From 2015dfd68f41616b3f0e5f9cb9c29dd126a2e3e2 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 9 Feb 2017 12:58:21 -0500
Subject: [PATCH] fixes
---
mhcflurry/class1_allele_specific/cross_validation.py | 2 +-
mhcflurry/parallelism.py | 1 +
test/test_class1_allele_specific_cv_and_train_command.py | 1 +
test/test_cross_validation.py | 2 +-
4 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/class1_allele_specific/cross_validation.py b/mhcflurry/class1_allele_specific/cross_validation.py
index 4d3dc41a..184bae58 100644
--- a/mhcflurry/class1_allele_specific/cross_validation.py
+++ b/mhcflurry/class1_allele_specific/cross_validation.py
@@ -192,4 +192,4 @@ def cross_validation_folds(
for (result_fold, imputation_result) in zip(
result_folds, imputation_results)
]
- return result_fold
+ return result_folds
diff --git a/mhcflurry/parallelism.py b/mhcflurry/parallelism.py
index c82b40e0..faecc871 100644
--- a/mhcflurry/parallelism.py
+++ b/mhcflurry/parallelism.py
@@ -14,6 +14,7 @@ class ParallelBackend(object):
self.module = module
self.verbose = verbose
+
class KubefaceParallelBackend(ParallelBackend):
"""
ParallelBackend that uses kubeface
diff --git a/test/test_class1_allele_specific_cv_and_train_command.py b/test/test_class1_allele_specific_cv_and_train_command.py
index f6e52d87..9f0c193b 100644
--- a/test/test_class1_allele_specific_cv_and_train_command.py
+++ b/test/test_class1_allele_specific_cv_and_train_command.py
@@ -61,6 +61,7 @@ def test_small_run():
"--alleles", "HLA-A0201", "HLA-A0301",
"--verbose",
"--num-local-threads", "1",
+ "--storage-prefix", "/tmp/",
]
print("Running cv_and_train_command with args: %s " % str(args))
diff --git a/test/test_cross_validation.py b/test/test_cross_validation.py
index cf95333b..c0d4296e 100644
--- a/test/test_cross_validation.py
+++ b/test/test_cross_validation.py
@@ -77,7 +77,7 @@ def test_cross_validation_with_imputation():
n_imputations=2, n_burn_in=1, n_nearest_columns=25)
train_data = (
mhcflurry.dataset.Dataset.from_csv(
- get_path("data_kim2014" , "bdata.2009.mhci.public.1.txt"))
+ get_path("data_kim2014", "bdata.2009.mhci.public.1.txt"))
.get_alleles(["HLA-A0201", "HLA-A0202", "HLA-A0301"]))
folds = cross_validation_folds(
--
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