ENH: added qiime-default-reference to setup.py
ENH: updated all use of template alignment to use default
ENH: added qiime-default-reference to print_qiime_config.py
ENH: assign taxonomy reference files now default to qiime_default_reference
MAINT: updated minimal dependency version
ENH: all otu pickers that use a reference now have a default
MAINT: remove qiime.filter.get_lane_mask in favor of qiime_default_reference
ENH: added functionality so it's clear what tree should be used with default reference; added ability to override all taxonomic assignemnt (since -t now has a default, this was no longer possible)
DOC: added note on new qiime_config value
DOC: simplified and modernized the QIIME install docs
ENH: changed default settings for clarity for qiime base install users
DOC: added version info for new dependencies
ENH: added some links to relevant documentation
ENH: added more annotation of output
ENH: added check for h5py, fixes #1596
DOC: modernized the upgrade instructions
DOC: modernization of the qiime config documentation
ENH: the default reference files are now part of qiime_config
MAINT: updated to pull values from qiime_config as getter functions are no longer necessary
MAINT: removed outdated imports