modifications in preparation for first alpha release

gregcaporaso commented 8 years ago

Command line interface now takes four new parameters (--source_sink_column, --source_column_value, --sink_column_value, source_category_column) which remove requirements on mapping file values. Defaults are still the same, so no changes to command line interface or APIs.
The API is now more formally privatized by having the file names start with _. This makes it clear to any advanced users that no part of the API should currently be considered public or stable. If you were previously using from sourcetracker.sourcetracker import _gibbs, you should now update that to from sourcetracker._sourcetracker import _gibbs.
Travis now runs a couple more commands.
Various other small clean-ups throughout.

@lkursell, @johnchase, @wdwvt1, it'd be great to have one of you take a quick look at this. If all is good I can create the release tomorrow morning.

johnchase commented 8 years ago

Very minor comment, otherwise it all looks good to me

gregcaporaso commented 8 years ago

Thanks guys - I'll make these changes before I do the release. Good catch on the source_category_column parameter/variable name.

caporaso-lab / sourcetracker2