Change the PCoA from cogent to skbio
Solving small PEP8 issue
Remove useless comments
Using skbio PCoA
Move misplaced alpha diversity tests

Unit tests for `single_file_cup` were in pycogent_backports tests instead of QIIME's alpha diversity tests. Also fixed issue where temporary files weren't being cleaned up.

Fixes #1488.
MAINT: adapting to handle numpy qual
MAINT: removing __iadd__ on a str
MAINT: trim_fastq not actually used, deleted
MAINT: using scikit-bio's format_fastq_record
MAINT: fixing broken tests
STY: removing unused vars
STY: removing unused imports
MAINT: almost done with qual updates
TST: updates to use actual phred scores
BUG: was converting phred val to str
MAINT: simplifying calls to range, thanks @ElDeveloper
BUG: passing in the phred offset now
initial changes to add index page to workflow output
TST: updating qual scores to reflect their actual offsets
updated so index page isn't supported in iterative mode, will add this in later as it's more complicated and less common - still needs testing with alignment, tree building, and tax assignment