Suppress pystan output

[bmmalone]

PyStan outputs information about sampling times for each call to the sampler. This output is not useful for this project.

By default, it is difficult to suppress this output. This thread has some details: https://groups.google.com/forum/#!topic/stan-users/Uel-8jy-Lrc

refresh=-1 and n_jobs=1 are already used.

[bmmalone]

This exact issue was also raised in facebook/prophet#223. There, randlet provided a context manager which suppresses pystan output. I pushed his solution in the pymisc repo. It is already being used in btea and just needs to be added here.

[eboileau]

I've added this in both estimates_orf_bayes_factors and riboutils.estimate_metagene_profile_bayes_factors. However, this is currently only in dev for pymisc, I'm not sure how you want to handle this. This is not a problem now, but will have to be sorted for a next release of rp-bp and riboseq-utils, otherwise the class won't be immediately available.

[bmmalone]

I will soon (hopefully this weekend) push a new version of pymisc which includes the context manager in the master branch. I'll let you know once I do that.

[eboileau]

Implemented in latest patch version 1.1.12. Closing this issue.