Merge pull request #94 from hammerlab/bump-keras-version

Bump keras version, set mhcflurry version to 0.9.1

downloads-generation/models_class1/GENERATE.sh

@@ -31,7 +31,7 @@ time mhcflurry-class1-train-allele-specific-models \
     --data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
     --hyperparameters hyperparameters.json \
     --out-models-dir models \
-    --min-measurements-per-allele 100
+    --min-measurements-per-allele 200
 
 cp $SCRIPT_ABSOLUTE_PATH .
 bzip2 LOG.txt

downloads-generation/models_class1_experiments1/GENERATE.sh

@@ -31,7 +31,7 @@ time mhcflurry-class1-train-allele-specific-models \
     --only-quantitative \
     --hyperparameters hyperparameters-standard.json \
     --out-models-dir models-standard-quantitative \
-    --min-measurements-per-allele 100
+    --min-measurements-per-allele 100 &
 
 # Model variations on qualitative + quantitative
 for mod in 0local_noL1 0local 1local dense16 dense64 noL1 
@@ -42,8 +42,9 @@ do
         --data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
         --hyperparameters hyperparameters-${mod}.json \
         --out-models-dir models-${mod} \
-        --min-measurements-per-allele 100
+        --min-measurements-per-allele 100 &
 done
+wait
 
 cp $SCRIPT_ABSOLUTE_PATH .
 bzip2 LOG.txt

downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.json

@@ -20,7 +20,7 @@
         ],
         "random_negative_affinity_min": 20000.0,
         "random_negative_affinity_max": 50000.0,
-        "dense_layer_l1_regularization": 0.001,
+        "dense_layer_l1_regularization": 0.0,
         "dropout_probability": 0.0
     }
-]
\ No newline at end of file
+]

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__ = "0.9.0"
+__version__ = "0.9.1"
 
 __all__ = [
     "Class1NeuralNetwork",

mhcflurry/downloads.yml

@@ -8,7 +8,7 @@
 # by name, the downloads with "default=true" are downloaded.
 
 # This should usually be the latest release.
-current-release: 1.0.0
+current-release: 0.9.1
 
 # An integer indicating what models the current MHCflurry code base is compatible
 # with. Increment this integer when changes are made to MHCflurry that would break
@@ -17,27 +17,27 @@ current-compatibility-version: 2
 
 # Add new releases here as they are made.
 releases:
-    1.0.0:
+    0.9.1:
         compatibility-version: 2
         downloads:
             - name: models_class1
-              url: http://github.com/hammerlab/mhcflurry/releases/download/pre-1.0.0-alpha/models_class1.tar.bz2
+              url: http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1.tar.bz2
               default: true
 
             - name: data_curated
-              url: https://github.com/hammerlab/mhcflurry/releases/download/pre-1.0.0-alpha/data_curated.tar.bz2
+              url: https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_curated.tar.bz2
               default: true
 
             - name: data_kim2014
-              url: http://github.com/hammerlab/mhcflurry/releases/download/0.0.8/data_kim2014.tar.bz2
+              url: http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_kim2014.tar.bz2
               default: false
 
             - name: data_iedb
-              url: https://github.com/hammerlab/mhcflurry/releases/download/pre-1.0.0-alpha/data_iedb.tar.bz2
+              url: https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_iedb.tar.bz2
               default: false
 
             - name: models_class1_experiments1
-              url: http://github.com/hammerlab/mhcflurry/releases/download/pre-1.0.0-alpha/models_class1_experiments1.tar.bz2
+              url: http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1_experiments1.tar.bz2
               default: false
 
     0.2.0:

requirements.txt

 six
 numpy>= 1.11
 pandas>=0.13.1
-Keras==2.0.4
+Keras==2.0.6
 appdirs
 tensorflow
 scikit-learn

setup.py

@@ -52,7 +52,7 @@ if __name__ == '__main__':
         'six',
         'numpy>=1.11',
         'pandas>=0.13.1',
-        'Keras==2.0.4',
+        'Keras==2.0.6',
         'appdirs',
         'tensorflow',
         'scikit-learn',