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Mar 22, 2008

  1. More news for release 1.45.

    authored March 22, 2008

Mar 21, 2008

  1. Biopython release 1.45.

    authored March 21, 2008
  2. Add some news for the 1.45 release.

    authored March 21, 2008
  3. Updating version number for Biopython release 1.45.

    authored March 21, 2008
  4. Peter Cock

    Deprecated Bio.biblio as no one seems to use it, and its doesn't work…

    … anymore. At the very least the URLs for the EBI SOAP API have changed.
    authored March 21, 2008
  5. Peter Cock

    Added missing copyright and licence header, explicitly stating that w…

    …hile these files are part of Biopython, BioSQL itself (database schema and scipts) is available and licensed separately.
    authored March 21, 2008

Mar 20, 2008

  1. Peter Cock

    Bug 2422, records the taxonomy again

    authored March 20, 2008

Mar 19, 2008

  1. popen2.Popen3 is not available on Windows; use popen2.popen3 there.

    authored March 19, 2008

Mar 16, 2008

  1. Peter Cock

    Minor tweak in anticipation of the taxon id fix for Bug 2422.

    authored March 16, 2008
  2. Peter Cock

    Fixes a disagreement with the GenBank parser on how to store the NCBI…

    … taxonomy ID and the taxonomy lineage (list of species) in the annotations dictionary of a SeqRecord.
    authored March 16, 2008
  3. Peter Cock

    Minor updates on parsing GenBank files, e.g. "organism" versus "sourc…

    …e" for species names.
    authored March 16, 2008

Mar 15, 2008

  1. Peter Cock

    Adds missing licence headers and a tiny bit of documentation with lin…

    …ks to the wise2 website.
    authored March 15, 2008

Mar 14, 2008

  1. Peter Cock

    Be a little less strict when checking the sequence alphabet matches t…

    …he translation table alphabet. Resolves bug 2437
    authored March 14, 2008
  2. Remove deprecated functions from Bio.Entrez, and update the deprecati…

    …on warning here.
    authored March 14, 2008
  3. Removing deprecated functions to let Bio.Entrez start out clean.

    authored March 14, 2008

Mar 07, 2008

  1. C Clustering Library 1.38. Renamed DataFile to Record, and added a re…

    …ad function.
    authored March 07, 2008

Feb 25, 2008

  1. Peter Cock

    Dos/Unix line endings

    authored February 25, 2008
  2. Changing bottle.png binary status - commiting as binary

    authored February 25, 2008
  3. Changing bottle.png binary status - initial remove

    authored February 25, 2008
  4. Moving Bio/Entrez.py to Bio/Entrez/__init__.py.

    authored February 25, 2008
  5. Moving Bio/Entrez.py to Bio/Entrez/__init__.py.

    authored February 25, 2008
  6. Moving Bio/Entrez.py to Bio/Entrez/__init__.py.

    authored February 25, 2008
  7. Resurrecting Bio.Entrez. The __init__.py file you see here is ancient…

    …, and is
    
    about to be replaced by what is currently in Bio/Entrez.py.
    authored February 25, 2008
  8. Using the new module Bio.Entrez instead of DBRegistry. See bug #2393.

    authored February 25, 2008

Feb 24, 2008

  1. Peter Cock

    Updated a couple of mentions of the deprecation Bio.WWW module to use…

    … its replacements.
    authored February 24, 2008

Feb 23, 2008

  1. Documentation for Bio.Entrez added.

    authored February 23, 2008

Feb 17, 2008

  1. Conforming to NCBI requirements.

    authored February 17, 2008

Feb 15, 2008

  1. Allow batch-processing (for example fetching records for a list of pu…

    …bmed ids).
    authored February 15, 2008
  2. Add missing functions from Entrez, and update the documentation of the

    existing functions.
    authored February 15, 2008
  3. Updated these functions with the latest information from NCBI.

    authored February 15, 2008
  4. Using modern Python.

    authored February 15, 2008
  5. Moving Bio.WWW.NCBI to Bio.Entrez; Bio.WWW.NCBI is deprecated, Bio.En…

    …trez will
    
    be updated and further developed.
    authored February 15, 2008
  6. Moving Bio.WWW.NCBI to Bio.Entrez. Bio.WWW.NCBI will be deprecated;

    Bio.Entrez will be updated and further developed.
    authored February 15, 2008

Feb 01, 2008

  1. Deprecating the Bio.Blast.NCBIXML.BlastParser.parse method in favor of

    the Bio.Blast.NCBIXML.parse function.
    authored February 01, 2008
  2. Use currently recommended usage of Bio.Blast.NCBIXML.

    authored February 01, 2008
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