diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py index 9f22176db08e141fbfc12f059a7c650941923c24..277c683b8b23c3750daa82e75c2be09a21f75059 100644 --- a/mhcflurry/class1_neural_network.py +++ b/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]) diff --git a/mhcflurry/testing_utils.py b/mhcflurry/testing_utils.py index f6cc079b375acbad60ddac2e7974ac72377b06fe..157a11af9f62891be7e61d64f1fae93b5463e830 100644 --- a/mhcflurry/testing_utils.py +++ b/mhcflurry/testing_utils.py @@ -1,7 +1,13 @@ +""" +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() diff --git a/test/test_calibrate_percentile_ranks_command.py b/test/test_calibrate_percentile_ranks_command.py index 4c97e80c04e5d47c6b3ff9872bce5c32d015f602..2dc44a0b018a74113b5314bff7ecc79486115fb3 100644 --- a/test/test_calibrate_percentile_ranks_command.py +++ b/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=[]): diff --git a/test/test_changing_allele_representations.py b/test/test_changing_allele_representations.py index 7c70048d0ed9ab6924cd184ac554a31a91cdae1f..38b9e12c339fd8bb2c6d40624c84bab92b4df636 100644 --- a/test/test_changing_allele_representations.py +++ b/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( diff --git a/test/test_class1_affinity_predictor.py b/test/test_class1_affinity_predictor.py index 563b6dcf3aa4830aa70b42a19a30896cec834773..8f2b4aa057bf1e42abc99752330ac45d28dded72 100644 --- a/test/test_class1_affinity_predictor.py +++ b/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. diff --git a/test/test_class1_neural_network.py b/test/test_class1_neural_network.py index e614d602b576d4c4a9ecbeec14029eea8bcc1195..4620334a38e96b917f41ec9db515ac33384711ce 100644 --- a/test/test_class1_neural_network.py +++ b/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(): diff --git a/test/test_class1_pan.py b/test/test_class1_pan.py index cdb483cf17260d93a59ba9ad940727393f9785bd..9ad87d69e1ced68490c29fca4a657ab2473da2a3 100644 --- a/test/test_class1_pan.py +++ b/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 = { diff --git a/test/test_custom_loss.py b/test/test_custom_loss.py index 4c177666f378284ed99960224cd8376a297ed387..2426f48db03242e4427b1bf7fd59a527551401aa 100644 --- a/test/test_custom_loss.py +++ b/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): diff --git a/test/test_download_models_class1.py b/test/test_download_models_class1.py index 5e4332724c01ba845e80c4f13676f3c93385cce8..ffbf8b3cf6ac172cef426a2cadd9d0efa9ecd101 100644 --- a/test/test_download_models_class1.py +++ b/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( diff --git a/test/test_multi_output.py b/test/test_multi_output.py index efbcccf0f9331239219133018e9043a548c2038f..b4254b56d7b1e7282c3127b00d15cf6593b98795 100644 --- a/test/test_multi_output.py +++ b/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(): diff --git a/test/test_network_merging.py b/test/test_network_merging.py index 8d1aca244fbdcc1572e696d704837cb76015c307..56683a52dbd8bfe63ad60b06ddaa76111d5d186f 100644 --- a/test/test_network_merging.py +++ b/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(): diff --git a/test/test_predict_command.py b/test/test_predict_command.py index 7d4d93406ae72715e6ac56e473c4178fb19f4a89..507d7c4a6c62939636ccb7315707957850a99c0a 100644 --- a/test/test_predict_command.py +++ b/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 diff --git a/test/test_released_predictors_on_hpv_dataset.py b/test/test_released_predictors_on_hpv_dataset.py index 02928f6db74a3a918be884f34e6311f9ff14e15f..3369257455157cc4047aedde6818139dee54b52f 100644 --- a/test/test_released_predictors_on_hpv_dataset.py +++ b/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): diff --git a/test/test_released_predictors_well_correlated.py b/test/test_released_predictors_well_correlated.py index 67d0e98e266e86d4779c70569f9d166a17f35d3f..82071d653e3db2c6147e73d97e8d1f146b785d84 100644 --- a/test/test_released_predictors_well_correlated.py +++ b/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( diff --git a/test/test_speed.py b/test/test_speed.py index 4f0d473e229b44160325ac7b184f53b16baa9157..eb604a5087458df6c517b7dde5db189d7ebe11e0 100644 --- a/test/test_speed.py +++ b/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 diff --git a/test/test_train_and_related_commands.py b/test/test_train_and_related_commands.py index 09ae60e569b9423fc92dc995777f23e8ffa5fde1..7b893f7be0914669115e0477284aa70fc300a88d 100644 --- a/test/test_train_and_related_commands.py +++ b/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"] = "" diff --git a/test/test_train_pan_allele_models_command.py b/test/test_train_pan_allele_models_command.py index dd69e81053420e35a4588dfa848a8ef87190ab14..51c7c3ffb5bc16ba4e92504702e06fe8e4ee8d58 100644 --- a/test/test_train_pan_allele_models_command.py +++ b/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"] = ""