Add .travis.yml

[adamrp]

Fix #138

[wasade]

I'm nervous.

[ElDeveloper]

I would suggest installing scipy, numpy, matplotlib and all the things that take a while with conda.

[adamrp]

Okay, thanks for the tip @ElDeveloper! This is my first time adding travis to a repo, so I'm still figuring things out.

[adamrp]

@wasade can you make your code (taxtree and test_taxtree) compatible with biom 1.3.1? If so, we are close to being able to add Travis (flake8 failures notwithstanding).

In a future PR, we should upgrade the package to use biom 2.x, but for now there is far more code that depends on the 1.3.1 API.

[wasade]

The processing pipeline is QIIME 1.9, and much of the code in americangut is already BIOM 2.x.

note, I think select_gamma can be tossed as we've changed the filtering for blooms

[adamrp]

There seem to be more errors when using BIOM 2.x than when I switch to BIOM 1.3.1, but I'll look into it.

On Thu, Mar 26, 2015 at 10:36 AM, Daniel McDonald notifications@github.com wrote:

The processing pipeline is QIIME 1.9, and much of the code in americangut is already BIOM 2.x.

note, I think select_gamma can be tossed as we've changed the filtering for blooms

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/139#issuecomment-86608699.

[adamrp]

Phew. Okay. It's passing. The vast majority of the changes are flake8 fixes (which i squashed into one commit, so for reviewing purposes it's probably safe to ignore the STY commit).

Note that right now, I have flake8 in Travis ignoring the py files in tests, since there are a ton of complaints...

[ElDeveloper]

Looks good, a few minor comments.

[adamrp]

Ready for another review or merge