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Commits on Oct 28, 2005
  1. Updated contributers for 1.41 release.

    mdehoon committed Oct 28, 2005
  2. More news for the 1.41 release.

    mdehoon committed Oct 28, 2005
  3. Biopython release 1.41.

    mdehoon committed Oct 28, 2005
  4. Bumped version number for Biopython 1.41 release.

    mdehoon committed Oct 28, 2005
Commits on Oct 27, 2005
  1. Removed the sorting of the fragments, since a) the result without sor…

    …ting is more intuitive, and b) comparison between Seq objects is not defined, so the result of sorting is random, causing errors in test_Restriction.
    mdehoon committed Oct 27, 2005
Commits on Oct 26, 2005
  1. Need to return sys.stderr to its original values, otherwise subsequen…

    …t tests
    
    may inadvertently fail.
    mdehoon committed Oct 26, 2005
Commits on Oct 25, 2005
  1. Corrected Polypeptide construction

    nisse committed Oct 25, 2005
  2. Misc

    nisse committed Oct 25, 2005
  3. Fixed Model error

    nisse committed Oct 25, 2005
Commits on Oct 24, 2005
  1. Updated received from Jason Hackney.

    mdehoon committed Oct 24, 2005
  2. Output of test_MEME.py, initial commit.

    mdehoon committed Oct 24, 2005
Commits on Oct 23, 2005
  1. Fixing typo (?) in Doctest output.

    mdehoon committed Oct 23, 2005
  2. Forgot to add the first line in the output.

    mdehoon committed Oct 23, 2005
  3. Updated with output from Python 2.4.1.

    mdehoon committed Oct 23, 2005
  4. Need to reset sys.stderr to its original value. Otherwise, tests foll…

    …owing
    
    test_PDB may inadvertently fail. (In this case, failure to reset sys.stderr
    in test_PDB caused test_Wise to fail).
    mdehoon committed Oct 23, 2005
  5. Removed the name of the temporary file, as it will depend on the plat…

    …form
    
    and may cause the test to inadvertently fail (for example, on Windows and
    Cygwin).
    mdehoon committed Oct 23, 2005
Commits on Oct 22, 2005
  1. adjusted minor format changes

    fkauff committed Oct 22, 2005
  2. Fixed bug setting defaults

    fkauff committed Oct 22, 2005
Commits on Oct 20, 2005
  1. Test for Bio.Blast.NCBIXML, submitted by Peter.

    mdehoon committed Oct 20, 2005
  2. Add Bio.MEME to the packages to be installed.

    mdehoon committed Oct 20, 2005
Commits on Oct 19, 2005
  1. whrandom is deprecated, use random instead.

    mdehoon committed Oct 19, 2005
  2. whrandom has been deprecated, use random instead.

    mdehoon committed Oct 19, 2005
  3. whrandom is deprecated, replacing by random.

    mdehoon committed Oct 19, 2005
Commits on Oct 18, 2005
  1. C Clustering Library version 1.30. This update will affect k-means cl…

    …ustering
    
    runs with distance measures other than the Euclidean distance and city-block
    distance.
    mdehoon committed Oct 18, 2005
Commits on Oct 17, 2005
Commits on Oct 14, 2005
  1. Several bugfixes which accumulated over time

    fkauff committed Oct 14, 2005
Commits on Oct 8, 2005
  1. major optimization to cpairwise2module

    when getting score_only, will not generate traceback matrix
    much faster
    jchang committed Oct 8, 2005
  2. minor update to parser format

    jchang committed Oct 8, 2005
Commits on Oct 5, 2005
  1. Made XML output the default when running qblast, as the XML parser is…

    … more
    
    stable than the HTML (in NCBIWWW) and text (in NCBIStandalone) parsers.
    (Currently, the XML parser is the only parser that works correctly).
    mdehoon committed Oct 5, 2005
  2. Updated the Tutorial to describe the NCBIXML parser as a replacement …

    …of the
    
    NCBIWWW and NCBIStandalone parsers.
    mdehoon committed Oct 5, 2005