Big refactor to prepare for release
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
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- .dockerignore 2 additions, 3 deletions.dockerignore
- .gitignore 12 additions, 0 deletions.gitignore
- .travis.yml 7 additions, 24 deletions.travis.yml
- Dockerfile 14 additions, 3 deletionsDockerfile
- README.md 40 additions, 19 deletionsREADME.md
- RELEASING.md 21 additions, 0 deletionsRELEASING.md
- downloads-generation/README.md 5 additions, 0 deletionsdownloads-generation/README.md
- downloads-generation/data_combined_iedb_kim2014/GENERATE.sh 46 additions, 0 deletionsdownloads-generation/data_combined_iedb_kim2014/GENERATE.sh
- downloads-generation/data_combined_iedb_kim2014/README.md 13 additions, 0 deletionsdownloads-generation/data_combined_iedb_kim2014/README.md
- downloads-generation/data_combined_iedb_kim2014/create-combined-class1-dataset.py 9 additions, 32 deletions...a_combined_iedb_kim2014/create-combined-class1-dataset.py
- downloads-generation/data_combined_iedb_kim2014/create-iedb-class1-dataset.py 11 additions, 26 deletions.../data_combined_iedb_kim2014/create-iedb-class1-dataset.py
- downloads-generation/data_kim2014/GENERATE.sh 33 additions, 0 deletionsdownloads-generation/data_kim2014/GENERATE.sh
- downloads-generation/data_kim2014/README.md 15 additions, 0 deletionsdownloads-generation/data_kim2014/README.md
- downloads-generation/models_class1_allele_specific_single/GENERATE.sh 52 additions, 0 deletions...neration/models_class1_allele_specific_single/GENERATE.sh
- downloads-generation/models_class1_allele_specific_single/README.md 20 additions, 0 deletions...generation/models_class1_allele_specific_single/README.md
- downloads-generation/models_class1_allele_specific_single/imputer.json 8 additions, 0 deletions...eration/models_class1_allele_specific_single/imputer.json
- downloads-generation/models_class1_allele_specific_single/models.py 15 additions, 0 deletions...generation/models_class1_allele_specific_single/models.py
- mhcflurry/__init__.py 13 additions, 2 deletionsmhcflurry/__init__.py
- mhcflurry/args.py 0 additions, 175 deletionsmhcflurry/args.py
- mhcflurry/class1_allele_specific/__init__.py 15 additions, 0 deletionsmhcflurry/class1_allele_specific/__init__.py
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