Fix connectors_benchmark.py [RFC/WIP]

PyNN:
* use file mode `wb` in save_positions as we write binary data
* zipfile now only accepts `w` (no `wb`)

connectors_benchmark.py
* `3` AllToAllConnector should not need delays?
* `7` is somehow broken? Wrong save/load format?
* `8` SmallWorldConnector doesn't seem to be supported by nest/mock

Author: muffgaga

pyNN/common/populations.py

@@ -579,7 +579,7 @@ def save_positions(self, file):
         Save positions to file. The output format is ``index x y z``
         """
         if isinstance(file, basestring):
-            file = recording.files.StandardTextFile(file, mode='w')
+            file = recording.files.StandardTextFile(file, mode='wb')
         cells = self.all_cells
         result = numpy.empty((len(cells), 4))
         result[:, 0] = numpy.array([self.id_to_index(id) for id in cells])
@@ -1310,7 +1310,7 @@ def save_positions(self, file):
         Save positions to file. The output format is id x y z
         """
         if isinstance(file, basestring):
-            file = files.StandardTextFile(file, mode='w')
+            file = files.StandardTextFile(file, mode='wb')
         cells = self.all_cells
         result = numpy.empty((len(cells), 4))
         result[:, 0] = numpy.array([self.id_to_index(id) for id in cells])

pyNN/recording/files.py

@@ -29,6 +29,10 @@
     have_hdf5 = False
 from pyNN.core import iteritems
 
+try:
+    basestring
+except NameError:
+    basestring = str
 
 DEFAULT_BUFFER_SIZE = 10000
 
@@ -61,7 +65,7 @@ def savez(file, *args, **kwds):
             raise ValueError("Cannot use un-named variables and keyword %s" % key)
         namedict[key] = val
 
-    zip = zipfile.ZipFile(file, mode="wb")
+    zip = zipfile.ZipFile(file, mode="w")
 
     # Place to write temporary .npy files
     #  before storing them in the zip. We need to path this to have a working

test/benchmarks/connectors_benchmark.py

@@ -80,7 +80,7 @@ def test(cases=[1]):
             conn = FixedProbabilityConnector(0.02, safe=safe, callback=callback, allow_self_connections=autapse, rng=rng)
             fig_name = "FixedProbability_%s_np_%d.png" % (simulator_name, np)
         elif case == 3:
-            conn = AllToAllConnector(delays=delay, safe=safe, callback=callback, allow_self_connections=autapse)
+            conn = AllToAllConnector(safe=safe, callback=callback, allow_self_connections=autapse)
             fig_name = "AllToAll_%s_np_%d.png" % (simulator_name, np)
         elif case == 4:
             conn = FixedNumberPostConnector(50, safe=safe, callback=callback, allow_self_connections=autapse, rng=rng)
@@ -92,7 +92,7 @@ def test(cases=[1]):
             conn = OneToOneConnector(safe=safe, callback=callback)
             fig_name = "OneToOne_%s_np_%d.png" % (simulator_name, np)
         elif case == 7:
-            conn = FromFileConnector(files.NumpyBinaryFile('Results/connections.dat', mode='r'), safe=safe, callback=callback, distributed=True)
+            conn = FromFileConnector(files.NumpyBinaryFile('Results/connections.dat', mode='rb'), safe=safe, callback=callback, distributed=False)
             fig_name = "FromFile_%s_np_%d.png" % (simulator_name, np)
         elif case == 8:
             conn = SmallWorldConnector(degree=0.1, rewiring=0., safe=safe, callback=callback, allow_self_connections=autapse)