From eef907330c2c14829906b7c8996f2ec0a4dcb180 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 9 Sep 2019 12:19:50 -0400
Subject: [PATCH] better test cleanups
---
test/test_class1_affinity_predictor.py | 15 ++++++++----
test/test_download_models_class1.py | 14 +++++++++--
test/test_network_merging.py | 20 ++++++++++++----
...test_released_predictors_on_hpv_dataset.py | 24 +++++++++++++------
...est_released_predictors_well_correlated.py | 24 ++++++++++++-------
test/test_speed.py | 22 ++++++++++++++++-
6 files changed, 92 insertions(+), 27 deletions(-)
diff --git a/test/test_class1_affinity_predictor.py b/test/test_class1_affinity_predictor.py
index 277e78cb..563b6dcf 100644
--- a/test/test_class1_affinity_predictor.py
+++ b/test/test_class1_affinity_predictor.py
@@ -15,14 +15,21 @@ from nose.tools import eq_, assert_raises
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)
+
+def setup():
+ global DOWNLOADED_PREDICTOR
+ DOWNLOADED_PREDICTOR = Class1AffinityPredictor.load()
+ logging.basicConfig(level=logging.DEBUG)
+
+
+def teardown():
+ global DOWNLOADED_PREDICTOR
+ DOWNLOADED_PREDICTOR = None
+ mhcflurry.testing_utils.module_cleanup()
# To hunt down a weird warning we were seeing in pandas.
diff --git a/test/test_download_models_class1.py b/test/test_download_models_class1.py
index 23b25c3d..5e433272 100644
--- a/test/test_download_models_class1.py
+++ b/test/test_download_models_class1.py
@@ -6,10 +6,20 @@ 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()
+DOWNLOADED_PREDICTOR = None
+
+
+def setup():
+ global DOWNLOADED_PREDICTOR
+ DOWNLOADED_PREDICTOR = Class1AffinityPredictor.load()
+
+
+def teardown():
+ global DOWNLOADED_PREDICTOR
+ DOWNLOADED_PREDICTOR = None
+ module_cleanup()
def predict_and_check(
diff --git a/test/test_network_merging.py b/test/test_network_merging.py
index a180df49..8d1aca24 100644
--- a/test/test_network_merging.py
+++ b/test/test_network_merging.py
@@ -6,14 +6,24 @@ 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(
- get_path("models_class1_pan", "models.with_mass_spec"),
- max_models=4,
- optimization_level=0,)
+PAN_ALLELE_PREDICTOR = None
+
+
+def setup():
+ global PAN_ALLELE_PREDICTOR
+ PAN_ALLELE_PREDICTOR = Class1AffinityPredictor.load(
+ get_path("models_class1_pan", "models.with_mass_spec"),
+ max_models=4,
+ optimization_level=0,)
+
+
+def teardown():
+ global PAN_ALLELE_PREDICTOR
+ PAN_ALLELE_PREDICTOR = None
+ module_cleanup()
def test_merge():
diff --git a/test/test_released_predictors_on_hpv_dataset.py b/test/test_released_predictors_on_hpv_dataset.py
index 10f0fc23..02928f6d 100644
--- a/test/test_released_predictors_on_hpv_dataset.py
+++ b/test/test_released_predictors_on_hpv_dataset.py
@@ -14,7 +14,6 @@ from mhcflurry import Class1AffinityPredictor
from mhcflurry.downloads import get_path
from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
def data_path(name):
@@ -25,14 +24,24 @@ def data_path(name):
return os.path.join(os.path.dirname(__file__), "data", name)
-PREDICTORS = {
- 'allele-specific': Class1AffinityPredictor.load(
- get_path("models_class1", "models")),
- 'pan-allele': Class1AffinityPredictor.load(
- get_path("models_class1_pan", "models.with_mass_spec"))
+DF = pandas.read_csv(data_path("hpv_predictions.csv"))
+PREDICTORS = None
+
+
+def setup():
+ global PREDICTORS
+ PREDICTORS = {
+ 'allele-specific': Class1AffinityPredictor.load(
+ get_path("models_class1", "models")),
+ 'pan-allele': Class1AffinityPredictor.load(
+ get_path("models_class1_pan", "models.with_mass_spec"))
}
-DF = pandas.read_csv(data_path("hpv_predictions.csv"))
+
+def teardown():
+ global PREDICTORS
+ PREDICTORS = None
+ module_cleanup()
def test_on_hpv(df=DF):
@@ -63,6 +72,7 @@ def test_on_hpv(df=DF):
if __name__ == '__main__':
# If run directly from python, leave the user in a shell to explore results.
+ setup()
result = test_on_hpv()
# Leave in ipython
diff --git a/test/test_released_predictors_well_correlated.py b/test/test_released_predictors_well_correlated.py
index 6b8a6a7e..67d0e98e 100644
--- a/test/test_released_predictors_well_correlated.py
+++ b/test/test_released_predictors_well_correlated.py
@@ -16,17 +16,24 @@ from mhcflurry.downloads import get_path
from mhcflurry.common import random_peptides
from mhcflurry.testing_utils import module_cleanup
-teardown = module_cleanup
+PREDICTORS = None
-PREDICTORS = {
- 'allele-specific': Class1AffinityPredictor.load(
- get_path("models_class1", "models")),
- 'pan-allele': Class1AffinityPredictor.load(
- get_path("models_class1_pan", "models.with_mass_spec"))
-}
-# PREDICTORS["pan-allele"].optimize()
+def setup():
+ global PREDICTORS
+ PREDICTORS = {
+ 'allele-specific': Class1AffinityPredictor.load(
+ get_path("models_class1", "models")),
+ 'pan-allele': Class1AffinityPredictor.load(
+ get_path("models_class1_pan", "models.with_mass_spec"))
+ }
+
+
+def teardown():
+ global PREDICTORS
+ PREDICTORS = None
+ module_cleanup()
def test_correlation(
@@ -83,6 +90,7 @@ parser.add_argument(
if __name__ == '__main__':
# If run directly from python, leave the user in a shell to explore results.
+ setup()
args = parser.parse_args(sys.argv[1:])
result = test_correlation(alleles=args.alleles, debug=True)
diff --git a/test/test_speed.py b/test/test_speed.py
index b35327fe..4f0d473e 100644
--- a/test/test_speed.py
+++ b/test/test_speed.py
@@ -19,7 +19,6 @@ 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"))
@@ -27,6 +26,26 @@ ALLELE_SPECIFIC_PREDICTOR = Class1AffinityPredictor.load(
PAN_ALLELE_PREDICTOR = Class1AffinityPredictor.load(
get_path("models_class1_pan", "models.with_mass_spec"))
+
+PREDICTORS = None
+
+
+def setup():
+ global PREDICTORS
+ PREDICTORS = {
+ 'allele-specific': Class1AffinityPredictor.load(
+ get_path("models_class1", "models")),
+ 'pan-allele': Class1AffinityPredictor.load(
+ get_path("models_class1_pan", "models.with_mass_spec"))
+ }
+
+
+def teardown():
+ global PREDICTORS
+ PREDICTORS = None
+ module_cleanup()
+
+
DEFAULT_NUM_PREDICTIONS = 10000
@@ -137,6 +156,7 @@ if __name__ == '__main__':
# to explore results.
args = parser.parse_args(sys.argv[1:])
+ setup()
if "allele-specific" in args.predictor:
print("Running allele-specific test")
--
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