I initially decided against including it because we don't usually include other tools' dependencies here (though they often overlap with direct QIIME dependencies). For example, biom-format also depends on dateutil and Cython, but we don't have those listed here. Likewise, PyCogent depends on MySQL-python and SQLAlchemy but those are missing too. I can add pyqi if you want, just wanted to explain my reasoning for originally not doing so.