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Commits on Mar 10, 2010
  1. Deleted extra pyc files and added AsciiDammit.py (public domain) code…

    authored
    … to GeneralUtils to save people the trouble (GeneralUtils needs it).
Commits on Aug 19, 2009
  1. Fixed filename.

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

    authored
    …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
Commits on Aug 17, 2009
  1. Pencils down update; removed some stuff that suddenly developed a bug…

    authored
    …. Tests and test files put in appropriate directory; biopython wiki page being updated.
  2. Pencils down update; removed some stuff that suddenly developed a bug…

    authored
    …. Tests and test files put in appropriate directory; biopython wiki page being updated.
Commits on Aug 16, 2009
  1. Replaced Trees.py file in Bio/Nexus with Brad Chapman's revised Trees…

    authored
    ….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.
Commits on Aug 7, 2009
Commits on Aug 4, 2009
  1. Code dealing with GBIF xml output completely refactored into the foll…

    authored
    …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.
Commits on Jul 29, 2009
  1. Code completely refactored into object methods; GIS functions still n…

    authored
    …eed work but tree and basic GBIF parsing functions. tree_functions makes use of Bio.Nexus.Tree, dependency on lagrange eliminated.
Commits on Jul 2, 2009
  1. Week 5 updates, added additional functions to geogUtils for parsing x…

    authored
    …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.
Commits on Jun 24, 2009
  1. Week 4 updates, added functions to geogUtils for parsing newick files…

    authored
    … and phylogenies, and extracting information from them; and _test script for week 4
  2. Week 4 updates, added functions to geogUtils for parsing newick files…

    authored
    … and phylogenies, and extracting information from them; and _test script for week 4
Commits on Jun 15, 2009
  1. Week 3 updates, added functions download & parse large numbers of rec…

    authored
    …ords, get TaxonOccurrence gbifKeys, and search with those keys.
  2. Week 3 updates, added functions download & parse large numbers of rec…

    authored
    …ords, get TaxonOccurrence gbifKeys, and search with those keys.
Commits on Jun 11, 2009
  1. Fixed unicode/HTML binding reading, now searches, downloads, parses, …

    authored
    …and classifies in one script (wk 2)
Commits on Jun 10, 2009
  1. Week 2 updates, added functions to geogUtils for accessing GBIF & par…

    authored
    …sing; and _test script for week 2
Commits on Jun 2, 2009
Commits on May 22, 2009
Commits on Apr 1, 2009
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    Partial step to resolving Bug 2176, oddities in the XML output carrie…

    peterjc authored
    …d over from the plain text output.
  5. @peterjc
  6. Fixing a typo.

    mdehoon authored
Commits on Mar 31, 2009
  1. @peterjc

    Check split methods

    peterjc authored
  2. @peterjc

    Check more string methods

    peterjc authored
  3. @peterjc
  4. @peterjc

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

    peterjc authored
    …dn't check for an invalid alphabet.
  5. @peterjc
  6. @peterjc
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