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biocore / American-Gut

American Gut open-access data and IPython notebooks
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WIP: Do the 10k #177

Closed wasade closed 8 years ago

wasade commented 8 years ago

This is a work in progress that refactors path management, and includes support for generating many other datasets of interest for downstream use.

Path management is not complete yet as, in the ideal case, there is a data access object to facilitate developers (e.g., AGData.bdiv('notrim', '1k', 'fecal') to get back the corresponding DistanceMatrix). In addition, the shear number of paths tracked is large but the patterns suggest it should be possible to not explicitly define them. However, right now, development is on a near path of least resistance.

wasade commented 8 years ago

...Prior to asking for review, I need to pull in the changes necessary for compute on the dataset as a whole and get those changes back in sync.

jwdebelius commented 8 years ago

Is it approaching the point where this can be cleaned up for review?

wasade commented 8 years ago

Should be basically there On Nov 10, 2015 14:32, "J W Debelius" notifications@github.com wrote:

Is it approaching the point where this can be cleaned up for review?

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/177#issuecomment-155589060.

wasade commented 8 years ago

Lit up green

jwdebelius commented 8 years ago

Sweet. The only thing I couldn't get to work when I ran through this branch was associated with the click command, and processing subsequent to the click commands. Given that this PR didn't touch that, I'm inclined that, other than the one comment, about text, I think it should be good.

jwdebelius commented 8 years ago

Thanks!

...Sorry, one more thing? Is this still a WIP? If not, Im happy to merge, but want to confirm first.