Remove scripts for now

Tweak Dockerfile

Big refactor to prepare for release

Return the titin epitope tests back to the original more stringent threshold of 500nm (instead of 700nm)

Make test_imputation unit test fair by training the model with imputation for the same number of epochs as the model without imputation

Fix bug in model loading when the models dir is changes. Refactored into a Class1AlleleSpecificPredictorLoader class

Fix failing test test_class1_allele_specific_cv_and_train_command and switch downloads.yml to point to models without imputation for now

Lazily putting this all in one commit.

* infrastructure for downloading datasets and published trained models (the `mhcflurry-downloads` command)
* docs and scripts (in `downloads-generation`) to generate the pubilshed datsets and trained models
* parallelized cross validation and model training implementation, including support for imputation (based on the old mhcflurry-cloud repo, which is now gone)
* a single front-end script for class1 allele-specific cross validation and model training / testing (`mhcflurry-class1-allele-specific-cv-and-train`)
* refactor how we deal with hyper-parameters and how we instantiate Class1BindingPredictors
* make Class1BindingPredictor pickleable and remove old serialization code
* move code particular to class 1 allele-specific predictors into its own submodule
* remove unused code including arg parsing, plotting, and ensembles
* had to bump the binding prediction threshold for the Titin1 epitope from 500 to 700, as this test was sporadically failing for me (see test_known_class1_epitopes.py)
* Attempt to make tests involving randomness somewhat more reproducible by setting numpy random seed
* update README

Remove experiements and notebooks

Split python2 into separate Dockerfile to speed up build (docker hub …

dockerize take 2

This is an attempt to have a single docker image that can be used as a base for cloud runs (with mhcflurry-cloud) and also eventually as a way for users to experiment with mhcflurry. Plan is to have this built automatically at https://hub.docker.com/r/hammerlab/mhcflurry/

 * supports cpu and theoretically gpu (not tested though)
 * supports python 2 and 3
 * putting Dockerfile in the root of our repo lets us just copy the current checkout of the mhcflurry repo into the image instead of pulling it from github, so it works with branches and non-released versions
 * by default this runs a python 3 jupyter notebook on port 8888 with mhcflurry and some convenience packages installed
 * does not try to train any models or run tests. Models will eventually be downloaded from google cloud storage once we have that working
 * it’s pretty hefty unfortunately, around 2 gig

Also: removed the pin on keras<1.0 in requirements.txt

Add notebook that builds simple model running on TF backend

Didn't get to multiple outputs but did some experiments on shared embedding