Add scipy, bipy, and pyqi as dependencies

Fixes #1330.
Change required pyqi version to 0.3.1

Deps were impossible to satisfy because biom-format 1.3.1 requires pyqi 0.3.1, but we were installing 0.3.1-dev.
update to address @gregcaporaso's comments
add optional pycogent deps to extra_requires
Merge branch 'master' into issue-1330

Conflicts:
	ChangeLog.md
Merge pull request #1331 from jrrideout/issue-1330

Add scipy, bipy, and pyqi as dependencies