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Commits on Nov 21, 2008
  1. @peterjc

    Doing the 1.49 release today

    peterjc committed Nov 21, 2008
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    Need to import string here (Bug 2680), previously imported via Bio.Pa…

    peterjc committed Nov 21, 2008
    …rserSupport which worked up until Biopython 1.48
  5. @peterjc

    Included NC_005816.1 GenBank file in the BioSQL unit test which requi…

    peterjc committed Nov 21, 2008
    …red fixing a couple of minor things on references (handling missing authors, not testing consortium)
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    Updating date in anticpation of the Biopython 1.49 release. Rewording…

    peterjc committed Nov 21, 2008
    … Seq introduction to resolve Bug 2662. Fixing a typo.
  8. @peterjc

    Based on a patch from Cymon Cox (Bug 2766), this addresses feature lo…

    peterjc committed Nov 21, 2008
    …cation's strand, db ref and the sub-feature order. It does not yet record the feature operator (which still defaults to 'join')
Commits on Nov 19, 2008
  1. @peterjc

    Don't use 'from XXXy import *' but instead 'import XXX' (Bug 2676). F…

    peterjc committed Nov 19, 2008
    …ix from Bruce Southey.
  2. @peterjc

    Don't using 'from numpy import *' but instead 'import numppy' (Bug 26…

    peterjc committed Nov 19, 2008
    …75). Fix from Bruce Southey.
  3. @peterjc
  4. More changes for Python 2.5. See bug #2609.

    mdehoon committed Nov 19, 2008
Commits on Nov 18, 2008
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Commits on Nov 17, 2008
  1. @peterjc

    Fixing an occasional unit test failure reported on the mailing list b…

    peterjc committed Nov 17, 2008
    …y Bruce Southey: Commenting out the assertion in DiversitySelectionTest.t_no_retrive_organism, since a 100% random new genome could by chance already be in the population.
  2. @peterjc

    Fix for occasional infinite loop when creating the input population i…

    peterjc committed Nov 17, 2008
    …n TournamentSelectionTest.t_select_best(); see mailing list discussion.
  3. @peterjc

    Since Biopython 1.45, or to be exact Bio/Seq.py CVS revision 1.20 (se…

    peterjc committed Nov 17, 2008
    …e Bug 2386), the Seq object's count method will not accept an integer argument. Fixes Bug 2651.
  4. @peterjc

    Coverted tabs to spaces in test_PDB.py and added a simple test of Bio…

    peterjc committed Nov 17, 2008
    ….PDB.NeighborSearch based on that module's self test.
  5. Distinguish between memory errors and not finding any entries.

    mdehoon committed Nov 17, 2008
    See bug #2666.
  6. @peterjc
  7. See bug #2657; making this code faster.

    mdehoon committed Nov 17, 2008
Commits on Nov 16, 2008
Commits on Nov 15, 2008
  1. Updating for Python 2.5. See bug #2609.

    mdehoon committed Nov 15, 2008
  2. Make the compiler shut up.

    mdehoon committed Nov 15, 2008
  3. This assertion is no longer needed (see revision 1.13 of Bio/KDTree/K…

    mdehoon committed Nov 15, 2008
    …DTree.py
    
    and revision 1.3 of Bio/KDTree/KDTreemodule.c, and bug #2649), and the typecode
    method no longer exists in NumPy. See bug #2658.
Commits on Nov 14, 2008
  1. @peterjc
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    Filename case fix for Windows

    peterjc committed Nov 14, 2008
  5. @peterjc

    Adding a general example doctest to the main docstring for the SeqRec…

    peterjc committed Nov 14, 2008
    …ord class (see Bug 2640)
  6. @peterjc
  7. @peterjc
  8. @peterjc

    Fixed case problems with finding SIMCOAL2.EXE under Windows (but unit…

    peterjc committed Nov 14, 2008
    … test still fails for me on Windows)
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