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Mar 10, 2010

  1. nmatzke

    Deleted extra pyc files and added AsciiDammit.py (public domain) code…

    … to GeneralUtils to save people the trouble (GeneralUtils needs it).
    authored March 09, 2010
  2. nmatzke

    Added a check for None to ~line 150 of GbifXml.py; thanks to James Pr…

    …ingle for noticing.
    authored March 09, 2010

Aug 19, 2009

  1. nmatzke

    Fixed filename.

    authored August 19, 2009
  2. nmatzke

    Fixed bug involving <annoying website links> in XML results. Function…

    …s that now work: downloading and processing an arbitrary number of records from GBIF in increments of size 'inc'; classifying records into geographic areas using the point-in-polygon operation in GeogUtils. Also deleted old loose files, updated wiki page at: http://biopython.org/wiki/BioGeography
    authored August 19, 2009

Aug 17, 2009

  1. nmatzke

    Actually uploading test files into Tests and Tests/output directory.

    authored August 17, 2009
  2. nmatzke

    Fixed accidental deletion of files in Bio.Nexus.

    authored August 17, 2009
  3. nmatzke

    Pencils down update; removed some stuff that suddenly developed a bug…

    …. Tests and test files put in appropriate directory; biopython wiki page being updated.
    authored August 17, 2009
  4. nmatzke

    Pencils down update; removed some stuff that suddenly developed a bug…

    …. Tests and test files put in appropriate directory; biopython wiki page being updated.
    authored August 17, 2009

Aug 16, 2009

  1. nmatzke

    Replaced Trees.py file in Bio/Nexus with Brad Chapman's revised Trees…

    ….py file, which correctly reads Newick files with branchlenghts and adds/substracts branchlengths etc. Revised other code to make use of this Trees.py, deleted local copy of Treesv2.py and references to it. Note that BioGeography code will not all run on 1.51 beta without the updated Trees.py file.
    authored August 16, 2009

Aug 07, 2009

  1. nmatzke

    Revised class names, Records object, and functions for parsing xml da…

    …ta to records objects.
    authored August 07, 2009

Aug 04, 2009

  1. nmatzke

    Code dealing with GBIF xml output completely refactored into the foll…

    …owing classes: ObsRecs (observation records & search results/summary), ObsRec (an individual observation record), XmlString (functions for cleaning xml returned by Gbif), GbifXml (extention of capabilities for ElementTree xml trees, parsed from GBIF xml returns.
    authored August 04, 2009

Jul 29, 2009

  1. nmatzke

    Code completely refactored into object methods; GIS functions still n…

    …eed work but tree and basic GBIF parsing functions. tree_functions makes use of Bio.Nexus.Tree, dependency on lagrange eliminated.
    authored July 28, 2009

Jul 02, 2009

  1. nmatzke

    Week 5 updates, added additional functions to geogUtils for parsing x…

    …mltree structures derived from ElementTree parsing of XML results from databases. No test script yet since it is mixed with other stuff that still has bugs.
    authored July 02, 2009

Jun 24, 2009

  1. nmatzke

    Week 4 updates, added functions to geogUtils for parsing newick files…

    … and phylogenies, and extracting information from them; and _test script for week 4
    authored June 23, 2009
  2. nmatzke

    Week 4 updates, added functions to geogUtils for parsing newick files…

    … and phylogenies, and extracting information from them; and _test script for week 4
    authored June 23, 2009

Jun 15, 2009

  1. nmatzke

    Week 3 updates, added functions download & parse large numbers of rec…

    …ords, get TaxonOccurrence gbifKeys, and search with those keys.
    authored June 14, 2009
  2. nmatzke

    Week 3 updates, added functions download & parse large numbers of rec…

    …ords, get TaxonOccurrence gbifKeys, and search with those keys.
    authored June 14, 2009

Jun 11, 2009

  1. nmatzke

    Fixed unicode/HTML binding reading, now searches, downloads, parses, …

    …and classifies in one script (wk 2)
    authored June 10, 2009

Jun 10, 2009

  1. nmatzke

    Week 2 updates, added functions to geogUtils for accessing GBIF & par…

    …sing; and _test script for week 2
    authored June 10, 2009
  2. nmatzke

    added week2 code. Run _test_functions_wk2.py to run

    authored June 10, 2009

Jun 02, 2009

  1. nmatzke

    added week1 code. Run _test_functions_wk1.py to run

    authored June 02, 2009

May 22, 2009

  1. nmatzke

    added temp1.py to test git etc. and created 'Geography' directory

    authored May 22, 2009

Apr 01, 2009

  1. Peter Cock

    Catch using non-alignments with Bio.Align.write() when passed to Bio.…

    …SeqIO (Bug 2803)
    authored April 01, 2009
  2. Peter Cock

    Support UnknownSeq (Bug 2799) in BioSQL. Cope when comments is a list…

    … (Bug 2802)
    authored April 01, 2009
  3. Peter Cock

    Comment corrections, and minor docstring clarifications.

    authored April 01, 2009
  4. Peter Cock

    Partial step to resolving Bug 2176, oddities in the XML output carrie…

    …d over from the plain text output.
    authored April 01, 2009
  5. Peter Cock

    Adding a stub for writing features.

    authored April 01, 2009
  6. Fixing a typo.

    authored April 01, 2009
  7. Adding deprecation information for Bio.SwissProt.SProt.

    authored April 01, 2009

Mar 31, 2009

  1. Peter Cock

    Check split methods

    authored March 31, 2009
  2. Peter Cock

    Check more string methods

    authored March 31, 2009
  3. Peter Cock

    Check string methods with optional start and end values (find, rfind,…

    … count)
    authored March 31, 2009
  4. Peter Cock

    UnknownSeq's count was ignoring the optional start/end values, and di…

    …dn't check for an invalid alphabet.
    authored March 31, 2009
  5. Peter Cock

    Basic unittest for Bio.Seq objects

    authored March 31, 2009
  6. Peter Cock

    Fix for a corner case of the UnknownSeq's count method.

    authored March 31, 2009
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