rename

mhcflurry/class1_neural_network.py

@@ -1416,10 +1416,4 @@ class Class1NeuralNetwork(object):
                 original_model.fit = \
                 original_model.fit_generator = throw
 
-        session = K.get_session()
-        (weights_variable,) = layer.non_trainable_weights
-        session.run(weights_variable.initializer)
-        session.run(tf.assign(weights_variable, reshaped))
-        #
-        # Previously had this but was getting sporadic not initialized errors
-        # layer.set_weights([reshaped])
+        layer.set_weights([reshaped])

mhcflurry/testing_utils.py

+"""
+Utilities used in MHCflurry unit tests.
+"""
 from . import Class1NeuralNetwork
 
 
-def module_cleanup():
+def cleanup():
+    """
+    Clear tensorflow session and other process-wide resources.
+    """
     import keras.backend as K
     Class1NeuralNetwork.clear_model_cache()
     K.clear_session()

test/test_calibrate_percentile_ranks_command.py

@@ -14,8 +14,8 @@ from mhcflurry.downloads import get_path
 
 os.environ["CUDA_VISIBLE_DEVICES"] = ""
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 
 def run_and_check(n_jobs=0, delete=True, additional_args=[]):

test/test_changing_allele_representations.py

@@ -8,8 +8,8 @@ from mhcflurry.downloads import get_path
 
 from numpy.testing import assert_equal
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 ALLELE_TO_SEQUENCE = pandas.read_csv(
     get_path(

test/test_class1_affinity_predictor.py

@@ -29,7 +29,7 @@ def setup():
 def teardown():
     global DOWNLOADED_PREDICTOR
     DOWNLOADED_PREDICTOR = None
-    mhcflurry.testing_utils.module_cleanup()
+    mhcflurry.testing_utils.cleanup()
 
 
 # To hunt down a weird warning we were seeing in pandas.

test/test_class1_neural_network.py

@@ -13,8 +13,8 @@ from mhcflurry.class1_neural_network import Class1NeuralNetwork
 from mhcflurry.downloads import get_path
 from mhcflurry.common import random_peptides
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 
 def test_class1_neural_network_a0205_training_accuracy():

test/test_class1_pan.py

@@ -11,8 +11,8 @@ from mhcflurry import Class1AffinityPredictor,Class1NeuralNetwork
 from mhcflurry.allele_encoding import AlleleEncoding
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 
 HYPERPARAMETERS = {

test/test_custom_loss.py

@@ -11,8 +11,8 @@ import keras.backend as K
 
 from mhcflurry.custom_loss import CUSTOM_LOSSES
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 
 def evaluate_loss(loss, y_true, y_pred):

test/test_download_models_class1.py

@@ -5,7 +5,7 @@ from numpy.testing import assert_equal
 
 from mhcflurry import Class1AffinityPredictor, Class1NeuralNetwork
 
-from mhcflurry.testing_utils import module_cleanup
+from mhcflurry.testing_utils import cleanup
 
 
 DOWNLOADED_PREDICTOR = None
@@ -19,7 +19,7 @@ def setup():
 def teardown():
     global DOWNLOADED_PREDICTOR
     DOWNLOADED_PREDICTOR = None
-    module_cleanup()
+    cleanup()
 
 
 def predict_and_check(

test/test_multi_output.py

@@ -12,8 +12,8 @@ logging.getLogger('tensorflow').disabled = True
 from mhcflurry.class1_neural_network import Class1NeuralNetwork
 from mhcflurry.common import random_peptides
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 
 def test_multi_output():

test/test_network_merging.py

@@ -5,7 +5,7 @@ from mhcflurry import Class1AffinityPredictor, Class1NeuralNetwork
 from mhcflurry.common import random_peptides
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
+from mhcflurry.testing_utils import cleanup
 
 logging.getLogger('tensorflow').disabled = True
 
@@ -23,7 +23,7 @@ def setup():
 def teardown():
     global PAN_ALLELE_PREDICTOR
     PAN_ALLELE_PREDICTOR = None
-    module_cleanup()
+    cleanup()
 
 
 def test_merge():

test/test_predict_command.py

@@ -6,8 +6,8 @@ from numpy.testing import assert_equal
 
 from mhcflurry import predict_command
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 TEST_CSV = '''
 Allele,Peptide,Experiment

test/test_released_predictors_on_hpv_dataset.py

@@ -13,7 +13,7 @@ from nose.tools import eq_, assert_less, assert_greater, assert_almost_equal
 from mhcflurry import Class1AffinityPredictor
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
+from mhcflurry.testing_utils import cleanup
 
 
 def data_path(name):
@@ -41,7 +41,7 @@ def setup():
 def teardown():
     global PREDICTORS
     PREDICTORS = None
-    module_cleanup()
+    cleanup()
 
 
 def test_on_hpv(df=DF):

test/test_released_predictors_well_correlated.py

@@ -15,7 +15,7 @@ from mhcflurry.encodable_sequences import EncodableSequences
 from mhcflurry.downloads import get_path
 from mhcflurry.common import random_peptides
 
-from mhcflurry.testing_utils import module_cleanup
+from mhcflurry.testing_utils import cleanup
 
 PREDICTORS = None
 
@@ -33,7 +33,7 @@ def setup():
 def teardown():
     global PREDICTORS
     PREDICTORS = None
-    module_cleanup()
+    cleanup()
 
 
 def test_correlation(

test/test_speed.py

@@ -18,7 +18,7 @@ from mhcflurry.encodable_sequences import EncodableSequences
 from mhcflurry.common import random_peptides
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
+from mhcflurry.testing_utils import cleanup
 
 ALLELE_SPECIFIC_PREDICTOR = Class1AffinityPredictor.load(
     get_path("models_class1", "models"))
@@ -43,7 +43,7 @@ def setup():
 def teardown():
     global PREDICTORS
     PREDICTORS = None
-    module_cleanup()
+    cleanup()
 
 
 DEFAULT_NUM_PREDICTIONS = 10000

test/test_train_and_related_commands.py

@@ -14,8 +14,8 @@ from numpy.testing import assert_array_less, assert_equal
 from mhcflurry import Class1AffinityPredictor
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 os.environ["CUDA_VISIBLE_DEVICES"] = ""
 

test/test_train_pan_allele_models_command.py

@@ -15,8 +15,8 @@ from numpy.testing import assert_equal, assert_array_less
 from mhcflurry import Class1AffinityPredictor,Class1NeuralNetwork
 from mhcflurry.downloads import get_path
 
-from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+from mhcflurry.testing_utils import cleanup
+teardown = cleanup
 
 os.environ["CUDA_VISIBLE_DEVICES"] = ""