Update mhc_rank/class1_processing_neural_network.py

See merge request !2

Recover lost data

See merge request !1

models from first round of training + some files to enable predictions to be to be run as SLURM jobs

added functionality to model creation that allows for learned embeddings (or combo of learned and hardcoded). Also, adjusted amino_acid.py to make X's index = 0 so that it can be used as a mask.

Deleted mhcflurry/__init__.py, mhcflurry/allele_encoding.py, mhcflurry/amino_acid.py, mhcflurry/calibrate_percentile_ranks_command.py, mhcflurry/class1_affinity_predictor.py, mhcflurry/class1_neural_network.py, mhcflurry/class1_presentation_predictor.py, mhcflurry/class1_processing_neural_network.py, mhcflurry/class1_processing_predictor.py, mhcflurry/cluster_parallelism.py, mhcflurry/common.py, mhcflurry/custom_loss.py, mhcflurry/data_dependent_weights_initialization.py, mhcflurry/downloads.py, mhcflurry/downloads.yml, mhcflurry/downloads_command.py, mhcflurry/encodable_sequences.py, mhcflurry/ensemble_centrality.py, mhcflurry/fasta.py, mhcflurry/flanking_encoding.py, mhcflurry/hyperparameters.py, mhcflurry/local_parallelism.py, mhcflurry/percent_rank_transform.py, mhcflurry/predict_command.py, mhcflurry/predict_scan_command.py, mhcflurry/random_negative_peptides.py, mhcflurry/regression_target.py, mhcflurry/scoring.py, mhcflurry/select_allele_specific_models_command.py, mhcflurry/select_pan_allele_models_command.py, mhcflurry/select_processing_models_command.py, mhcflurry/testing_utils.py, mhcflurry/train_allele_specific_models_command.py, mhcflurry/train_pan_allele_models_command.py, mhcflurry/train_presentation_models_command.py, mhcflurry/train_processing_models_command.py, mhcflurry/version.py, train_APmodels.sh files

altered training init to work with SLURM and corrected typo (BLOSUM --> BLOSUM62) in hyperparameters, specifically encoding options

fixed nonsensical import of subpackage in middle of script to point to mhc_rank instead of mhcflurry

trying to figure out why cleave_radius is an unexpected keyword arg in vector_encode even though vector encode has an explicit argument cleave_radisu...