Bump version, upgrade to Keras 2.0.9

* Switch from JSON to YAML for hyperparameters
* Pin tensorflow (hoping will help with #110)

mhcflurry/__init__.py

@@ -17,7 +17,7 @@ from .class1_affinity_prediction.class1_neural_network import (
 from .class1_affinity_prediction.class1_affinity_predictor import (
     Class1AffinityPredictor)
 
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 
 __all__ = [
     "Class1NeuralNetwork",

mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py

@@ -5,7 +5,7 @@ Train Class1 single allele models.
 import os
 import sys
 import argparse
-import json
+import yaml
 
 import pandas
 
@@ -31,7 +31,7 @@ parser.add_argument(
     "--hyperparameters",
     metavar="FILE.json",
     required=True,
-    help="JSON of hyperparameters")
+    help="JSON or YAML of hyperparameters")
 parser.add_argument(
     "--allele",
     default=None,
@@ -61,7 +61,7 @@ def run(argv=sys.argv[1:]):
 
     configure_logging(verbose=args.verbosity > 1)
 
-    hyperparameters_lst = json.load(open(args.hyperparameters))
+    hyperparameters_lst = yaml.load(open(args.hyperparameters))
     assert isinstance(hyperparameters_lst, list)
     print("Loaded hyperparameters list: %s" % str(hyperparameters_lst))
 

requirements.txt

 six
-numpy>= 1.11
+numpy>=1.11
 pandas>=0.13.1
-Keras==2.0.8
+Keras==2.0.9
+tensorflow>=1.4.0
 appdirs
-tensorflow
 scikit-learn
 typechecks
 mhcnames
+pyyaml

setup.py

@@ -51,12 +51,13 @@ if __name__ == '__main__':
         'six',
         'numpy>=1.11',
         'pandas>=0.13.1',
-        'Keras==2.0.8',
+        'Keras==2.0.9',
         'appdirs',
-        'tensorflow',
+        'tensorflow>=1.4.0',
         'scikit-learn',
         'typechecks',
         'mhcnames',
+        'pyyaml',
     ]
     if PY2:
         # concurrent.futures is a standard library in Py3 but Py2