Merge pull request #455 from AurelienJaquier/withopen

use with context manager when reading/writing files

Author: AurelienJaquier

bluepyopt/deapext/algorithms.py

@@ -123,7 +123,8 @@ def eaAlphaMuPlusLambdaCheckpoint(
 
     if continue_cp:
         # A file name has been given, then load the data from the file
-        cp = pickle.load(open(cp_filename, "rb"))
+        with open(cp_filename, "rb") as f:
+            cp = pickle.load(f)
         population = cp["population"]
         parents = cp["parents"]
         start_gen = cp["generation"]
@@ -185,7 +186,8 @@ def eaAlphaMuPlusLambdaCheckpoint(
                       logbook=logbook,
                       rndstate=random.getstate(),
                       param_names=param_names)
-            pickle.dump(cp, open(cp_filename_tmp, "wb"))
+            with open(cp_filename_tmp, "wb") as f:
+                pickle.dump(cp, f)
             if os.path.isfile(cp_filename_tmp):
                 shutil.copy(cp_filename_tmp, cp_filename)
                 logger.debug('Wrote checkpoint to %s', cp_filename)

bluepyopt/deapext/optimisationsCMA.py

@@ -265,7 +265,8 @@ def run(
         if continue_cp:
 
             # A file name has been given, then load the data from the file
-            cp = pickle.load(open(cp_filename, "rb"))
+            with open(cp_filename, "rb") as f:
+                cp = pickle.load(f)
             gen = cp["generation"]
             self.hof = cp["halloffame"]
             logbook = cp["logbook"]
@@ -361,7 +362,8 @@ def run(
                     CMA_es=CMA_es,
                     param_names=param_names,
                 )
-                pickle.dump(cp, open(cp_filename_tmp, "wb"))
+                with open(cp_filename_tmp, "wb") as f:
+                    pickle.dump(cp, f)
                 if os.path.isfile(cp_filename_tmp):
                     shutil.copy(cp_filename_tmp, cp_filename)
                     logger.debug("Wrote checkpoint to %s", cp_filename)

bluepyopt/tests/test_deapext/test_algorithms.py

@@ -1,7 +1,7 @@
 """bluepyopt.optimisations tests"""
 
 import numpy
-import mock
+from unittest import mock
 
 import deap.creator
 import deap.benchmarks
@@ -75,7 +75,7 @@ def test_eaAlphaMuPlusLambdaCheckpoint_with_checkpoint():
 
     with mock.patch('pickle.dump'):
         with mock.patch('bluepyopt.deapext.algorithms.open',
-                        return_value=None):
+                        mock.mock_open()):
             population, hof, logbook, history = \
                 bluepyopt.deapext.algorithms.eaAlphaMuPlusLambdaCheckpoint(
                     population=population,
@@ -99,7 +99,7 @@ def test_eaAlphaMuPlusLambdaCheckpoint_with_checkpoint():
                                                  'rndstate': random.getstate(),
                                                  'generation': 1}):
         with mock.patch('bluepyopt.deapext.algorithms.open',
-                        return_value=None):
+                        mock.mock_open()):
             new_population, hof, logbook, history = \
                 bluepyopt.deapext.algorithms.eaAlphaMuPlusLambdaCheckpoint(
                     population=population,

bluepyopt/tests/test_ephys/test_simulators.py

@@ -27,7 +27,7 @@
 import pytest
 import numpy
 
-import mock
+from unittest import mock
 import numpy
 
 import bluepyopt.ephys as ephys

tox.ini

@@ -18,7 +18,6 @@ extras = tests
 deps =
     coverage
     flake8
-    mock
     neuron-nightly
     sh
     pytest-cov