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
Fix floating point issue in otu_significance test

Use a larger epsilon when comparing observed to expected bootstrapped p-value.

Fixes #1347.
Merge pull request #1364 from jrrideout/issue-1347-2nd-part

Fix floating point issue in otu_significance.py test
Merge branch 'master' into issue-1330

Conflicts:
	ChangeLog.md
Removed deprecated 'commands' import
Merge pull request #1373 from lkursell/issue_1352

Removed deprecated 'commands' import
Merge pull request #1331 from jrrideout/issue-1330

Add scipy, bipy, and pyqi as dependencies