fix subtle python 2 issues

mhcflurry/__init__.py

@@ -12,8 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import class1_allele_specific
-from .class1_allele_specific import Class1BindingPredictor
+from .class1_allele_specific.class1_binding_predictor import (
+    Class1BindingPredictor)
 from .predict import predict
 from .package_metadata import __version__
 from . import parallelism
@@ -22,7 +22,6 @@ parallelism.configure_joblib()
 
 __all__ = [
     "Class1BindingPredictor",
-    "class1_allele_specific",
     "predict",
     "parallelism",
     "__version__",

mhcflurry/class1_allele_specific/class1_binding_predictor.py

@@ -22,6 +22,7 @@ from __future__ import (
 )
 
 import tempfile
+import os
 
 import numpy as np
 
@@ -121,9 +122,16 @@ class Class1BindingPredictor(Class1AlleleSpecificKmerIC50PredictorBase):
     def __setstate__(self, state):
         model_bytes = state.pop('model_bytes')
         self.__dict__.update(state)
-        with tempfile.NamedTemporaryFile(suffix='.hdf5', delete=True) as fd:
+        fd = tempfile.NamedTemporaryFile(suffix='.hdf5', delete=False)
+        try:
             fd.write(model_bytes)
+
+            # HDF5 has issues when the file is open multiple times, so we close
+            # it here before loading it into keras.
+            fd.close()
             self.model = keras.models.load_model(fd.name)
+        finally:
+            os.unlink(fd.name)
 
     def get_weights(self):
         """

mhcflurry/class1_allele_specific/cross_validation.py

@@ -12,8 +12,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import collections
 import logging
 

mhcflurry/class1_allele_specific/cv_and_train_command.py

@@ -36,7 +36,11 @@ the 'fork' mode causes a library we use to hang. We have to instead use
 the 'spawn' or 'forkserver' modes. See:
 https://pythonhosted.org/joblib/parallel.html#bad-interaction-of-multiprocessing-and-third-party-libraries
 '''
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import sys
 import argparse
 import json

mhcflurry/class1_allele_specific/load.py

@@ -14,7 +14,11 @@
 '''
 Load predictors
 '''
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import pickle
 from os.path import join
 

mhcflurry/class1_allele_specific/scoring.py

-from __future__ import absolute_import
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import sklearn
 import numpy
 import scipy

mhcflurry/class1_allele_specific/train.py

@@ -12,8 +12,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import collections
 import logging
 import time
@@ -277,7 +280,7 @@ def train_across_models_and_folds(
     pandas.DataFrame
     '''
     if cartesian_product_of_folds_and_models:
-        tasks_per_model = int(math.ceil(len(folds) / folds_per_task))
+        tasks_per_model = int(math.ceil(float(len(folds)) / folds_per_task))
         fold_index_groups = [[] for _ in range(tasks_per_model)]
         index_group = 0
         for index in range(len(folds)):

mhcflurry/downloads_command.py

@@ -28,7 +28,11 @@ Get the path to a download:
 Summarize available and fetched downloads:
     $ mhcflurry-downloads info
 '''
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import sys
 import argparse
 import logging

mhcflurry/hyperparameters.py

@@ -11,7 +11,11 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
+from __future__ import (
+    print_function,
+    division,
+    absolute_import,
+)
 import itertools