Diff for "days29/bugs"

Use this page to keep track of the bugs fixed during Sage Days 29.

• William Stein:

  • 10937 -- bug in Dokchitser L.init_Johncoeffs (positive review -- Robert Bradshaw)

  • 10975 -- creation of certain prime finite fields is double dog slow (compared to Magma) (positive review -- David Roe)

  • 9705 -- trouble with long lines in notebook magma mode (positive review -- Martin Raum)

  • 8998 -- galois_action on cusps has a bug (positive review)

  • 11007 -- heegner points -- fix nonsquarefree case (with patch; needs review)

  • 10836 -- primitive root is broken (positive review)

• Rob Beezer:

  • 10974 -- Overhaul, fix matrix augment, stack (positive review -- Keshav Kini)

  • 10470 -- Don't list infinite vector spaces (positive review -- John Palmieri)

  • 10545 -- Add the outer product of two vectors (positive -- John Palmieri)

  • 10737 -- Extended echelon form (positive review -- John Palmieri)

  • 10977 -- Document vector constructor behavior (positive review -- Martin Raum)

  • 11004 -- make subdivisions optional for tensor products of matrices (positive review -- John Palmieri)

• John Palmieri:

  • 4983 -- replace subdivisions attribute for matrices with a function (positive review -- Rob Beezer)

  • 7105 -- open search results in new tabs (needs review)

  • 9960 -- require SAGE_CHECK to be "yes" (positive review -- Leif Leonhardy, Ivan Andrus, David Kirkby). This patch also fixes 4029 -- sage-env kills the shell when called from "wrong" directory.

  • 10752 -- matrix pivots should be immutable (positive review -- Rob Beezer)

  • 10822 -- sage -sh doesn't set the path right if default shell is zsh on OSX (needs review)

• Rob Beezer and John Palmieri:

  • 10595 -- vector constructor fails on empty list (positive review -- Dmitrii Pasechnik, Rob Beezer, and John Palmieri)

• Martin Raum:

  • 5731 -- update to NTL 5.5.2 (needs review)

  • 10553 -- Review: Diamond bracket operators are terribly slow (positive review -- Martin Raum)

  • 8614 -- Optimize creation of modular symbols spaces by speeding up quotienting out by 2-term relations (under review by John Cremona)

  • 4578 -- Optimize modular symbols decomposition algorithm (needs review)

  • 10987 -- Add optional arguement to decomposition_of_subspace making restrict not check the subspace (positive review -- Rob Beezer)

  • 6670 -- Port group algebras to the current coercion system (needs review)

  • 11017 -- GP blocks files when reallocating memory; Workaround (positive review by John Cremona)

  • 11024 -- Update Dokchitser calculator to compiled version (under review by John Cremona)

  • 10863 -- Review: Add check for orthogonal/unitary matrices (positive review -- Martin Raum)

  • 10802 -- Review: Singular values of matrices over CDF (positive review -- Martin Raum)

  • 10791 -- Review: Fix and upgrade Gram-Schmidt ( in progress )

  • 11027 -- Review: Schur matrix decomposition over RDF/CDF ( enhancement, in progress )

• Moritz Minzlaff:

  • 9053 -- fixes computation of pivots (positive review -- Keshav Kini)

• Maarten Derickx:

  • 10570 -- sage leaves a lot of stackframes alive at startup (needs review)

  • 10933 -- time fails inside function (positive review -- Martin Raum)

  • 9094 -- is_square and sqrt for polynomials and fraction fields (positive review -- Robert Bradshaw)

• Robert Bradshaw

  • 10548 -- The coercion model is keeping references to tracebacks which causes memory leaks. (positive review -- Maarten Derickx)

  • 11040 -- Sage startup time. (needs review)

  • 11043 -- Sage startup time (again). (needs review)

• Robert Miller

  • 11033 -- Fixes bugs in automorphism groups of linear codes. (needs review)

  • 10994 -- Bug in permutation_automorphism_group for linear codes. (fixed by #11033)

  • 11032 -- automorphism_group_binary_code crashes Sage when it can't allocate enough memory. (fixed by #11033)

  • 10976 -- computing order of a certain subgroup of a permutation group is double dog slow (compared to Magma) worked on 10804 which implements the first round of data structures designed to replace GAP in computations of this type

• Simon Spicer:

  • 9028 -- Review: Basic Stats - Standard Deviation (positive review -- Simon Spicer)

  • 10799 -- Review: Solved the problem to compute resultants on certain variable orders (positive review -- Simon Spicer)

  • 10601 -- Fixed the QuaternionAlgebra constructor to accept Python ints, longs and floats as input. (positive review -- Rob Beezer)

  • 9306 -- Alters the round() command to defer to an element's .round() method if no precision is specified. (positive review -- Keshav Kini)

  • 10761 -- Fixed numerical_approx() when called on complex-valued AlgebraicNumbers (positive review -- Rob Beezer)

  • 10794 -- Review: QR decomposition for matrices over exact rings (positive review -- Simon Spicer)

  • 10934 -- Review: Implement is_maximal() for ideals of quotient rings of ZZ (positive review -- Simon Spicer)

• Chris Swierczewski:

  • 6371 -- Implement Riemann theta functions (needs review)

• Gagan Sekhon

  • 10832 -- Simon 2-descent (all the work was done by Cremona, I just fixed some doctest) (positive review -- Jamie Weigandt)

• John Cremona

  • 10840 -- bug in saturation for elliptic curves over Q (positive review by Gagan Sekhon)

  • 10999 -- Elliptic curve generators from the database lie on the wrong curve (needs review)

  • Enhancement: 11005 -- Update Simon's GP scripts and convert to use via gp2c (under review by Martin Raum)

• Justin Walker

  • 4120 -- New code for binary quadratic forms (under review by John Cremona)

  • 10521 -- bug in integral_points (for elliptic curves over Q) (May be fixed by 10973)

  • 10973 -- Integral points on elliptic curves over number fields (Close, but needs work)

• Jamie Weigandt

  • Enhancement: 9371 -- Implemented 2-Torsion Rank over General Fields

• Michael Droettboom

  • 8125 -- problem with "text" in matplotlib Fixed in matplotlib

  • 10717 -- Prime typeset badly on plots Fixed in matplotlib

  • 10980 -- Make sure symbolic gridline values are okay Fixed in matplotlib

  • mpl 3236567 -- backend_wx draws images at wrong position Fixed in matplotlib

• Ivan Andrus

  • 11000 -- GAP interface doesn't handle input with multiple lines correctly (positive review -- Keshav Kini)

  • 10469 -- Don't source sage-env more than once (positive review -- Ivan Andrus, Keshav Kini, John Palmieri)

  • 7766 -- Update valgrind (needs review)

• Paul Ivanov
  • Matplotlib work

    • Fixed large memory leak fixed in matplotlib test suite (trunk) pull request 56

    • Fixed memory leak in matplotlib-py3 caused be old version of CXX. pull request 23

    • Include matplotlib testsuite behave consistently using matplotlib.test() and nosetests pull request 58

    • (enhancement) 'scrub' keyword for matplotlib clear figure command. pull request 56

    • mpl 3189536 -- radio_buttons example has only one (the last) button active Fixed in matplotlib.

    • mpl 3187521 -- Crash when enumerating fonts containing a dot in their name fixed in matplotlib pull request 59.

    • (work in progress) mpl 3187864 matplotlib with QGIS memory error on Suse 11.3
    • (work in progress) mpl 3205391 gtkagg.so hanging plot creation

  • Ipython work IPython pull request 309

    • (work in progress) filed and added test for GH-306 - multiline strings at end of input cause noop

    • (work in progress) filed and added test for GH-307 - lines ending with semicolon should not go to cache

    • (work in progress) added test for GH-284 - ensure In variable is works

    • (work in progress) added test for GH-238 - %run's aggressive name cleaning

• Keshav Kini and Maarten Derickx

  • 11008 -- spkg test suite successes are not correctly written to the appropriate file in spkg/installed (positive review -- John Palmieri)

• Volker Braun

  • 6391 -- libGAP! -- create a Cython library interface to gap first working version, needs review.

  • 9232 -- jmol on commandline broken (needs review)

• IPython team (Fernando Perez, Min Ragan-Kelley, Thomas Kluyver) Issues Closed and Pull Requests merged (66)

  • Closed: 3 Implement PBS support in ipcluster

  • Closed: 6 Update the Sphinx docs for the new ipcluster

  • Closed: 9 Getting "DeadReferenceError: Calling Stale Broker" after ipcontroller restart

  • Closed: 15 Implement SGE support in ipcluster

  • Closed: 18 %cpaste freeze sync frontend

  • Closed: 24 ipcluster does not start all the engines

  • Closed: 25 unicode bug - encoding input

  • Closed: 27 generics.complete_object broken

  • Closed: 28 Offer finer control for initialization of input streams

  • Closed: 31 Issues in magic_whos code

  • Closed: 43 Implement SSH support in ipcluster

  • Closed: 44 Merge history from multiple sessions

  • Closed: 46 Input to %timeit is not preparsed

  • Closed: 51 Out not working with ipythonx

  • Closed: 52 Document testing process better

  • Closed: 53 Internal Python error in the inspect module

  • Closed: 58 ipython change char '0xe9' to 4 spaces

  • Closed: 60 Improve absolute import management for iptest.py

  • Closed: 68 Problems with Control-C stopping ipcluster on Windows/Python2.6

  • Closed: 74 Manager() [from multiprocessing module] hangs ipythonx but not ipython

  • Closed: 77 ipython oops in cygwin

  • Closed: 86 Make IPython work with multiprocessing

  • Closed: 88 Error when inputting UTF8 CJK characters

  • Closed: 93 when looping, cursor appears at leftmost point in newline

  • Closed: 100 Overzealous introspection

  • Closed: 108 ipython disables python logger

  • Closed: 109 WinHPCLauncher is a hard dependency that causes errors in the test suite

  • Closed: 111 Iterator version of TaskClient.map() that returns results as they become available

  • Closed: 115 multiline specials not defined in 0.11 branch

  • Closed: 120 inspect.getsource fails for functions defined on command line

  • Closed: 121 If plot windows are closed via window controls, no more plotting is possible.

  • Closed: 126 Can't transfer command line argument to script

  • Closed: 127 %edit does not work on filenames consisted of pure numbers

  • Closed: 130 Deadlock when importing a module that creates an IPython client

  • Closed: 132 Ipython prevent south from working

  • Closed: 133 whitespace after Source introspection

  • Closed: 134 multline block scrolling

  • Closed: 143 Ipython.gui.wx.ipython_view.IPShellWidget: ignores user*_ns arguments

  • Closed: 145 Bug on MSW sytems: idle can not be set as default IPython editor. Fix Suggested.

  • Closed: 182 ipython q4thread in version 10.1 not starting properly

  • Merged: 191 Unbundle external libraries

  • Closed: 196 IPython can't deal with unicode file name.

  • Merged: 199 Magic arguments

  • Closed: 200 Unicode error when starting ipython in a folder with non-ascii path

  • Closed: 201 use session.send throughout zmq code

  • Closed: 202 Matplotlib native 'MacOSX' backend broken in '-pylab' mode

  • Merged: 204 Emacs completion bugfix

  • Closed: 205 In the Qt console, Tab should insert 4 spaces when not completing

  • Closed: 212 IPython ignores exceptions in the first evaulation of class attrs

  • Merged: 235 Fix history magic command's bugs wrt to full history and add -O option to display full history

  • Merged: 236 History minus p flag

  • Closed: 240 Incorrect method displayed in %psource

  • Merged: 252 Unicode issues

  • Merged: 261 Adapt magic commands to new history system.

  • Merged: 282 SQLite history

  • Closed: 285 ipcluster local -n 4 fails

  • Closed: 290 try/except/else clauses can't be typed, code input stops too early.

  • Merged: 292 Issue 31

  • Merged: 293 Issue 133

  • Merged: 294 Issue 290

  • Closed: 305 more readline shortcuts in qtconsole

  • Closed: 308 Test suite should set sqlite history to work in :memory:

  • Merged: 311 Qtconsole exit

  • Merged: 312 History memory

  • Merged: 313 Readline shortcuts

  • Closed: 314 Multi-line, multi-block cells can't be executed.

• NumPy (Chuck Harris, Mark Wiebe) From http://projects.scipy.org/numpy/timeline

  • Bugs fixed:
    • Ticket #1779 (array.tolist() speed enhancement) closed by mwiebe
    • Ticket #1780 (nditer broadcasting test failure under python 2.4) closed by mwiebe
    • Ticket #766 (fastCopyAndTranspose segfaults) closed by mwiebe

    • Ticket #1675 (No support for __format__ in scalars/arrays) closed by mwiebe

  • Bugs closed from triage:
    • Ticket #38 (strides accepted as an argument to records.array) closed by mwiebe

    • Ticket #213 (SharedLibrary builder for numpy.distutils) closed by mwiebe

    • Ticket #244 (Build fails with Intel Visual Fortran compiler) closed by mwiebe
    • Ticket #260 (Add mechanism for registering objects to be deallocated and memory-to-be ...) closed by mwiebe
    • Ticket #338 (Valgrind warning when calling scipy.interpolate.interp1d) closed by mwiebe
    • Ticket #398 (Compatibility loader for old Numeric pickles) closed by mwiebe
    • Ticket #400 (C API access to fft for C scipy extension ?) closed by mwiebe
    • Ticket #402 (newaxis incompatible with array indexing) closed by mwiebe
    • Ticket #416 (The docstrings of functions which take an out= parameter should mention ...) closed by mwiebe
    • Ticket #417 (Numpy 1.0.1 compilation fails on IRIX 6.5) closed by mwiebe
    • Ticket #468 (Use ellipses to auto complete indices for slice assignments) closed by mwiebe
    • Ticket #619 (remove split_quoted in numpy.distutils.ccompiler) closed by mwiebe
    • Ticket #695 (No test for r4836) closed by mwiebe
    • Ticket #721 (0-dimensional boolean arrays should work as masks for array scalars) closed by mwiebe
    • Ticket #722 (Write tests to confirm that methods preserve arrays/matrices) closed by mwiebe
    • Ticket #741 (Extend numpy.dot() to accept more than 2 arrays.) closed by mwiebe
    • Ticket #756 (String conversion should be supported for arithmetic operators.) closed by mwiebe
    • Ticket #758 (g3 f2py clean up) closed by mwiebe
    • Ticket #762 (Figure out why fixing #743 fixed #733 too.) closed by mwiebe
    • Ticket #772 (Valgrind warning when running test for compress2d) closed by mwiebe
    • Ticket #819 (.flat reorders data) closed by mwiebe
    • Ticket #1608 (numpy.sort on x.flat modifies x) closed by mwiebe
    • Ticket #867 (Array generation fail) closed by mwiebe

    • Ticket #875 (numpy.lib.io.save fails with NameError) closed by mwiebe

    • Ticket #909 (fromstring() / fromfile() Enhancements) closed by mwiebe
    • Ticket #980 (NaN's are silenty converted to ints) closed by mwiebe
    • Ticket #982 (Problem accessing data attribute of ndarray object created with certain ...) closed by mwiebe
    • Ticket #987 (random.exponential() seems to use the reciprocal rate prarameter instead ...) closed by mwiebe
    • Ticket #1012 (dtype attributes change after an arithmetic operation involving a scalar) closed by mwiebe
    • Ticket #1024 (Untested changes to numpy.lib.io in r6345) closed by mwiebe
    • Ticket #1032 (Crash on fastputmask on win32) closed by mwiebe
    • Ticket #1035 (Fix up Nan handling for max/amax/argmax/fmac + min/sort equivalent) closed by mwiebe
    • Ticket #1037 (Pickling/unpickling empty unicode types does not work) closed by mwiebe
    • Ticket #1046 (+SKIP option to doctests is not supported by python 2.4) closed by mwiebe
    • Ticket #1054 (Feature request: intent(transpose) option in f2py) closed by mwiebe
    • Ticket #1056 (typedef npy_intp to Py_ssize_t (cf. PEP353)) closed by mwiebe
    • Ticket #1097 (polydiv should be duck-typing safe) closed by charris
    • Ticket #1081 (Strange behavior of array() in a corner case) closed by charris
    • Ticket #1068 (numpy crashes on long double computation on windows for amd64) closed by charris
    • Ticket #1082 (numpybook doesn't build) closed by mwiebe
    • Ticket #1091 (crackfortran patch needed) closed by mwiebe
    • Ticket #1094 (masked array autotest fails with bus error) closed by mwiebe
    • Ticket #1136 (Multiplying Python float to numpy.array of objects works but fails with a ...) closed by mwiebe

    • Ticket #1174 (FAIL: test_testUfuncRegression (test_old_ma.TestUfuncs)) closed by mwiebe

    • Ticket #1180 (numpy.average: add an option to skip 'None' values from count) closed by mwiebe
    • Ticket #1224 (discrepencies in found tests between numscons and distutils builds) closed by mwiebe
    • Ticket #1225 (datetime64 and timedelta64 tests) closed by mwiebe

    • Ticket #1265 (64bit System: take raises TypeError when using int64 indices) closed by charris

    • Ticket #1258 (numpy.array does not upconvert from float to store complex types) closed by mwiebe
    • Ticket #1277 (Constructing real arrays with complex numbers leads to funny errors) closed by mwiebe
    • Ticket #1304 (Bug in handling '|S0' format string) closed by mwiebe
    • Ticket #1321 (A dtype should be immutable) closed by mwiebe
    • Ticket #1718 ("shape mismatch" error is not informative) closed by mwiebe
    • Ticket #1640 (structured array incorrectly gives a broadcast error) closed by mwiebe