upgrading software

[antgonza]

• open_file completely changed from skbio 0.3.0 to 0.4.2, the main changes are due to supporting both python 2.7 and 3. After discussing with @josenavas we decided that it was easier to simply reuse the code and then address once we solve Add python 3 back in to travis CI #250.
• After making that decision we realized that open_file was already within our code in qiita_ware so decided to move it to qiita_db
• flatten doesn't exist anymore in skbio, the suggestion is to use list(chain(*, which we are doing here
• updated test so we use ipython 3.2.0

[codecov-io]

Codecov Report

Merging #2261 into remove-moi will increase coverage by 2.8%.
The diff coverage is 98.63%.

@@              Coverage Diff              @@
##           remove-moi    #2261     +/-   ##
=============================================
+ Coverage       92.82%   95.62%   +2.8%     
=============================================
  Files             171       75     -96     
  Lines           18930    13021   -5909     
=============================================
- Hits            17571    12451   -5120     
+ Misses           1359      570    -789

Impacted Files	Coverage Δ
qiita_db/search.py	92.56% <100%> (+0.05%)	⬆️
qiita_db/util.py	96.68% <100%> (+0.12%)	⬆️
qiita_db/metadata_template/util.py	90.9% <100%> (-0.07%)	⬇️
qiita_db/test/test_util.py	99.61% <98.07%> (-0.18%)	⬇️
...andlers/study_handlers/tests/test_edit_handlers.py
qiita_pet/handlers/upload.py
qiita_pet/test/test_download.py
..._pet/handlers/analysis_handlers/tests/test_util.py
qiita_pet/test/test_logger.py
qiita_pet/uimodules/prep_template_tab.py
... and 89 more

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[josenavas]

Tests are expected to fail, and this is going to a different development branch, which is a WIP branch. The vast majority of this changes are just moving code around so I will merge as everything looks fine.