ran 2to3 stage 1

examples/brunel.py

@@ -1,4 +1,5 @@
 from __future__ import division
+from __future__ import print_function
 import os.path
 from itertools import groupby
 from operator import itemgetter
@@ -157,11 +158,11 @@
                                 max_delay=ReferenceBrunel2000.max_delay,
                                 dt=args.timestep * un.ms, seed=seed) as sim:
         # Construct the network
-        print "Constructing the network in {}".format(simulator.upper())
+        print("Constructing the network in {}".format(simulator.upper()))
         networks[simulator] = pype9_network_classes[simulator](
             model, build_mode=args.build_mode)
-        print "Finished constructing the network in {}".format(
-            simulator.upper())
+        print("Finished constructing the network in {}".format(
+            simulator.upper()))
         # Record spikes and voltages
         for pop in networks[simulator].component_arrays:
             pop[:args.num_record].record('spikes')
@@ -170,7 +171,7 @@
 
         # Create the reference simulation if required
         if simulator == 'nest' and args.reference:
-            print "Constructing the reference NEST implementation"
+            print("Constructing the reference NEST implementation")
             if args.no_init_v:
                 init_v = {'Exc': 0.0, 'Inh': 0.0}
             else:
@@ -183,7 +184,7 @@
                        to_plot=pops_to_plot, timestep=args.timestep)
 
         # Run the simulation(s)
-        print "Running the simulation in {}".format(simulator.upper())
+        print("Running the simulation in {}".format(simulator.upper()))
         if args.progress_bar:
             kwargs = {'callbacks': [
                 SimulationProgressBar(args.simtime / 77, args.simtime)]}
@@ -193,7 +194,7 @@
 
 if mpi_rank == 0:
     # Plot the results
-    print "Plotting the results"
+    print("Plotting the results")
     num_subplots = len(args.simulators) + int(args.reference)
     for pop_name in pops_to_plot:
         spike_fig, spike_subplots = plt.subplots(num_subplots, 1,
@@ -288,4 +289,4 @@
                                            '{}_v'.format(pop_name)))
     if save_path is None:
         plt.show()
-    print "done"
+    print("done")

examples/izhikevich.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import nineml.units as un
 from argparse import ArgumentParser
 import ninemlcatalog
@@ -166,7 +167,7 @@ def construct_reference(input_signal, dt):
     # allow the backend to be set
     from matplotlib import pyplot as plt  # @IgnorePep8
 
-    print "Plotting the results"
+    print("Plotting the results")
     plt.figure(figsize=args.figsize)
     if args.fast_spiking:
         title = "Izhikevich Fast Spiking"
@@ -193,4 +194,4 @@ def construct_reference(input_signal, dt):
         plt.savefig(args.save_fig)
     else:
         plt.show()
-    print "done"
+    print("done")

pype9/cmd/__init__.py

@@ -1,4 +1,5 @@
-import convert
-import simulate
-import plot
-import help  # @ReservedAssignment
+from __future__ import absolute_import
+from . import convert
+from . import simulate
+from . import plot
+from . import help  # @ReservedAssignment

pype9/cmd/_utils.py

@@ -7,6 +7,7 @@
 import ninemlcatalog
 from argparse import ArgumentTypeError
 from pype9.exceptions import Pype9UsageError, Pype9UnitStrError
+from functools import reduce
 
 
 def existing_file(fname):

pype9/cmd/help.py

@@ -1,6 +1,7 @@
 """
 Prints help information associated with a PyPe9 command
 """
+from __future__ import print_function
 from argparse import ArgumentParser
 
 
@@ -35,7 +36,7 @@ def _get_description(cmd):
 
 def run(argv):
     if not argv:
-        print available_cmds_message()
+        print(available_cmds_message())
     else:
         args = argparser().parse_args(argv)
         get_parser(args.cmd).print_help()

pype9/simulate/common/units.py

@@ -21,6 +21,7 @@
 from pype9.exceptions import Pype9RuntimeError
 from pype9.utils import classproperty
 from fractions import gcd
+from functools import reduce
 numpy.seterr(all='raise')
 
 

pype9/simulate/nest/cells/code_gen/base.py

@@ -200,7 +200,7 @@ def clean_compile_dir(self, compile_dir, **kwargs):  # @UnusedVariable @IgnorePe
         try:
             if not path.exists(compile_dir):
                 os.makedirs(compile_dir)
-        except IOError, e:
+        except IOError as e:
             raise Pype9BuildError(
                 "Could not make compile directory '{}': {}"
                 .format(compile_dir, e))

pype9/utils/testing.py

@@ -3,6 +3,7 @@
 NEST
 """
 from __future__ import absolute_import, division
+from __future__ import print_function
 import os.path
 import re
 from itertools import combinations
@@ -541,8 +542,8 @@ def __init__(self, case, order, external_input=None, connections=None,
          J_ex, J_in, p_rate) = self.parameters(case, order)
 
         if override_input is not None:
-            print "changing poisson rate from {} to {}".format(p_rate,
-                                                               override_input)
+            print("changing poisson rate from {} to {}".format(p_rate,
+                                                               override_input))
             p_rate = override_input
 
         nest.SetDefaults("iaf_psc_alpha", neuron_params)
@@ -739,7 +740,7 @@ def assertEqual(self, first, second, msg=None):
             if msg is None:
                 msg = '{} and {} are not equal'.format(repr(first),
                                                        repr(second))
-            print msg
+            print(msg)
 
     def assertAlmostEqual(self, first, second, places=None, msg=None):
         if places is None:
@@ -748,37 +749,37 @@ def assertAlmostEqual(self, first, second, places=None, msg=None):
             if msg is None:
                 msg = '{} and {} are not equal'.format(repr(first),
                                                        repr(second))
-            print msg
+            print(msg)
 
     def assertLess(self, first, second, msg=None):
         if first >= second:
             if msg is None:
                 msg = '{} is not less than {}'.format(repr(first),
                                                       repr(second))
-            print msg
+            print(msg)
 
     def assertLessEqual(self, first, second, msg=None):
         if first > second:
             if msg is None:
                 msg = '{} is not less than or equal to {}'.format(
                     repr(first), repr(second))
-            print msg
+            print(msg)
 
     def assertNotEqual(self, first, second, msg=None):
         if first == second:
             if msg is None:
                 msg = '{} is equal to {}'.format(
                     repr(first), repr(second))
-            print msg
+            print(msg)
 
     def assertTrue(self, statement, msg=None):
         if not statement:
             if msg is None:
                 msg = '{} is not true'.format(repr(statement))
-            print msg
+            print(msg)
 
     def assertNotTrue(self, statement, msg=None):
         if statement:
             if msg is None:
                 msg = '{} is true'.format(repr(statement))
-            print msg
+            print(msg)

setup.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function
 import os
 import re
 import platform

test/test_cmds/test_convert.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import os.path
 import tempfile
 import shutil
@@ -42,7 +43,7 @@ def test_convert_format(self):
         in_path = os.path.join(os.path.relpath(ninemlcatalog.root),
                                  'neuron', 'Izhikevich.xml')
         out_path = os.path.join(self.tmpdir, 'Izhikevich.yml')
-        print out_path
+        print(out_path)
         args = '{} {}'.format(in_path, out_path)
         convert.run(args.split())
         # Check the output file is yaml

test/test_seeding.py

@@ -1,4 +1,5 @@
 from __future__ import division
+from __future__ import print_function
 from itertools import chain
 import ninemlcatalog
 import numpy
@@ -67,9 +68,9 @@ def test_network_seed(self):
             with Simulation(dt=0.01 * un.ms, seed=1) as sim:
                 network1 = Network(brunel_model)
                 network1.component_array('Ext').record('spike_output')
-                print "Sim 1 - prop: {}, dyn: {}, global: {}".format(
+                print("Sim 1 - prop: {}, dyn: {}, global: {}".format(
                     sim.all_properties_seeds, sim.all_dynamics_seeds,
-                    sim.global_seed)
+                    sim.global_seed))
                 sim.run(20 * un.ms)
             ext1_spikes = network1.component_array(
                 'Ext').recording('spike_output')
@@ -78,9 +79,9 @@ def test_network_seed(self):
             with Simulation(dt=0.01 * un.ms, seed=1) as sim:
                 network2 = Network(brunel_model)
                 network2.component_array('Ext').record('spike_output')
-                print "Sim 2 - prop: {}, dyn: {}, global: {}".format(
+                print("Sim 2 - prop: {}, dyn: {}, global: {}".format(
                     sim.all_properties_seeds, sim.all_dynamics_seeds,
-                    sim.global_seed)
+                    sim.global_seed))
                 sim.run(20 * un.ms)
             ext2_spikes = network2.component_array(
                 'Ext').recording('spike_output')
@@ -89,9 +90,9 @@ def test_network_seed(self):
             with Simulation(dt=0.01 * un.ms, seed=2) as sim:
                 network3 = Network(brunel_model)
                 network3.component_array('Ext').record('spike_output')
-                print "Sim 3 - prop: {}, dyn: {}, global: {}".format(
+                print("Sim 3 - prop: {}, dyn: {}, global: {}".format(
                     sim.all_properties_seeds, sim.all_dynamics_seeds,
-                    sim.global_seed)
+                    sim.global_seed))
                 sim.run(20 * un.ms)
             ext3_spikes = network3.component_array(
                 'Ext').recording('spike_output')
@@ -100,9 +101,9 @@ def test_network_seed(self):
             with Simulation(dt=0.01 * un.ms, properties_seed=1) as sim:
                 network4 = Network(brunel_model)
                 network4.component_array('Ext').record('spike_output')
-                print "Sim 4 - prop: {}, dyn: {}, global: {}".format(
+                print("Sim 4 - prop: {}, dyn: {}, global: {}".format(
                     sim.all_properties_seeds, sim.all_dynamics_seeds,
-                    sim.global_seed)
+                    sim.global_seed))
                 sim.run(20 * un.ms)
             ext4_spikes = network4.component_array(
                 'Ext').recording('spike_output')

test/test_simulations/test_cells.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function
 import sys
 import quantities as pq
 import os.path
@@ -96,7 +97,7 @@ def test_izhi(self, plot=PLOT_DEFAULT, print_comparisons=False,
         comparisons = comparer.compare()
         if print_comparisons:
             for (name1, name2), diff in comparisons.iteritems():
-                print '{} v {}: {}'.format(name1, name2, diff)
+                print('{} v {}: {}'.format(name1, name2, diff))
         if plot:
             comparer.plot()
         if 'nest' in simulators and 'neuron' in simulators:
@@ -169,7 +170,7 @@ def test_hh(self, plot=PLOT_DEFAULT, print_comparisons=False,
         comparisons = comparer.compare()
         if print_comparisons:
             for (name1, name2), diff in comparisons.iteritems():
-                print '{} v {}: {}'.format(name1, name2, diff)
+                print('{} v {}: {}'.format(name1, name2, diff))
         if plot:
             comparer.plot()
         # FIXME: Need to work out what is happening with the reference NEURON
@@ -219,7 +220,7 @@ def test_liaf(self, plot=PLOT_DEFAULT, print_comparisons=False,
         comparisons = comparer.compare()
         if print_comparisons:
             for (name1, name2), diff in comparisons.iteritems():
-                print '{} v {}: {}'.format(name1, name2, diff)
+                print('{} v {}: {}'.format(name1, name2, diff))
         if plot:
             comparer.plot()
         if 'neuron' in simulators:
@@ -344,7 +345,7 @@ def test_alpha_syn(self, plot=PLOT_DEFAULT, print_comparisons=False,
         comparisons = comparer.compare()
         if print_comparisons:
             for (name1, name2), diff in comparisons.iteritems():
-                print '{} v {}: {}'.format(name1, name2, diff)
+                print('{} v {}: {}'.format(name1, name2, diff))
         if plot:
             comparer.plot()
         if 'nest' in simulators and 'neuron' in simulators:
@@ -389,7 +390,7 @@ def test_izhiFS(self, plot=PLOT_DEFAULT, print_comparisons=False,
         comparisons = comparer.compare()
         if print_comparisons:
             for (name1, name2), diff in comparisons.iteritems():
-                print '{} v {}: {}'.format(name1, name2, diff)
+                print('{} v {}: {}'.format(name1, name2, diff))
         if plot:
             comparer.plot()
         if 'nest' in simulators and 'neuron' in simulators:
@@ -431,9 +432,9 @@ def test_poisson(self, duration=100 * un.s, rate=100 * un.Hz,
             ref_rate = pq.Quantity(UnitHandlerNEST.to_pq_quantity(rate), 'Hz')
             rate_difference = abs(ref_rate - recorded_rate)
             if print_comparisons:
-                print "Reference rate: {}".format(ref_rate)
-                print "{} recorded rate: {}".format(sim_name, recorded_rate)
-                print "{} difference: {}".format(sim_name, rate_difference)
+                print("Reference rate: {}".format(ref_rate))
+                print("{} recorded rate: {}".format(sim_name, recorded_rate))
+                print("{} difference: {}".format(sim_name, rate_difference))
             self.assertLess(
                 rate_difference, 5 * pq.Hz,
                 ("Recorded rate of {} poisson generator ({}) did not match "
@@ -491,4 +492,4 @@ def test_poisson(self, duration=100 * un.s, rate=100 * un.Hz,
     test = getattr(tester, 'test_' + args.test)
     test(plot=args.plot, print_comparisons=args.print_comparisons,
          simulators=args.simulators, build_mode=args.build_mode, **kwargs)
-    print "done"
+    print("done")

test/test_simulations/test_network.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 from __future__ import division
+from __future__ import print_function
 from itertools import groupby, izip
 from operator import itemgetter
 import itertools
@@ -557,7 +558,7 @@ def test_activity_with_neuron(self, case='AI', order=10, simtime=100.0,
                         percent_psth_stdev_error)))
         if plot:
             plt.show()
-        print "done"
+        print("done")
 
     def test_flatten(self, **kwargs):  # @UnusedVariable
         brunel_network = ninemlcatalog.load(