Add teardown to tests to clear keras session

.travis.yml

@@ -44,5 +44,4 @@ script:
   # download data and models, then run tests
   - mhcflurry-downloads fetch data_curated models_class1 models_class1_pan allele_sequences
   - mhcflurry-downloads info  # just to test this command works
-  #- travis_wait 30 nosetests --with-timer -sv
-  - bash -c 'for i in $(ls test/test_*.py) ; do echo "Invoking test: $i" ; nosetests -sv $i ; done'
+  - nosetests --with-timer -sv test

mhcflurry/testing_utils.py

+
+
+def module_cleanup():
+    import keras.backend as K
+    K.clear_session()

test/test_calibrate_percentile_ranks_command.py

@@ -14,6 +14,9 @@ from mhcflurry.downloads import get_path
 
 os.environ["CUDA_VISIBLE_DEVICES"] = ""
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 
 def run_and_check(n_jobs=0, delete=True, additional_args=[]):
     source_models_dir = get_path("models_class1_pan", "models.with_mass_spec")

test/test_changing_allele_representations.py

@@ -8,6 +8,9 @@ from mhcflurry.downloads import get_path
 
 from numpy.testing import assert_equal
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 ALLELE_TO_SEQUENCE = pandas.read_csv(
     get_path(
         "allele_sequences", "allele_sequences.csv"),

test/test_class1_affinity_predictor.py

@@ -16,6 +16,10 @@ from numpy import testing
 
 from mhcflurry.downloads import get_path
 
+import mhcflurry.testing_utils
+teardown = mhcflurry.testing_utils.module_cleanup
+
+
 DOWNLOADED_PREDICTOR = Class1AffinityPredictor.load()
 
 logging.basicConfig(level=logging.DEBUG)
@@ -252,3 +256,4 @@ def test_predict_implementations_equivalent():
                 peptides=peptides,
                 centrality_measure=centrality_measure).prediction.values
             testing.assert_almost_equal(pred1, pred2, decimal=2)
+

test/test_class1_neural_network.py

@@ -13,6 +13,9 @@ 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
+
 
 def test_class1_neural_network_a0205_training_accuracy():
     # Memorize the dataset.

test/test_class1_pan.py

@@ -11,6 +11,9 @@ 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
+
 
 HYPERPARAMETERS = {
     'activation': 'tanh',

test/test_custom_loss.py

@@ -11,6 +11,9 @@ import keras.backend as K
 
 from mhcflurry.custom_loss import CUSTOM_LOSSES
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 
 def evaluate_loss(loss, y_true, y_pred):
     y_true = numpy.array(y_true)

test/test_download_models_class1.py

@@ -5,6 +5,9 @@ from numpy.testing import assert_equal
 
 from mhcflurry import Class1AffinityPredictor, Class1NeuralNetwork
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 
 DOWNLOADED_PREDICTOR = Class1AffinityPredictor.load()
 

test/test_multi_output.py

@@ -12,6 +12,9 @@ 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
+
 
 def test_multi_output():
     hyperparameters = dict(

test/test_network_merging.py

@@ -5,6 +5,9 @@ from mhcflurry import Class1AffinityPredictor, Class1NeuralNetwork
 from mhcflurry.common import random_peptides
 from mhcflurry.downloads import get_path
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 logging.getLogger('tensorflow').disabled = True
 
 PAN_ALLELE_PREDICTOR = Class1AffinityPredictor.load(

test/test_predict_command.py

@@ -6,6 +6,9 @@ from numpy.testing import assert_equal
 
 from mhcflurry import predict_command
 
+from mhcflurry.testing_utils import module_cleanup
+teardown = module_cleanup
+
 TEST_CSV = '''
 Allele,Peptide,Experiment
 HLA-A0201,SYNFEKKL,17

test/test_released_predictors_on_hpv_dataset.py

@@ -13,6 +13,9 @@ 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
+teardown = module_cleanup
+
 
 def data_path(name):
     '''

test/test_released_predictors_well_correlated.py

@@ -15,6 +15,9 @@ 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
+teardown = module_cleanup
+
 
 PREDICTORS = {
     'allele-specific': Class1AffinityPredictor.load(

test/test_speed.py

@@ -18,6 +18,9 @@ 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
+teardown = module_cleanup
+
 ALLELE_SPECIFIC_PREDICTOR = Class1AffinityPredictor.load(
     get_path("models_class1", "models"))
 

test/test_train_and_related_commands.py

@@ -14,6 +14,9 @@ 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
+
 os.environ["CUDA_VISIBLE_DEVICES"] = ""
 
 HYPERPARAMETERS = [

test/test_train_pan_allele_models_command.py

@@ -15,6 +15,9 @@ 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
+
 os.environ["CUDA_VISIBLE_DEVICES"] = ""