Create the cognoml package to implement an MVP API

[dhimmel]

I'll remove WIP (work in progress) when this pull request is complete.

See https://github.com/cognoma/machine-learning/issues/31 for API design discussion.

See https://github.com/cognoma/machine-learning/issues/44 for MVP (minimal viable product) feature inclusion decisions.

[dhimmel]

This pull request is ready for some review. Suggesting @yl565 @awm33 @cgreene @gwaygenomics.

The package name is cognoml. Feedback on name welcome.

The package is pip installable, but there are outstanding issues:

• data management: I'm not sure the best way to have our package access the data. Should you always have to pass a path for the directory that contains the data? If the data doesn't exist in that directory, it can be downloaded.
• algorithm support: currently only SGDClassifier is supported. It's not clear how we want to modularly support different pipelines. If we want to support different algos, how should this info get passed to this module?
• feature name bug
• currently the returned JSON may contain numpy values which break the builtin JSON encoder. Alternatively, cognoml.utils.JSONEncoder should work. However, if writing to the database, maybe we should just sanitize all JSON values before returning.

To run the example, use:

python cognoml/main.py > data/api/hippo-output.json

[gwaybio]

ok, i think this looks good to me. Although you may want to wait on @yl565 for those specific questions.

[dhimmel]

I propose we merge this sooner rather than later. The pull request is already quite large.

@gwaygenomics, @cgreene, @yl565 does one of you want to submit a review for up to 2291a0cd0afc74d3888cf04a52a169ca3435de19?