From 2401d7b9a9d08176325d038c1c45e6c50713bb1e Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 6 Sep 2019 19:49:10 -0400
Subject: [PATCH] attempted fix for travis tests
---
mhcflurry/class1_neural_network.py | 1 +
test/test_class1_neural_network.py | 4 ++--
test/test_released_predictors_well_correlated.py | 2 +-
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index d75f66b7..86a0cdf5 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -1368,6 +1368,7 @@ class Class1NeuralNetwork(object):
m is the length of the vectors used to represent amino acids
"""
from keras.models import clone_model
+ import keras.backend as K
reshaped = allele_representations.reshape(
(allele_representations.shape[0], -1))
original_model = self.network()
diff --git a/test/test_class1_neural_network.py b/test/test_class1_neural_network.py
index 0566b6a6..8baaded0 100644
--- a/test/test_class1_neural_network.py
+++ b/test/test_class1_neural_network.py
@@ -90,7 +90,7 @@ def test_inequalities():
hyperparameters = dict(
peptide_amino_acid_encoding="one-hot",
activation="tanh",
- layer_sizes=[16],
+ layer_sizes=[64],
max_epochs=200,
minibatch_size=32,
random_negative_rate=0.0,
@@ -108,7 +108,7 @@ def test_inequalities():
loss="custom:mse_with_inequalities_and_multiple_outputs")
df = pandas.DataFrame()
- df["peptide"] = random_peptides(1000, length=9)
+ df["peptide"] = random_peptides(100, length=9)
# First half are binders
df["binder"] = df.index < len(df) / 2
diff --git a/test/test_released_predictors_well_correlated.py b/test/test_released_predictors_well_correlated.py
index a6034b3e..395a6e80 100644
--- a/test/test_released_predictors_well_correlated.py
+++ b/test/test_released_predictors_well_correlated.py
@@ -23,7 +23,7 @@ PREDICTORS = {
get_path("models_class1_pan", "models.with_mass_spec"))
}
-PREDICTORS["pan-allele"].optimize()
+# PREDICTORS["pan-allele"].optimize()
def test_correlation(
--
GitLab