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MAINT: removed outdated imports
DOC: updated based on changes to how qiime-default-reference values are loaded
MAINT: fixed missing import
DOC: modernization of docs
MAINT: small fixes
DOC: modernization
MAINT: relax matplotlib version requirement
Merge branch 'mpl-relax-version-req' of https://github.com/jairideout/qiime into issue1696