Karl-Dieter Crisman - Katherine Stange [first contribution] - Kelvin Li - Keshav Kini - Kiran Kedlaya - Kwankyu Lee - Leif Leonhardy - Leonardo Sampaio - Luca De Feo - Luis Felipe Tabera Alonso - Maarten Derickx - Marco Streng - Mariah Lenox - Mario Pernici [first contribution] - Marshall Hampton - Martin Albrecht - Martin Raum - Martin von Gagern [first contribution] - Mike Hansen - Mike Zabrocki - Minh Van Nguyen - Mitesh Patel - Nathann Cohen - Nicolas Borie - Nicolas Estibals [first contribution] - Nicolas M. Thiéry - Nils Bruin - Pablo Angulo - Paulo César Pereira de Andrade - Paul-Olivier Dehaye - Paul Zimmermann - Peter Bruin - Punarbasu Purkayastha [first contribution] - Radoslav Kirov - R. Andrew Ohana - Reg Burgess [first contribution] - Rob Beezer - Robert Bradshaw - Robert Miller - Ryan Grout - Sébastien Labbé - Simon King - Simon Spicer - Steven Trogdon [first contribution] - Tom Boothby - Tom Denton - Vincent Delecroix - Volker Braun - Wai Yan Pong [first contribution] - Willem Jan Palenstijn - William Stein - Zafeirakis Zafeirakopoulos [first contribution] * Release manager: Jeroen Demeyer. * We closed 251 tickets in this release. For details, see http://boxen.math.washington.edu/home/release/sage-4.7.2/tickets.html Closed tickets: #8269: cygwin: maxima does not build on cygwin, possibly due to ECL bug. [Reviewed by Karl-Dieter Crisman, Mike Hansen] #9382: atlas not respecting SAGE_FAT_BINARY on i686 systems [Reviewed by Leif Leonhardy, Volker Braun] #10235: Karl-Dieter Crisman: singular-3-1-1-4.p3 is missing Singular.rc.in [Reviewed by Leif Leonhardy] #10715: upgrade Sphinx to upstream version 1.0.7 [Reviewed by John Palmieri] #11494: Get linbox to build on Cygwin [Reviewed by Karl-Dieter Crisman] #11519: Kiran Kedlaya: Singular hiccups when identifying its version [Reviewed by Simon King] #11636: Do not use PARI's hash_GEN() for gen.__hash__ -- it is buggy [Reviewed by William Stein] #6146: the detection of SAGE_ROOT in $SAGE_ROOT/sage script should expand symlinks recursively (fix this on systems that do *NOT* support readlink -f) [Reviewed by Jeroen Demeyer] #7347: numerical_integral(SR(0), 0, 1) gives an error [Reviewed by Karl-Dieter Crisman, Douglas McNeil] #9044: Use mpmath for the erf() function [Reviewed by Karl-Dieter Crisman] #9848: 'sage -advanced' does not mention the '-R' flag, which starts the R interpreter [Reviewed by Karl-Dieter Crisman] #11626: make the error function work in arbitrary precision [Reviewed by Paul Zimmermann, Karl-Dieter Crisman] #11629: Evaluating the order of an ideal class fails [Reviewed by Francis Clarke] #11707: Remove `readlink -n` and `realpath` from $SAGE_ROOT/sage [Reviewed by Jeroen Demeyer] #748: [waiting on upstream] update iml to the 1.0.3 release + our patches [Reviewed by Leif Leonhardy] #1904: elliptic curves -- some period lattice functions are not implemented [Reviewed by John Cremona, David Loeffler, Paul Zimmermann] #2110: Cython annotation should be available more easily [Reviewed by Robert Bradshaw] #8085: 1d line plot [Reviewed by Karl-Dieter Crisman] #8217: Marshall Hampton: make 4ti2 an optional package [Reviewed by David Perkinson] #10152: bug in integral_points (for elliptic curves over Q) [Reviewed by William Stein] #10252: ecm does not compile on some 32-bit Linux systems [Reviewed by Leif Leonhardy] #11242: python spkg build fails on Ubuntu 11.04 [Reviewed by Jan Groenewald, Leif Leonhardy] #11405: magma interface needs work in presence of newlines [Reviewed by William Stein] #11421: Mariah Lenox: upgrade optional package NZMATH to version 1.1.0 [Reviewed by William Stein] #11427: optional spkg database_gap-4.4.12.p0.spkg fails test on sage-4.7.1.alpha1 [Reviewed by William Stein] #11504: Karl-Dieter Crisman: Tachyon fails to build on Cygwin - again [Reviewed by Reg Burgess, Leif Leonhardy] #11723: Implement completion: LaurentPolynomialRing -> LaurentSeriesRing [Reviewed by Tom Boothby] #11728: Multiplication(?) buggy in AA [Reviewed by William Stein] #11733: do not load sagenb.misc.misc on startup [Reviewed by Julian Rueth] #11746: Unify the definition of "monomial", introduce "term" [Reviewed by William Stein] #11833: Class for ternary quadratic forms [Reviewed by Leif Leonhardy] #11834: Gustavo Rama: Class for ternary quadratic forms [Reviewed by Leif Leonhardy] #298: autotesting of examples [Reviewed by John Palmieri, Keshav Kini] #8995: @ sign in notebook username prevents TinyMCE from working [Reviewed by Karl-Dieter Crisman, Dmitrii Pasechnik] #11769: Singular does not build on Ubuntu Oneiric [Reviewed by Volker Braun] #11788: Symmetrica fails to build under stricter gcc-4.6.x link rules [Reviewed by Volker Braun] Merged in sage-4.7.2.alpha0: #2100: Jason Grout, Karl-Dieter Crisman: sensible defaults for aspect ratio [Reviewed by Andrey Novoseltsev, Karl-Dieter Crisman, Ryan Grout] #7496: Volker Braun, Karl-Dieter Crisman: symbolic variable names should be valid identifiers, or ridiculousness follows [Reviewed by Karl-Dieter Crisman, Volker Braun] #9080: Kwankyu Lee: add F-distribution support for RealDistribution [Reviewed by Karl-Dieter Crisman] #9180: Robert Bradshaw: Absolute interval arithmetic [Reviewed by Kiran Kedlaya] #9453: André Apitzsch: Implement Aurifeuillian factorization [Reviewed by Mariah Lenox] #10146: Dan Drake: update SageTeX spkg to version 2.3.1 [Reviewed by Mariah Lenox, Andrey Novoseltsev] #10226: Volker Braun: Rewrite ATLAS spkg-install [Reviewed by Dan Drake, David Kirkby] #10594: Ryan Grout, Keshav Kini: Upgrade Mercurial to 1.8.x [Reviewed by Dan Drake, Ryan Grout, John Palmieri] #10666: Volker Braun: document the SAGE_ATLAS_ARCH environment variable [Reviewed by Dan Drake] #10692: Christian Stump: new method RootSystem.root_poset [Reviewed by Frédéric Chapoton] #10724: Paul-Olivier Dehaye: include support for beta variables for partitions [Reviewed by Benjamin Jones] #10736: Robert Bradshaw: int raised to a RealNumber gives an error [Reviewed by Dan Drake, Mariah Lenox] #10747: Burcin Erocal, Zafeirakis Zafeirakopoulos: symbolic functions can be defined with a constant argument [Reviewed by Karl-Dieter Crisman] #10771: Simon King: gcd and lcm for fraction fields [Reviewed by Marco Streng, Mariah Lenox] #10839: Rob Beezer: LU decomposition for rectangular matrices [Reviewed by Ryan Grout] #10845: Mario Pernici: fixed errors in documentation in two ETuple methods [Reviewed by Ivo Hedtke] #11196: Florent Hivert: Compute heights of Dyck words and compare them [Reviewed by Mike Hansen] #11232: Dima Pasechnik: we should not build patch on Cygwin on Windows 7 [Reviewed by David Kirkby, Karl-Dieter Crisman] #11244: François Bissey: In python-2.7 deprecation warnings are not shown to the user by default [Reviewed by Mariah Lenox] #11246: Dima Pasechnik, Jeroen Demeyer: flint-1.5.0.p5's extraneous #includes break typedef ulong in sys/types.h [Reviewed by Karl-Dieter Crisman, Leif Leonhardy] #11251: Florent Hivert: Add todo extension to Sphinx [Reviewed by John Palmieri] #11287: Nicolas M. Thiéry: Interface to runsnake and import_statements [Reviewed by Franco Saliola, Simon King, Christian Stump] #11312: Volker Braun: Speed up the computation of the Hilbert basis of a cone [Reviewed by Andrey Novoseltsev] #11376: François Bissey: Remove the hardcoding of python version in setup.py and SConstruct to build sage_clib and sage itself [Reviewed by Mariah Lenox] #11392: Volker Braun: Toric ideals over fraction fields [Reviewed by Andrey Novoseltsev] #11411: Frédéric Chapoton: some q binomial coefficients should be zero [Reviewed by Florent Hivert] #11454: Marco Streng: Extend the Magma interface to Conics [Reviewed by Mariah Lenox] #11498: Andrey Novoseltsev: Improve LaTeXing of strings [Reviewed by John Palmieri] #11522: Ivo Hedtke: partition centralizer_size doc is badly set up [Reviewed by John Palmieri] #11524: Alex Raichev: Function to test for algebraic dependence of polynomials [Reviewed by Martin Albrecht] #11527: Karl-Dieter Crisman: Add revolution_plot3d to reference manual [Reviewed by John Palmieri, Ivo Hedtke] #11530: Simon King, Rob Beezer: Conversion of finite field elements to PARI disregards characteristic and mangles "Mod" [Reviewed by Jeroen Demeyer] #11533: William Stein: allow unicode strings for specifying elliptic curve cremona labels [Reviewed by Robert Bradshaw] #11549: Joris Vankerschaver, Jeroen Demeyer: Arithmetic with symbolic vectors always creates a new FreeModuleElement_generic_dense [Reviewed by David Roe] #11550: Mike Hansen, Karl-Dieter Crisman: Singular does not build on Cygwin on Windows 7 [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer] Merged in sage-4.7.2.alpha1: #8821: Simon King: Adding a section on coercion to the tutorial (guided tour) [Reviewed by John Palmieri, Leif Leonhardy] #8938: Francis Clarke, Andrey Novoseltsev: Multivariate polynomials can be incorrectly formatted in LaTeX [Reviewed by Martin Albrecht, John Palmieri] #10319: Johan Bosman: segmentation fault in sparse rational matrix manipulations [Reviewed by Rob Beezer] #10848: Rob Beezer: Checks for Hermitian matrices [Reviewed by Mike Hansen] #10926: Chris Wuthrich: is_gamma0_equiv on Cusps is wrong [Reviewed by David Loeffler] #11106: Achim Fassbender, Radoslav Kirov: Make location of notebook style files configurable [Reviewed by Burcin Erocal] #11144: Ivo Hedtke: trivial typo messes up interact doc [Reviewed by John Palmieri] #11183: Tom Denton: Stembridge local characterization for crystal bases [Reviewed by Anne Schilling] #11224: Nicolas M. Thiéry: Support for the descriptor protocol for lazy_import'ed objects [Reviewed by Mike Hansen] #11261: Alexander Dreyer: Update PolyBoRi to upstream release 0.7-1 [Reviewed by Burcin Erocal, François Bissey, Karl-Dieter Crisman] #11265: Kwankyu Lee: "\dots" in docstring is not converted to "..." properly. [Reviewed by Ivo Hedtke] #11298: Simon King: Extend the capabilities of Sage's introspection [Reviewed by John Palmieri] #11304: Francis Clarke: Problems with S-class groups of number fields [Reviewed by John Cremona] #11316: Kwankyu Lee: Weighted degree term orders added [Reviewed by Simon King] #11350: Simon King: Fraction fields should know whether they are finite or not. [Reviewed by Robert Bradshaw, Jeroen Demeyer, John Palmieri] #11356: Rob Beezer: Companion matrix constructor [Reviewed by David Loeffler] #11424: Vincent Delecroix: Build Integer from Unicode [Reviewed by Mariah Lenox] #11435: Paul-Olivier Dehaye: empty partition causes error for down_list [Reviewed by Nathann Cohen] #11456: Marco Streng: Make the Magma interface able to convert number field elements from Magma to Sage [Reviewed by William Stein] #11468: Jean-Pierre Flori: Memleak in singular.pyx [Reviewed by Mariah Lenox, Jonathan Bober] #11489: Bruce Cohen: iframe command [Reviewed by Keshav Kini, Ryan Grout] #11495: Willem Jan Palenstijn: Trac #1092 small memleaks exposed by ntl_ZZ_pE (from 2.8.12.alpha0) [Reviewed by Jonathan Bober] #11546: Anne Schilling: Implementation of energy function for crystals [Reviewed by Tom Denton] #11547: Mike Hansen, Karl-Dieter Crisman: Copy needed dll to so files on Cygwin [Reviewed by Dmitrii Pasechnik] #11557: Volker Braun: Machine-readable timeit() output [Reviewed by John Palmieri] #11558: Volker Braun: Echelonize with transformation=True oddness for sparse matrix [Reviewed by Rob Beezer] #11578: William Stein: elliptic curve isogeny: error in documentation and a comment [Reviewed by Dan Shumow] #11589: Martin Albrecht, Simon King: faster zero matrix creation [Reviewed by Simon King, Martin Albrecht] #11592: Eviatar Bach: Improvements to units convert function [Reviewed by Burcin Erocal] #11611: Jeroen Demeyer: Equal PARI integers have different hashes [Reviewed by William Stein] #11617: William Stein: sending certain large strings to the gp PARI pexpect interface fails [Reviewed by Mike Hansen] #11659: Jeroen Demeyer: Increase LaTeX SAVE_SIZE in Sphinx [Reviewed by Leif Leonhardy] Merged in sage-4.7.2.alpha2: #4578: Martin Raum: optimize modular symbols decomposition algorithm [Reviewed by David Loeffler] #6670: Martin Raum, John Palmieri: Port group algebras to the current coercion system [Reviewed by John Palmieri, Martin Raum] #7654: Martin Albrecht: Conversion bug in MPolynomialRing_libsingular [Reviewed by Simon King] #9631: William Stein, Mitesh Patel: Remerge #9501 after resolving NFS and/or doctest problems with @fork [Reviewed by Volker Braun] #10497: Nathann Cohen: Constraint Generation for TSP/Hamiltonian Cycle [Reviewed by Leonardo Sampaio] #10530: Eviatar Bach: De Bruijn Sequence construction for combinat [Reviewed by Nicolas M. Thiéry, Nathann Cohen] #10793: Andrey Novoseltsev: Matrices can be "constructed" from matrices of wrong dimensions [Reviewed by Volker Braun] #11053: Nathann Cohen: improving shortest path all pairs through BFS computations [Reviewed by Leonardo Sampaio] #11121: Keshav Kini, John Palmieri: Set up good defaults for sage's mercurial [Reviewed by John Palmieri, Keshav Kini] #11166: Nicolas Borie: Typo in initialization of FreeModule_generic_field [Reviewed by Kelvin Li, Rob Beezer] #11267: Simon King: cdef public attributes of a class should only appear in the docs if they have a proper docstring [Reviewed by John Palmieri] #11379: Sébastien Labbé: Add Quantumino solver to sage/games [Reviewed by Rob Beezer] #11388: Robert Bradshaw: Allow start/stop recording exceptions in the coercion model [Reviewed by Luis Felipe Tabera Alonso] #11480: Rob Beezer: ZigZag and rational (canonical) forms [Reviewed by David Loeffler] #11499: Karl-Dieter Crisman: Sage library fails to build on Cygwin [Reviewed by Reg Burgess] #11535: Rob Beezer: Linear dependence/independence of vectors [Reviewed by Ivo Hedtke] #11540: Maarten Derickx: Make elliptic curve reduction consistent with has_good_reduction [Reviewed by Chris Wuthrich] #11552: Rob Beezer: Fix surjectivity testing for free module morphisms [Reviewed by John Palmieri] #11577: Leif Leonhardy, John Palmieri: save(x,filename) fails for pure Python objects for x if filename contains a dot [Reviewed by John Palmieri, Leif Leonhardy] #11600: Rob Beezer: Add alias for free module morphism lift method [Reviewed by Martin Raum] #11602: John Palmieri: install_scripts should use "$@" instead of $* [Reviewed by Leif Leonhardy] #11610: Simon King: Reduce memory consumption of generic Strassen-Winograd implementation [Reviewed by Ivo Hedtke] #11618: Leif Leonhardy: solve with solution_dict=True doesn't always return a list [Reviewed by Karl-Dieter Crisman] #11620: Robert Miller: Bugs persist in graph_isom_equivalent_non_edge_labeled_graph [Reviewed by Nathann Cohen] #11623: Robert Miller: small optimization to girth [Reviewed by Nathann Cohen] #11624: Martin Raum: List Sidon g-sets [Reviewed by Nicolas Borie] #11658: Leif Leonhardy: the timeout option is not working correctly in parallel computing [Reviewed by Volker Braun] #11665: Leif Leonhardy: Don't delete built Sage documentation until Sphinx has been successfully (re)installed [Reviewed by John Palmieri] #11686: John Palmieri: Race condition in matplotlib mkdir() [Reviewed by Leif Leonhardy] Merged in sage-4.7.2.alpha3: #813: Simon King: forced coercion vs. automatic coercion [Reviewed by Julian Rueth] #3052: Keshav Kini: mercurial --> plain text --> mercurial [Reviewed by Volker Braun] #5847: Mike Hansen, Leif Leonhardy, Jeroen Demeyer: Update GMP-ECM to 6.3 [Reviewed by Leif Leonhardy, Dmitrii Pasechnik, Mariah Lenox, Maarten Derickx] #6315: Mariah Lenox, William Stein: optional doctest failure -- caused by mistakes in lectures on number theory rst book [Reviewed by Marco Streng] #6329: Mariah Lenox, William Stein: optional doctest failure -- breakage in the sage<-->magma interface [Reviewed by Mike Hansen] #7714: Martin Albrecht: bug in matrix pivots over multivariate polynomial ring [Reviewed by Luis Felipe Tabera Alonso] #7852: Rob Beezer, Leif Leonhardy: solve_left for RDF matrices is WRONG [Reviewed by Martin Raum, Leif Leonhardy, Rob Beezer] #7879: Robert Bradshaw: Remove unnecessary signal handling for low prec mpfr operations. [Reviewed by Alex Ghitza, Mariah Lenox, William Stein] #8094: Harald Schilly, Jason Grout, Martin Raum: shortcuts properties for matrix transpose, complex conjugate, conjugate transpose, and inverse [Reviewed by Rob Beezer, Martin Raum] #8469: Minh Van Nguyen: add "Number Theory and the RSA Public Key Cryptosystem" to "Thematic Tutorials" [Reviewed by Pablo Angulo, Rob Beezer, Martin Albrecht] #9739: Mitesh Patel, John Palmieri: Handle duplicate file basenames when testing multiple files in parallel [Reviewed by Robert Bradshaw, Leif Leonhardy] #10335: Mike Hansen, Jason Hill, David Loeffler: Add domains for permutation groups [Reviewed by Robert Miller, Rob Beezer, Nicolas Borie, Nicolas M. Thiéry] #10453: David Loeffler: Problem with old submodule [Reviewed by Johan Bosman] #10464: Katherine Stange: m-th power residue symbol [Reviewed by Francis Clarke, David Loeffler] #10635: Christopher Hall: refactor polynomial_element.pyx factor function [Reviewed by Mariah Lenox, William Stein, Simon Spicer] #10801: William Stein, Keshav Kini: Create a new option: "sage -strip" which deletes things that aren't needed for a binary distribution of sage, or for people that will never develop or upgrade [Reviewed by Benjamin Jones, Keshav Kini] #10850: Francis Clarke: composition and comparison of number-field homomorphisms [Reviewed by David Loeffler] #10952: Robert Bradshaw, Rob Beezer: better numerical accuracy testing [Reviewed by Jason Grout, Mariah Lenox, William Stein, John Palmieri] #10975: William Stein: creation of certain prime finite fields is double dog slow (compared to Magma) [Reviewed by David Roe, Tom Boothby] #10981: William Stein: algebraic real field partial_fraction_decomposition bug [Reviewed by Simon Spicer, Leif Leonhardy] #11036: Douglas McNeil, Maarten Derickx: improve solve_mod performance [Reviewed by John Cremona, Simon Spicer] #11120: Keshav Kini, John Palmieri: Autodetect installed 3-way merge programs (invalidates #4434) [Reviewed by John Palmieri, Keshav Kini] #11142: John Palmieri: clean up sage/misc/hg.py [Reviewed by Karl-Dieter Crisman, Keshav Kini] #11259: Rob Beezer: LU decomposition for matrices with exact base rings [Reviewed by Martin Raum] #11342: Simon King, Volker Braun: Make getattr faster on parents and elements [Reviewed by Jeroen Demeyer, Volker Braun, Simon King] #11351: Mariah Lenox: make flintqs-20070817 spkg build with -m64 rather than -march=opteron [Reviewed by Martin Albrecht] #11354: Mariah Lenox: remove dist directory from eclib spkg [Reviewed by William Stein] #11385: Volker Braun, Andrey Novoseltsev: Orbit closure as toric variety [Reviewed by Andrey Novoseltsev, Volker Braun] #11401: Nils Bruin: magma mode in 4.7 notebook broken [Reviewed by Marco Streng] #11422: Vincent Delecroix: modular subgroups [Reviewed by David Loeffler] #11431: Simon King: Conversion from Singular to Sage [Reviewed by Martin Albrecht] #11460: François Bissey, John Palmieri: upgrade ipython to 0.10.2 [Reviewed by François Bissey, John Palmieri] #11544: Rob Beezer: Viewing matrices of algebraic numbers can take a long time [Reviewed by Martin Raum] #11553: Rob Beezer: Matrix morphism additions [Reviewed by Martin Raum] #11574: Martin Albrecht: update M4RI to newest upstream release [Reviewed by Simon King, Alexander Dreyer] #11580: Nils Bruin: Magma interface cannot convert multivariate polynomials back to Sage [Reviewed by William Stein, Marco Streng] #11588: Nathann Cohen: copying a linear program crashes Sage [Reviewed by John Perry] #11595: Rob Beezer: Update exact eigenspace routines [Reviewed by Martin Raum, Leif Leonhardy] #11598: David Loeffler: Congruence testing for odd modular subgroups [Reviewed by Vincent Delecroix] #11627: Andrey Novoseltsev: Turn Fan(discard_warning) into an error [Reviewed by Volker Braun] #11640: R. Andrew Ohana: Remove DB_HOME in preference of SAGE_DATA [Reviewed by Tom Boothby] #11642: R. Andrew Ohana: Rewrite/improve/fix SQLDatabase and SQLQuery objects [Reviewed by Tom Boothby] #11657: William Stein, Rob Beezer: the vector(...) function is extremely slow [Reviewed by Rob Beezer, William Stein] #11680: Martin Albrecht: support extra_compile_args (e.g., C99) when loading/attaching .pyx (cython) files, and when using %cython in the notebook [Reviewed by William Stein, Leif Leonhardy] #11682: David Perkinson: Thematic Tutorial on Sandpiles [Reviewed by Rob Beezer, John Palmieri] #11684: Johan Bosman, Simon King: Obtaining coefficients of polynomials over finite fields is extremely slow [Reviewed by Simon King, Johan Bosman] #11685: Johan Bosman, Jeroen Demeyer: Pari finite field extension: element created by list not recognised as zero [Reviewed by Simon King, Johan Bosman, Peter Bruin] #11690: Martin Albrecht: fix AES equation systems when star=True [Reviewed by David Montminy] #11691: Ivan Andrus: scaling_term only appears in documentation [Reviewed by Nathann Cohen] #11692: Ivan Andrus: Creating a multiedged graph gives wrong error [Reviewed by Nathann Cohen] #11700: Anne Schilling: Methods concerning cores in Partitions [Reviewed by Mike Zabrocki] #11703: Frédéric Chapoton: another example of simplicial complex : the K3 surface [Reviewed by John Palmieri] #11706: William Stein, Leif Leonhardy: tachyon-0.98.9.p3 fails to build on ppc64 SUSE Linux power 7 (silius on skynet) [Reviewed by Leif Leonhardy, Karl-Dieter Crisman, Mike Hansen] #11711: Rob Beezer: Add charpoly as an alias for graph characteristic polynomials [Reviewed by Nathann Cohen] #11712: Martin Albrecht: Make it so typing `cython?` results in one seeing documentation for all pragmas for %cython mode and load/attach .pyx file [Reviewed by Mike Hansen] #11714: William Stein, Julian Rueth: ensure that numpy is not imported on startup [Reviewed by William Stein] #11716: Julian Rueth: Remove twisted.persisted.styles import [Reviewed by Mike Hansen] #11722: Maarten Derickx: document the SAGE_PARALLEL_SPKG_BUILD environment variable [Reviewed by Simon Spicer, John Palmieri] #11725: Rob Beezer: Generate random elements of the algebraic field [Reviewed by Simon Spicer, Leif Leonhardy] #11727: Karl-Dieter Crisman, Dmitrii Pasechnik: Even more minor Cygwin fixes for FLINT [Reviewed by Dmitrii Pasechnik, Karl-Dieter Crisman] #11732: Julian Rueth: faster import of sage.interacts.all [Reviewed by William Stein] #11734: Julian Rueth: sage_wraps should only read the sources of wrapped functions when needed. [Reviewed by Simon King] #11738: Diego de Estrada: Various issues in is_interval and is_chordal [Reviewed by Nathann Cohen] #11741: R. Andrew Ohana: pari.init_primes() can segfault for large input on many platforms [Reviewed by Aly Deines] #11744: Karl-Dieter Crisman: Add library gmp needed for real interval absolute [Reviewed by Mike Hansen] #11747: William Stein: is_monomial and is_term [Reviewed by Mike Hansen] #11749: Robert Bradshaw: Remove unneeded imports [Reviewed by Keshav Kini, Leif Leonhardy] #11750: Maarten Derickx: CRT_list not working for non-coprime moduli [Reviewed by Luis Felipe Tabera Alonso, Wai Yan Pong, Leif Leonhardy] #11751: Maarten Derickx, Julian Rueth: make free_module_generic_pid also work for pid's other than integers [Reviewed by Julian Rueth, Maarten Derickx] #11752: Paulo César Pereira de Andrade: ecl.pyx should not touch SIGPWR neither SIGXCPU when initializing ecl [Reviewed by Nils Bruin] #11753: Punarbasu Purkayastha: Fix step=0 in (x)srange [Reviewed by Dmitrii Pasechnik] #11756: Alexander Dreyer: PolyBoRi 0.7.1 needs to activate -msse2 [Reviewed by Martin Albrecht] #11767: Paul Zimmermann: elliptic_logarithm of high precision points often hangs forever [Reviewed by John Cremona, Leif Leonhardy, William Stein] #11778: Johan Bosman: p_iter_fork doesn't flush stdout properly [Reviewed by Leif Leonhardy] #11779: Dmitrii Pasechnik: python ints vs sage ints with respect to powers weirdness [Reviewed by William Stein] #11798: Paul Zimmermann: typo in the documentation of weierstrass_points [Reviewed by Luca De Feo] #11801: Jean-Pierre Flori: Ill-formed documentation of HilbertClassPolynomialDatabase [Reviewed by Paul Zimmermann] #11810: Nicolas Estibals: Formatting issue in documentation of divisor_group method [Reviewed by Jean-Pierre Flori] #11815: Simon King: Embedding information in doc strings must not be formatted [Reviewed by Volker Braun] #11816: Julian Rueth: Typo in the developer's guide [Reviewed by Leif Leonhardy] #11818: John Palmieri: sage