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biocore / American-Gut

American Gut open-access data and IPython notebooks
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Introduces the single bodysite notebook #182

Closed jwdebelius closed 8 years ago

jwdebelius commented 8 years ago

Creates a notebook for generating the single sample per bodysite packaged results.

jwdebelius commented 8 years ago

I fixed the pep8, but the parallel_alpha_diversity is still timing out.

mortonjt commented 8 years ago

I noticed the timing out issue with https://github.com/biocore/American-Gut/pull/181

Can you try replacing the last line in .travis.yml with

travis_wait ./scripts/run_the_ipys.sh ipynb/primary-processing/

This will allocate 20 minutes to run the scripts rather than just 10 minutes before travis crashes.

wasade commented 8 years ago

Few comments

jwdebelius commented 8 years ago

@mortonjt: I added the line, and now it can't parse the travis.yml file. I thought I'd copied correctly? I also thought Embriette had made this change already, so I'm kind of surprised its running into the error. If my PR doesn't fix this, would it be possible for someone with more experience with travis to address it systematically?

jwdebelius commented 8 years ago

@mortonjt, @squirrelo, @wasade, @EmbrietteH, could I get another review?

Thanks!

jwdebelius commented 8 years ago

Addressed comments. @mortonjt, how does it look?

jwdebelius commented 8 years ago

Bumping this because its needed for alpha diversity plots later

jwdebelius commented 8 years ago

Since all comments have been addressed and tests are passing, could this be merged?

Thanks.

wasade commented 8 years ago

Awesome!!

On Fri, Jan 8, 2016 at 1:05 PM, Embriette Hyde notifications@github.com wrote:

Merged #182 https://github.com/biocore/American-Gut/pull/182.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/182#event-509869448.