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Mar 17, 2007

  1. Getting ready for release 1.43.

    authored March 17, 2007
  2. Updated news for 1.43 release.

    authored March 17, 2007
  3. Updated links for 1.43 release.

    authored March 17, 2007
  4. Increase version number for 1.43 release.

    authored March 17, 2007
  5. Add links to protein.aln, m_cold.fasta.

    authored March 17, 2007
  6. Output of blastall, blastpgp is now in XML format by default.

    authored March 17, 2007
  7. Make blastall, blastpgp output in XML format by default.

    authored March 17, 2007

Mar 16, 2007

  1. kabat_file_dir is not used.

    authored March 16, 2007
  2. Bio.Kabat is on the nomination to be removed from Biopython, as its code

    seems to be out of date and currently it doesn't seem to have any users.
    authored March 16, 2007
  3. Show both relative paths (for offline use) and absolute paths to the …

    …website,
    
    which is more reliable.
    authored March 16, 2007
  4. Bio.Kabat now has a DeprecationWarning because its code seems to be o…

    …ut of
    
    date, and no users came forward. Removing the test for Bio.Kabat so that the
    DeprecationWarning won't show up when running the tests.
    authored March 16, 2007

Mar 14, 2007

  1. Change paths for example files to relative paths, so they can be found

    both on the web and in the source distribution.
    authored March 14, 2007
  2. Avoid printing output when run as a unittest.

    authored March 14, 2007
  3. Peter Cock

    Standardising on double quotes in the examples as these can be copied…

    … from both the PDF and HTML output for beginners to experiment. Single quotes can be rendered as apostrophes which spoil this.
    authored March 14, 2007
  4. Peter Cock

    A few little improvements

    authored March 14, 2007
  5. Peter Cock

    Link directly to ls_orchid.fasta and ls_orchid.gbk files which Michie…

    authored March 14, 2007
  6. Peter Cock

    Corrected some miss spellings of (un)ambiguous

    Updated some URLs, especially Biopython website links that had moved.
    
    Stop using nested \ahref{\url{...}} in the LaTex, as this was causing warnings in Hevea.
    authored March 14, 2007

Mar 13, 2007

  1. C Clustering Library 1.35. Use PyArray_ISCONTIGUOUS instead of CONTIG…

    …UOUS
    
    to make Bio.Cluster more compatible with NumPy. In NumPy, CONTIGUOUS exists
    in oldnumeric.h only; PyArray_ISCONTIGUOUS is in arrayobject.h both in NumPy
    and in Numeric.
    authored March 13, 2007

Mar 12, 2007

  1. Peter Cock

    Cope with cDNA in the LOCUS line of GenBank files

    Reported by Marc Colosimo in Bug 2231
    authored March 12, 2007
  2. Peter Cock

    Added new GenBank test case with NCBI header to test_GenBank.py

    authored March 12, 2007
  3. Peter Cock

    Added new GenBank test case with NCBI header to test_SeqIO.py

    authored March 12, 2007
  4. Peter Cock

    GenBank test case with an NCBI header

    authored March 12, 2007
  5. Peter Cock

    Fix regression bug 2229 for GenBank files with header\n\nAlso clarifi…

    …ed a few comments, and added links to documentation
    authored March 12, 2007
  6. Peter Cock

    Added explicit test case for assorted new line characters in the reco…

    …rd name, description and annotation.
    
    Also print out less records in the output (as its getting a little long now).
    authored March 12, 2007
  7. Peter Cock

    Rather than using hard-coded format lists, automatically test all the…

    … format writers in Bio.SeqIO
    
    This also lets us test their ValueError messages when given bad input.
    authored March 12, 2007
  8. Peter Cock

    Stupidly missed a few uses of os.linesep

    authored March 12, 2007
  9. Peter Cock

    Shouldn't have used os.linesep, a simple "\n" works fine on Windows/L…

    …inux/...
    authored March 12, 2007
  10. Peter Cock

    Made "clean" a method of the base writer class for use by FASTA and C…

    …lustal writers to remove newlines etc.
    authored March 12, 2007
  11. Peter Cock

    remove any newlines in the annotation when writing Stockholm files

    authored March 12, 2007
  12. Peter Cock

    Stricter checking of input sequences when writing: check for zero len…

    …gth alignment, as well as sequences of different lengths
    authored March 12, 2007
  13. Peter Cock

    Fixed newly added link to cor6_6.gb to work in hevea (was only workin…

    …g in pdflatex)
    authored March 12, 2007
  14. Peter Cock

    Some typos, tweaked some links to work both in pdflatex and hevea, mo…

    …ved a couple of paragraphs
    authored March 12, 2007

Mar 11, 2007

  1. Peter Cock

    Removing this example, as depended on Bio.Fasta._Scanner which was re…

    …moved back in Feb 2004.
    
    I don't see how the example could be adapted for the current code.
    authored March 11, 2007
  2. Peter Cock

    Added a new version of the example using Bio.SeqIO

    authored March 11, 2007
  3. Peter Cock

    Don't use the string module, and check for the prior existance of the…

    … index before building it.
    authored March 11, 2007
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