Closed adamrp closed 9 years ago
I'm nervous.
I would suggest installing scipy, numpy, matplotlib and all the things that take a while with conda.
Okay, thanks for the tip @ElDeveloper! This is my first time adding travis to a repo, so I'm still figuring things out.
@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.
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
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.
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...
Looks good, a few minor comments.
Ready for another review or merge
Fix #138