From f99b79e88b67f85d4c33e58cf7e2c440a03c24d4 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 9 Sep 2019 13:50:40 -0400
Subject: [PATCH] rename
---
mhcflurry/class1_neural_network.py | 8 +-------
mhcflurry/testing_utils.py | 8 +++++++-
test/test_calibrate_percentile_ranks_command.py | 4 ++--
test/test_changing_allele_representations.py | 4 ++--
test/test_class1_affinity_predictor.py | 2 +-
test/test_class1_neural_network.py | 4 ++--
test/test_class1_pan.py | 4 ++--
test/test_custom_loss.py | 4 ++--
test/test_download_models_class1.py | 4 ++--
test/test_multi_output.py | 4 ++--
test/test_network_merging.py | 4 ++--
test/test_predict_command.py | 4 ++--
test/test_released_predictors_on_hpv_dataset.py | 4 ++--
test/test_released_predictors_well_correlated.py | 4 ++--
test/test_speed.py | 4 ++--
test/test_train_and_related_commands.py | 4 ++--
test/test_train_pan_allele_models_command.py | 4 ++--
17 files changed, 37 insertions(+), 37 deletions(-)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index 9f22176d..277c683b 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 f6cc079b..157a11af 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 4c97e80c..2dc44a0b 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 7c70048d..38b9e12c 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 563b6dcf..8f2b4aa0 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 e614d602..4620334a 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 cdb483cf..9ad87d69 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 4c177666..2426f48d 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 5e433272..ffbf8b3c 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 efbcccf0..b4254b56 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 8d1aca24..56683a52 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 7d4d9340..507d7c4a 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 02928f6d..33692574 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 67d0e98e..82071d65 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 4f0d473e..eb604a50 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 09ae60e5..7b893f7b 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 dd69e810..51c7c3ff 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"] = ""
--
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