From 8df1eb5e0b237f2e63a8e051e00c621ffaf73b8c Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 20 Sep 2019 10:12:39 -0400
Subject: [PATCH] fix tests
---
mhcflurry/class1_ligandome_predictor.py | 2 +-
test/test_network_merging.py | 1 -
test/test_speed.py | 8 ++++----
3 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/mhcflurry/class1_ligandome_predictor.py b/mhcflurry/class1_ligandome_predictor.py
index 685f2083..2c32ad9d 100644
--- a/mhcflurry/class1_ligandome_predictor.py
+++ b/mhcflurry/class1_ligandome_predictor.py
@@ -150,7 +150,7 @@ class Class1LigandomePredictor(object):
return network
@staticmethod
- def loss(y_true, y_pred, delta=0.2, alpha=None):
+ def loss(y_true, y_pred, sample_weight=None, delta=0.2, alpha=None):
"""
Loss function for ligandome prediction.
"""
diff --git a/test/test_network_merging.py b/test/test_network_merging.py
index 31c63377..591d420f 100644
--- a/test/test_network_merging.py
+++ b/test/test_network_merging.py
@@ -10,7 +10,6 @@ from mhcflurry.downloads import get_path
from mhcflurry.testing_utils import cleanup, startup
-
PAN_ALLELE_PREDICTOR = None
diff --git a/test/test_speed.py b/test/test_speed.py
index 3f75579b..037ae61c 100644
--- a/test/test_speed.py
+++ b/test/test_speed.py
@@ -22,11 +22,11 @@ from mhcflurry.testing_utils import cleanup, startup
ALLELE_SPECIFIC_PREDICTOR = None
-PAN_ALLELE_PREDICTOR_NO_MASS_SPEC = None
+PAN_ALLELE_PREDICTOR = None
def setup():
- global ALLELE_SPECIFIC_PREDICTOR, PAN_ALLELE_PREDICTOR_NO_MASS_SPEC
+ global ALLELE_SPECIFIC_PREDICTOR, PAN_ALLELE_PREDICTOR
startup()
ALLELE_SPECIFIC_PREDICTOR = Class1AffinityPredictor.load(
get_path("models_class1", "models"))
@@ -36,7 +36,7 @@ def setup():
def teardown():
- global ALLELE_SPECIFIC_PREDICTOR, PAN_ALLELE_PREDICTOR_NO_MASS_SPEC
+ global ALLELE_SPECIFIC_PREDICTOR, PAN_ALLELE_PREDICTOR
ALLELE_SPECIFIC_PREDICTOR = None
PAN_ALLELE_PREDICTOR = None
cleanup()
@@ -97,7 +97,7 @@ def test_speed_allele_specific(profile=False, num=DEFAULT_NUM_PREDICTIONS):
def test_speed_pan_allele(profile=False, num=DEFAULT_NUM_PREDICTIONS):
- global PAN_ALLELE_PREDICTOR_NO_MASS_SPEC
+ global PAN_ALLELE_PREDICTOR
starts = collections.OrderedDict()
timings = collections.OrderedDict()
profilers = collections.OrderedDict()
--
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