Merge branch 'master' into io-rename
Merge branch 'master' of github.com:OpenTreeOfLife/peyotl into as-json-to-utility
refactored nexson_syntax tests into separate files for low-level conversion and use of the PhyloSchema class
new test reveals bug in unused functionality
bug fix in generating a phylesystem_url. Code not used.
several more test. and making the URL shorter when the default NexSON is requested
Merge pull request #73 from OpenTreeOfLife/cull-non-matching-trees
cull_nonmatching_trees method added

This gives a way to address:
https://github.com/OpenTreeOfLife/phylesystem-api/issues/135

If cull_nonmatching=true is passed into a call that would
previously return a NexSON tree fragment then the response
will now be a NexSON with the nonmatching trees omitted.

These trees will not be in the lists (and empty trees groups
will be culled). But there can be dangling reference to trees
in the full study in some of the annotations. So the client
code must be prepared to deal with some broken references if
it wants to traverse all of the annotations.
conversion to requested nexson version.

Unlike with other forms of slicing a study into pieces, when
we use the cull_nonmatching... feature, we can support
conversion to the user's requested version of the NexSON
syntax. This new code and test make sure that this works.
raise exception for unexpected cull_nonmatching value
initial bib file and minor edits
some blah-blah in the docs
more text
some editing and move to bioinformatics template
minor
more text and references
first draft - desperately needs to be proofread
first proofread
Merge pull request #75 from OpenTreeOfLife/papers

Papers
comment on style install