[Biopython-dev] GSoC Weekly Update 12: PhyloXML for Biopython

[Eric Talevich]

Hi folks,

Previously I (Aug. 3-7):

    - Refactored the PhyloXML parser somewhat, to behave more like the other
      Biopython parsers and also handle 'other' elements better
    - Reorganized Bio.Tree a bit, generalizing the Tree base class and
      improving BaseTree-PhyloXML interoperability
    - Worked on networkx export and graphviz display
    - Added some more tests (thanks, Diana!)
    - Added TreeIO.convert(), to match the AlignIO and SeqIO modules

Next week (Aug. 10-14) I will:

    - Update the wiki documentation
    - Fix any surprises that come up during testing

    Automated testing:
    - Check unit tests for complete coverage
    - Re-run performance benchmarks
    - Run tests and benchmarks on alternate platforms
    - Check epydoc's generated API documentation

Remarks:

    - Performance of the I/O functions is close to what it was before, in
the
      best of times; parsing Taxonomy nodes incrementally seems to have
helped.

    - Drawing trees with Graphviz is still ugly. Hopefully I can fix it this
      week, but if not, I'll probably do it after GSoC because I like pretty
      things.

    - Presumably, any discussion of merging with Biopython will have to wait
      until after the biopython-1.51 release. I'll be around. For GSoC
      requirements, I'm planning on just dumping the Bio.Tree and Bio.TreeIO
      modules along with the unit test suite as standalone files, rather
than
      as a patch set since the last upstream revision I pulled was just a
      random untagged one around the time of the last beta release.


Cheers,
Eric
http://github.com/etal/biopython/tree/phyloxml/Bio/PhyloXML
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Biopython_support_for_parsing_and_writing_phyloXML