def test_storing_loading():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, '''v : volt
x : 1
n : integer
b : boolean''')
v = np.arange(10)*volt
x = np.arange(10, 20)
n = np.arange(20, 30)
b = np.array([True, False]).repeat(5)
G.v = v
G.x = x
G.n = n
G.b = b
S = Synapses(G, G, '''v_syn : volt
x_syn : 1
n_syn : integer
b_syn : boolean''')
S.connect(j='i')
S.v_syn = v
S.x_syn = x
S.n_syn = n
S.b_syn = b
run(0*ms)
device.build(directory=None, with_output=False)
assert_allclose(G.v[:], v)
assert_allclose(S.v_syn[:], v)
assert_allclose(G.x[:], x)
assert_allclose(S.x_syn[:], x)
assert_allclose(G.n[:], n)
assert_allclose(S.n_syn[:], n)
assert_allclose(G.b[:], b)
assert_allclose(S.b_syn[:], b)
reset_device()
def test_cpp_standalone():
set_device('cpp_standalone', build_on_run=False)
##### Define the model
tau = 1 * ms
eqs = '''
dV/dt = (-40*mV-V)/tau : volt (unless refractory)
'''
threshold = 'V>-50*mV'
reset = 'V=-60*mV'
refractory = 5 * ms
N = 1000
G = NeuronGroup(N,
eqs,
reset=reset,
threshold=threshold,
refractory=refractory,
name='gp')
G.V = '-i*mV'
M = SpikeMonitor(G)
S = Synapses(G, G, 'w : volt', on_pre='V += w')
S.connect('abs(i-j)<5 and i!=j')
S.w = 0.5 * mV
S.delay = '0*ms'
net = Network(G, M, S)
net.run(100 * ms)
device.build(directory=None, with_output=False)
# we do an approximate equality here because depending on minor details of how it was compiled, the results
# may be slightly different (if -ffast-math is on)
assert len(M.i) >= 17000 and len(M.i) <= 18000
assert len(M.t) == len(M.i)
assert M.t[0] == 0.
reset_device()
def test_time_after_run(with_output=False):
set_device('cpp_standalone', build_on_run=False)
# Check that the clock and network time after a run is correct, even if we
# have not actually run the code yet (via build)
G = NeuronGroup(10, 'dv/dt = -v/(10*ms) : 1')
net = Network(G)
assert_allclose(defaultclock.dt, 0.1*ms)
assert_allclose(defaultclock.t, 0.*ms)
assert_allclose(G.t, 0.*ms)
assert_allclose(net.t, 0.*ms)
net.run(10*ms)
assert_allclose(defaultclock.t, 10.*ms)
assert_allclose(G.t, 10.*ms)
assert_allclose(net.t, 10.*ms)
net.run(10*ms)
assert_allclose(defaultclock.t, 20.*ms)
assert_allclose(G.t, 20.*ms)
assert_allclose(net.t, 20.*ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, run=True, compile=True,
with_output=with_output)
# Everything should of course still be accessible
assert_allclose(defaultclock.t, 20.*ms)
assert_allclose(G.t, 20.*ms)
assert_allclose(net.t, 20.*ms)
reset_device()
def test_spikegenerator_standalone_change_spikes(with_output=False):
'''
Basic test for `SpikeGeneratorGroup`.
'''
set_device('cpp_standalone', build_on_run=False)
indices1 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1])
times1 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2]) * ms
SG = SpikeGeneratorGroup(5, indices1, times1)
s_mon = SpikeMonitor(SG)
net = Network(SG, s_mon)
net.run(5*ms)
indices2 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1, 3, 3, 3, 1, 2])
times2 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2, 4.5, 4.7, 4.8, 4.5, 4.7])*ms + 5*ms
SG.set_spikes(indices2, times2)
net.run(5*ms)
indices3 = np.array([4, 1, 0])
times3 = np.array([1, 3, 4])*ms + 10*ms
SG.set_spikes(indices3, times3)
net.run(5*ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True, run=True, with_output=with_output)
_compare_spikes(5, indices1, times1, s_mon, end_time=5*ms)
_compare_spikes(5, indices2, times2, s_mon, start_time=5*ms, end_time=10*ms)
_compare_spikes(5, indices3, times3, s_mon, start_time=10*ms)
reset_device()
def test_timedarray(with_output=True):
set_device('cpp_standalone', build_on_run=False)
defaultclock.dt = 0.1*ms
ta1d = TimedArray(np.arange(10)*volt, dt=1*ms)
ta2d = TimedArray(np.arange(300).reshape(3, 100).T, dt=defaultclock.dt)
G = NeuronGroup(4, '''x = ta1d(t) : volt
y = ta2d(t, i) : 1''')
mon = StateMonitor(G, ['x', 'y'], record=True)
run(11*ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True,
run=True, with_output=with_output)
for idx in xrange(4):
# x variable should have neuron independent values
assert_equal(mon[idx].x[:],
np.clip(np.arange(11).repeat(10), 0, 9)*volt)
for idx in xrange(3):
# y variable is neuron-specific
assert_equal(mon[idx].y[:],
np.clip(np.arange(110), 0, 99) + idx*100)
# the 2d array only has 3 columns, the last neuron should therefore contain
# only NaN
assert_equal(mon[3].y[:], np.nan)
reset_device()
def test_spikegenerator_standalone_change_period(with_output=False):
'''
Basic test for `SpikeGeneratorGroup`.
'''
set_device('cpp_standalone', build_on_run=False)
indices1 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1])
times1 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2]) * ms
SG = SpikeGeneratorGroup(5, indices1, times1, period=5*ms)
s_mon = SpikeMonitor(SG)
net = Network(SG, s_mon)
net.run(10*ms)
indices2 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1, 3, 3, 3, 1, 2])
times2 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2, 4.5, 4.7, 4.8, 4.5, 4.7])*ms + 10*ms
SG.set_spikes(indices2, times2)
net.run(10*ms) # period should no longer be in effect
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True, run=True, with_output=with_output)
_compare_spikes(5, np.hstack([indices1, indices1]),
np.hstack([times1, times1+5*ms]),
s_mon, end_time=10*ms)
_compare_spikes(5, indices2, times2, s_mon, start_time=10*ms)
reset_device()
def test_sorted_indices_statemonitor():
previous_device = get_device()
results = {}
n_cells = 5
n_recorded = 10
delay = np.arange(n_cells) * defaultclock.dt
for devicename in ['cpp_standalone', 'cuda_standalone']:
set_device(devicename, build_on_run=False, with_output=False)
Synapses.__instances__().clear()
reinit_devices()
P = NeuronGroup(n_cells, model='', threshold='True')
S = Synapses(P, P, model='''w : 1''', on_pre='''w += 1''')
S.connect(j='i')
S.pre.delay = delay
state_mon = StateMonitor(S, 'w', record=range(n_recorded))
run(defaultclock.dt * (n_cells + 1))
device.build(directory=None, with_output=False)
results[devicename] = state_mon.w.astype(int)
assert_allclose(results['cpp_standalone'].sum(axis=0),
results['cuda_standalone'].sum(axis=0))
assert_allclose(results['cpp_standalone'], results['cuda_standalone'])
reset_device(previous_device)
def test_time_after_run():
set_device('cpp_standalone', build_on_run=False)
# Check that the clock and network time after a run is correct, even if we
# have not actually run the code yet (via build)
G = NeuronGroup(10, 'dv/dt = -v/(10*ms) : 1')
net = Network(G)
assert_allclose(defaultclock.dt, 0.1 * ms)
assert_allclose(defaultclock.t, 0. * ms)
assert_allclose(G.t, 0. * ms)
assert_allclose(net.t, 0. * ms)
net.run(10 * ms)
assert_allclose(defaultclock.t, 10. * ms)
assert_allclose(G.t, 10. * ms)
assert_allclose(net.t, 10. * ms)
net.run(10 * ms)
assert_allclose(defaultclock.t, 20. * ms)
assert_allclose(G.t, 20. * ms)
assert_allclose(net.t, 20. * ms)
device.build(directory=None, with_output=False)
# Everything should of course still be accessible
assert_allclose(defaultclock.t, 20. * ms)
assert_allclose(G.t, 20. * ms)
assert_allclose(net.t, 20. * ms)
reset_device()
def test_storing_loading():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, '''v : volt
x : 1
n : integer
b : boolean''')
v = np.arange(10)*volt
x = np.arange(10, 20)
n = np.arange(20, 30)
b = np.array([True, False]).repeat(5)
G.v = v
G.x = x
G.n = n
G.b = b
S = Synapses(G, G, '''v_syn : volt
x_syn : 1
n_syn : integer
b_syn : boolean''')
S.connect(j='i')
S.v_syn = v
S.x_syn = x
S.n_syn = n
S.b_syn = b
run(0*ms)
device.build(directory=None, with_output=False)
assert_allclose(G.v[:], v)
assert_allclose(S.v_syn[:], v)
assert_allclose(G.x[:], x)
assert_allclose(S.x_syn[:], x)
assert_allclose(G.n[:], n)
assert_allclose(S.n_syn[:], n)
assert_allclose(G.b[:], b)
assert_allclose(S.b_syn[:], b)
reset_device()
def test_cpp_standalone():
set_device('cpp_standalone', build_on_run=False)
##### Define the model
tau = 1*ms
eqs = '''
dV/dt = (-40*mV-V)/tau : volt (unless refractory)
'''
threshold = 'V>-50*mV'
reset = 'V=-60*mV'
refractory = 5*ms
N = 1000
G = NeuronGroup(N, eqs,
reset=reset,
threshold=threshold,
refractory=refractory,
name='gp')
G.V = '-i*mV'
M = SpikeMonitor(G)
S = Synapses(G, G, 'w : volt', on_pre='V += w')
S.connect('abs(i-j)<5 and i!=j')
S.w = 0.5*mV
S.delay = '0*ms'
net = Network(G, M, S)
net.run(100*ms)
device.build(directory=None, with_output=False)
# we do an approximate equality here because depending on minor details of how it was compiled, the results
# may be slightly different (if -ffast-math is on)
assert len(M.i)>=17000 and len(M.i)<=18000
assert len(M.t) == len(M.i)
assert M.t[0] == 0.
reset_device()
def test_timedarray(with_output=True):
set_device('cpp_standalone', build_on_run=False)
defaultclock.dt = 0.1 * ms
ta1d = TimedArray(np.arange(10) * volt, dt=1 * ms)
ta2d = TimedArray(np.arange(300).reshape(3, 100).T, dt=defaultclock.dt)
G = NeuronGroup(
4, '''x = ta1d(t) : volt
y = ta2d(t, i) : 1''')
mon = StateMonitor(G, ['x', 'y'], record=True)
run(11 * ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir,
compile=True,
run=True,
with_output=with_output)
for idx in xrange(4):
# x variable should have neuron independent values
assert_equal(mon[idx].x[:],
np.clip(np.arange(11).repeat(10), 0, 9) * volt)
for idx in xrange(3):
# y variable is neuron-specific
assert_equal(mon[idx].y[:], np.clip(np.arange(110), 0, 99) + idx * 100)
# the 2d array only has 3 columns, the last neuron should therefore contain
# only NaN
assert_equal(mon[3].y[:], np.nan)
reset_device()
def test_spikegenerator_standalone_change_period(with_output=False):
'''
Basic test for `SpikeGeneratorGroup`.
'''
set_device('cpp_standalone', build_on_run=False)
indices1 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1])
times1 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2]) * ms
SG = SpikeGeneratorGroup(5, indices1, times1, period=5 * ms)
s_mon = SpikeMonitor(SG)
net = Network(SG, s_mon)
net.run(10 * ms)
indices2 = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1, 3, 3, 3, 1, 2])
times2 = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2, 4.5, 4.7, 4.8, 4.5, 4.7
]) * ms + 10 * ms
SG.set_spikes(indices2, times2)
net.run(10 * ms) # period should no longer be in effect
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir,
compile=True,
run=True,
with_output=with_output)
_compare_spikes(5,
np.hstack([indices1, indices1]),
np.hstack([times1, times1 + 5 * ms]),
s_mon,
end_time=10 * ms)
_compare_spikes(5, indices2, times2, s_mon, start_time=10 * ms)
reset_device()
def test_schedule_warning():
previous_device = get_device()
from uuid import uuid4
# TestDevice1 supports arbitrary schedules, TestDevice2 does not
class TestDevice1(Device):
# These functions are needed during the setup of the defaultclock
def get_value(self, var):
return np.array([0.0001])
def add_array(self, var):
pass
def init_with_zeros(self, var, dtype):
pass
def fill_with_array(self, var, arr):
pass
class TestDevice2(TestDevice1):
def __init__(self):
super(TestDevice2, self).__init__()
self.network_schedule = ['start', 'groups', 'synapses',
'thresholds', 'resets', 'end']
# Unique names are important for getting the warnings again for multiple
# runs of the test suite
name1 = 'testdevice_' + str(uuid4())
name2 = 'testdevice_' + str(uuid4())
all_devices[name1] = TestDevice1()
all_devices[name2] = TestDevice2()
set_device(name1)
assert schedule_propagation_offset() == 0*ms
net = Network()
assert schedule_propagation_offset(net) == 0*ms
# Any schedule should work
net.schedule = list(reversed(net.schedule))
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 0, 'did not expect a warning'
assert schedule_propagation_offset(net) == defaultclock.dt
set_device(name2)
assert schedule_propagation_offset() == defaultclock.dt
# Using the correct schedule should work
net.schedule = ['start', 'groups', 'synapses', 'thresholds', 'resets', 'end']
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 0, 'did not expect a warning'
assert schedule_propagation_offset(net) == defaultclock.dt
# Using another (e.g. the default) schedule should raise a warning
net.schedule = None
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 1 and l[0][1].endswith('schedule_conflict')
reset_device(previous_device)
def test_schedule_warning():
previous_device = get_device()
from uuid import uuid4
# TestDevice1 supports arbitrary schedules, TestDevice2 does not
class TestDevice1(Device):
# These functions are needed during the setup of the defaultclock
def get_value(self, var):
return np.array([0.0001])
def add_array(self, var):
pass
def init_with_zeros(self, var, dtype):
pass
def fill_with_array(self, var, arr):
pass
class TestDevice2(TestDevice1):
def __init__(self):
super(TestDevice2, self).__init__()
self.network_schedule = [
'start', 'groups', 'synapses', 'thresholds', 'resets', 'end'
]
# Unique names are important for getting the warnings again for multiple
# runs of the test suite
name1 = 'testdevice_' + str(uuid4())
name2 = 'testdevice_' + str(uuid4())
all_devices[name1] = TestDevice1()
all_devices[name2] = TestDevice2()
set_device(name1)
net = Network()
# Any schedule should work
net.schedule = list(reversed(net.schedule))
with catch_logs() as l:
net.run(0 * ms)
assert len(l) == 0, 'did not expect a warning'
set_device(name2)
# Using the correct schedule should work
net.schedule = [
'start', 'groups', 'synapses', 'thresholds', 'resets', 'end'
]
with catch_logs() as l:
net.run(0 * ms)
assert len(l) == 0, 'did not expect a warning'
# Using another (e.g. the default) schedule should raise a warning
net.schedule = None
with catch_logs() as l:
net.run(0 * ms)
assert len(l) == 1 and l[0][1].endswith('schedule_conflict')
reset_device(previous_device)
def test_multiple_connects():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, 'v:1')
S = Synapses(G, G, 'w:1')
S.connect(i=[0], j=[0])
S.connect(i=[1], j=[1])
run(0 * ms)
device.build(directory=None, with_output=False)
assert len(S) == 2 and len(S.w[:]) == 2
reset_device()
def test_multiple_connects():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, 'v:1')
S = Synapses(G, G, 'w:1')
S.connect(i=[0], j=[0])
S.connect(i=[1], j=[1])
run(0*ms)
device.build(directory=None, with_output=False)
assert len(S) == 2 and len(S.w[:]) == 2
reset_device()
def test_cuda_scalar_writes():
# Test that writing to a scalar variable only is done once in a cuda_standalone
# setting
set_device('cuda_standalone', build_on_run=False)
G = NeuronGroup(10, 's : 1 (shared)')
G.run_regularly('s += 1')
run(defaultclock.dt)
device.build(directory=None, with_output=False)
assert_equal(G.s[:], 1.0)
reset_device()
def test_openmp_scalar_writes():
# Test that writing to a scalar variable only is done once in an OpenMP
# setting (see github issue #551)
set_device('cpp_standalone', build_on_run=False)
prefs.devices.cpp_standalone.openmp_threads = 4
G = NeuronGroup(10, 's : 1 (shared)')
G.run_regularly('s += 1')
run(defaultclock.dt)
device.build(directory=None, with_output=False)
assert_equal(G.s[:], 1.0)
reset_device()
def test_openmp_scalar_writes():
# Test that writing to a scalar variable only is done once in an OpenMP
# setting (see github issue #551)
set_device('cpp_standalone', build_on_run=False)
prefs.devices.cpp_standalone.openmp_threads = 4
G = NeuronGroup(10, 's : 1 (shared)')
G.run_regularly('s += 1')
run(defaultclock.dt)
device.build(directory=None, with_output=False)
assert_equal(G.s[:], 1.0)
reset_device()
def test_multiple_connects(with_output=False):
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, 'v:1')
S = Synapses(G, G, 'w:1')
S.connect(i=[0], j=[0])
S.connect(i=[1], j=[1])
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
run(0 * ms)
device.build(directory=tempdir, compile=True, run=True, with_output=True)
assert len(S) == 2 and len(S.w[:]) == 2
reset_device()
def test_multiple_connects(with_output=False):
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, 'v:1')
S = Synapses(G, G, 'w:1')
S.connect(i=[0], j=[0])
S.connect(i=[1], j=[1])
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
run(0*ms)
device.build(directory=tempdir, compile=True, run=True,
with_output=True)
assert len(S) == 2 and len(S.w[:]) == 2
reset_device()
def test_duplicate_names_across_nets(with_output=True):
set_device('cpp_standalone', build_on_run=False)
# In standalone mode, names have to be globally unique, not just unique
# per network
obj1 = BrianObject(name='name1')
obj2 = BrianObject(name='name2')
obj3 = BrianObject(name='name3')
obj4 = BrianObject(name='name1')
net1 = Network(obj1, obj2)
net2 = Network(obj3, obj4)
net1.run(0*ms)
net2.run(0*ms)
assert_raises(ValueError, lambda: device.build())
reset_device()
def test_state_monitor_record_single_timestep_cpp_standalone():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(1, 'dv/dt = -v/(5*ms) : 1')
G.v = 1
mon = StateMonitor(G, 'v', record=True)
# Recording before a run should not work
assert_raises(TypeError, lambda: mon.record_single_timestep())
run(0.5 * ms)
mon.record_single_timestep()
tempdir = tempfile.mkdtemp()
device.build(directory=tempdir, compile=True, run=True, with_output=False)
assert_allclose(mon.t[-1], 0.5 * ms)
assert len(mon.t) == 6
assert mon[0].v[-1] == G.v
reset_device()
def test_duplicate_names_across_nets():
set_device('cpp_standalone', build_on_run=False)
# In standalone mode, names have to be globally unique, not just unique
# per network
obj1 = BrianObject(name='name1')
obj2 = BrianObject(name='name2')
obj3 = BrianObject(name='name3')
obj4 = BrianObject(name='name1')
net1 = Network(obj1, obj2)
net2 = Network(obj3, obj4)
net1.run(0*ms)
net2.run(0*ms)
assert_raises(ValueError, lambda: device.build())
reset_device()
def test_state_monitor_record_single_timestep_cpp_standalone():
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(1, 'dv/dt = -v/(5*ms) : 1')
G.v = 1
mon = StateMonitor(G, 'v', record=True)
# Recording before a run should not work
assert_raises(TypeError, lambda: mon.record_single_timestep())
run(0.5*ms)
mon.record_single_timestep()
tempdir = tempfile.mkdtemp()
device.build(directory=tempdir, compile=True, run=True,
with_output=False)
assert_allclose(mon.t[-1], 0.5*ms)
assert len(mon.t) == 6
assert mon[0].v[-1] == G.v
reset_device()
def test_dt_changes_between_runs_standalone(with_output=False):
set_device('cpp_standalone', build_on_run=False)
defaultclock.dt = 0.1 * ms
G = NeuronGroup(1, 'v:1')
mon = StateMonitor(G, 'v', record=True)
run(.5 * ms)
defaultclock.dt = .5 * ms
run(.5 * ms)
defaultclock.dt = 0.1 * ms
run(.5 * ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True, run=True, with_output=True)
assert len(mon.t[:]) == 5 + 1 + 5
assert_allclose(
mon.t[:], [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 1., 1.1, 1.2, 1.3, 1.4] * ms)
reset_device()
def test_dt_changes_between_runs_standalone(with_output=False):
set_device('cpp_standalone', build_on_run=False)
defaultclock.dt = 0.1*ms
G = NeuronGroup(1, 'v:1')
mon = StateMonitor(G, 'v', record=True)
run(.5*ms)
defaultclock.dt = .5*ms
run(.5*ms)
defaultclock.dt = 0.1*ms
run(.5*ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True, run=True,
with_output=True)
assert len(mon.t[:]) == 5 + 1 + 5
assert_allclose(mon.t[:],
[0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 1., 1.1, 1.2, 1.3, 1.4]*ms)
reset_device()
def test_spikegenerator_standalone(with_output=False):
'''
Basic test for `SpikeGeneratorGroup` in standalone.
'''
set_device('cpp_standalone', build_on_run=False)
indices = np.array([3, 2, 1, 1, 2, 3, 3, 2, 1])
times = np.array([1, 4, 4, 3, 2, 4, 2, 3, 2]) * ms
SG = SpikeGeneratorGroup(5, indices, times)
s_mon = SpikeMonitor(SG)
net = Network(SG, s_mon)
net.run(5*ms)
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True, run=True, with_output=with_output)
_compare_spikes(5, indices, times, s_mon)
reset_device()
def example_run(debug=False, **build_options):
'''
Run a simple example simulation that test whether the Brian2/Brian2GeNN/GeNN
pipeline is working correctly.
Parameters
----------
debug : bool
Whether to display debug information (e.g. compilation output) during
the run. Defaults to ``False``.
build_options : dict
Additional options that will be forwarded to the ``set_device`` call,
e.g. ``use_GPU=False``.
'''
from brian2.devices.device import set_device, reset_device
from brian2 import ms, NeuronGroup, run
from brian2.utils.logger import std_silent
import numpy as np
from numpy.testing import assert_allclose
from tempfile import mkdtemp
import shutil
with std_silent(debug):
test_dir = mkdtemp(prefix='brian2genn_test')
set_device('genn', directory=test_dir, debug=debug, **build_options)
N = 100
tau = 10 * ms
eqs = '''
dV/dt = -V/tau: 1
'''
G = NeuronGroup(N,
eqs,
threshold='V>1',
reset='V=0',
refractory=5 * ms,
method='linear')
G.V = 'i/100.'
run(1 * ms)
assert_allclose(G.V, np.arange(100) / 100. * np.exp(-1 * ms / tau))
shutil.rmtree(test_dir, ignore_errors=True)
reset_device()
print('Example run was successful.')
def test_set_reset_device_implicit():
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
assert get_device() is test_device2
assert get_device()._options['my_opt'] == 2
assert get_device().build_on_run
reset_device()
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
reset_device()
assert get_device() is runtime_device
reset_device() # If there is no previous device, will reset to runtime device
assert get_device() is runtime_device
del all_devices['test1']
del all_devices['test2']
def test_set_reset_device_implicit():
import brian2.devices.device as device_module
old_prev_devices = list(device_module.previous_devices)
device_module.previous_devices = []
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
assert get_device() is test_device2
assert get_device()._options['my_opt'] == 2
assert get_device().build_on_run
reset_device()
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
reset_device()
assert get_device() is runtime_device
reset_device(
) # If there is no previous device, will reset to runtime device
assert get_device() is runtime_device
del all_devices['test1']
del all_devices['test2']
device_module.previous_devices = old_prev_devices
def test_set_reset_device_implicit():
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
assert get_device() is test_device2
assert get_device()._options['my_opt'] == 2
assert get_device().build_on_run
reset_device()
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
reset_device()
assert get_device() is runtime_device
reset_device() # If there is no previous device, will reset to runtime device
assert get_device() is runtime_device
del all_devices['test1']
del all_devices['test2']
def test_set_reset_device_implicit():
import brian2.devices.device as device_module
old_prev_devices = list(device_module.previous_devices)
device_module.previous_devices = []
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
assert get_device() is test_device2
assert get_device()._options['my_opt'] == 2
assert get_device().build_on_run
reset_device()
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
reset_device()
assert get_device() is runtime_device
reset_device() # If there is no previous device, will reset to runtime device
assert get_device() is runtime_device
del all_devices['test1']
del all_devices['test2']
device_module.previous_devices = old_prev_devices
def test_set_reset_device_explicit():
original_device = get_device()
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
test_device3 = ATestDevice()
all_devices['test3'] = test_device3
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
set_device('test3', build_on_run=False, my_opt=3)
reset_device('test1') # Directly jump back to the first device
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
del all_devices['test1']
del all_devices['test2']
del all_devices['test3']
reset_device(original_device)
def test_set_reset_device_explicit():
original_device = get_device()
test_device1 = ATestDevice()
all_devices['test1'] = test_device1
test_device2 = ATestDevice()
all_devices['test2'] = test_device2
test_device3 = ATestDevice()
all_devices['test3'] = test_device3
set_device('test1', build_on_run=False, my_opt=1)
set_device('test2', build_on_run=True, my_opt=2)
set_device('test3', build_on_run=False, my_opt=3)
reset_device('test1') # Directly jump back to the first device
assert get_device() is test_device1
assert get_device()._options['my_opt'] == 1
assert not get_device().build_on_run
del all_devices['test1']
del all_devices['test2']
del all_devices['test3']
reset_device(original_device)
def generate_results(num_repeats):
results = {}
for name in ['CUBA', 'COBA']:
for target in ['numpy', 'cython', 'weave']:
for dtype in [float32, float64]:
prefs.codegen.target = target
prefs.core.default_float_dtype = dtype
times = [run_benchmark(name) for repeat in range(num_repeats)]
results[name, target, dtype.__name__] = amin(times)
for name in ['CUBA', 'COBA']:
for dtype in [float32, float64]:
times = []
for _ in range(num_repeats):
reset_device()
reinit_devices()
set_device('cpp_standalone', directory=None, with_output=False)
prefs.core.default_float_dtype = dtype
times.append(run_benchmark(name))
results[name, 'cpp_standalone', dtype.__name__] = amin(times)
return results
def example_run(debug=False, **build_options):
'''
Run a simple example simulation that test whether the Brian2/Brian2GeNN/GeNN
pipeline is working correctly.
Parameters
----------
debug : bool
Whether to display debug information (e.g. compilation output) during
the run. Defaults to ``False``.
build_options : dict
Additional options that will be forwarded to the ``set_device`` call,
e.g. ``use_GPU=False``.
'''
from brian2.devices.device import set_device, reset_device
from brian2 import ms, NeuronGroup, run
from brian2.utils.logger import std_silent
import numpy as np
from numpy.testing import assert_allclose
from tempfile import mkdtemp
import shutil
with std_silent(debug):
test_dir = mkdtemp(prefix='brian2genn_test')
set_device('genn', directory=test_dir, debug=debug, **build_options)
N = 100
tau = 10*ms
eqs = '''
dV/dt = -V/tau: 1
'''
G = NeuronGroup(N, eqs, threshold='V>1', reset='V=0', refractory=5 * ms,
method='linear')
G.V = 'i/100.'
run(1*ms)
assert_allclose(G.V, np.arange(100)/100.*np.exp(-1*ms/tau))
shutil.rmtree(test_dir, ignore_errors=True)
reset_device()
print('Example run was successful.')
# backup prefs such that reinit_device in the pytest test teardown resets
# the preferences to what was set above (in restore_initial_state())
# TODO after change to pytest, might just use that pytest prefs plugin?
prefs._backup()
if args.only is None or args.only == 'single-run':
print ("Running standalone-compatible standard tests "
"(single run statement)\n")
sys.stdout.flush()
pref_plugin.device_options = {'directory': None, 'with_output': with_output}
argv = make_argv(tests, markers='standalone_compatible and not multiple_runs')
exit_code = pytest.main(argv + additional_args, plugins=[pref_plugin])
pref_success = pref_success and exit_code in [0, 5]
clear_caches()
reset_device()
if args.only is None or args.only == 'multi-run':
print ("Running standalone-compatible standard tests "
"(multiple run statements)\n")
sys.stdout.flush()
pref_plugin.device_options = {'directory': None, 'with_output': with_output,
'build_on_run': False}
argv = make_argv(tests, markers='standalone_compatible and multiple_runs')
exit_code = pytest.main(argv + additional_args, plugins=[pref_plugin])
pref_success = pref_success and exit_code in [0, 5]
clear_caches()
reset_device()
if args.only is None or args.only == 'standalone-only':
def test_openmp_consistency(with_output=False):
previous_device = get_device()
n_cells = 100
n_recorded = 10
numpy.random.seed(42)
taum = 20 * ms
taus = 5 * ms
Vt = -50 * mV
Vr = -60 * mV
El = -49 * mV
fac = (60 * 0.27 / 10)
gmax = 20*fac
dApre = .01
taupre = 20 * ms
taupost = taupre
dApost = -dApre * taupre / taupost * 1.05
dApost *= 0.1*gmax
dApre *= 0.1*gmax
connectivity = numpy.random.randn(n_cells, n_cells)
sources = numpy.random.random_integers(0, n_cells-1, 10*n_cells)
# Only use one spike per time step (to rule out that a single source neuron
# has more than one spike in a time step)
times = numpy.random.choice(numpy.arange(10*n_cells), 10*n_cells,
replace=False)*ms
v_init = Vr + numpy.random.rand(n_cells) * (Vt - Vr)
eqs = Equations('''
dv/dt = (g-(v-El))/taum : volt
dg/dt = -g/taus : volt
''')
results = {}
for (n_threads, devicename) in [(0, 'runtime'),
(0, 'cpp_standalone'),
(1, 'cpp_standalone'),
(2, 'cpp_standalone'),
(3, 'cpp_standalone'),
(4, 'cpp_standalone')]:
set_device(devicename, build_on_run=False, with_output=False)
Synapses.__instances__().clear()
if devicename=='cpp_standalone':
reinit_devices()
prefs.devices.cpp_standalone.openmp_threads = n_threads
P = NeuronGroup(n_cells, model=eqs, threshold='v>Vt', reset='v=Vr', refractory=5 * ms)
Q = SpikeGeneratorGroup(n_cells, sources, times)
P.v = v_init
P.g = 0 * mV
S = Synapses(P, P,
model = '''dApre/dt=-Apre/taupre : 1 (event-driven)
dApost/dt=-Apost/taupost : 1 (event-driven)
w : 1''',
pre = '''g += w*mV
Apre += dApre
w = w + Apost''',
post = '''Apost += dApost
w = w + Apre''')
S.connect()
S.w = fac*connectivity.flatten()
T = Synapses(Q, P, model = "w : 1", on_pre="g += w*mV")
T.connect(j='i')
T.w = 10*fac
spike_mon = SpikeMonitor(P)
rate_mon = PopulationRateMonitor(P)
state_mon = StateMonitor(S, 'w', record=range(n_recorded), dt=0.1*second)
v_mon = StateMonitor(P, 'v', record=range(n_recorded))
run(0.2 * second, report='text')
if devicename=='cpp_standalone':
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, compile=True,
run=True, with_output=with_output)
results[n_threads, devicename] = {}
results[n_threads, devicename]['w'] = state_mon.w
results[n_threads, devicename]['v'] = v_mon.v
results[n_threads, devicename]['s'] = spike_mon.num_spikes
results[n_threads, devicename]['r'] = rate_mon.rate[:]
for key1, key2 in [((0, 'runtime'), (0, 'cpp_standalone')),
((1, 'cpp_standalone'), (0, 'cpp_standalone')),
((2, 'cpp_standalone'), (0, 'cpp_standalone')),
((3, 'cpp_standalone'), (0, 'cpp_standalone')),
((4, 'cpp_standalone'), (0, 'cpp_standalone'))
]:
assert_allclose(results[key1]['w'], results[key2]['w'])
assert_allclose(results[key1]['v'], results[key2]['v'])
assert_allclose(results[key1]['r'], results[key2]['r'])
assert_allclose(results[key1]['s'], results[key2]['s'])
reset_device(previous_device)
def test_array_cache(with_output=False):
# Check that variables are only accessible from Python when they should be
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10, '''dv/dt = -v / (10*ms) : 1
w : 1
x : 1
y : 1
z : 1 (shared)''',
threshold='v>1')
S = Synapses(G, G, 'weight: 1', on_pre='w += weight')
S.connect(p=0.2)
S.weight = 7
# All neurongroup values should be known
assert_allclose(G.v, 0)
assert_allclose(G.w, 0)
assert_allclose(G.x, 0)
assert_allclose(G.y, 0)
assert_allclose(G.z, 0)
assert_allclose(G.i, np.arange(10))
# But the synaptic variable is not -- we don't know the number of synapses
assert_raises(NotImplementedError, lambda: S.weight[:])
# Setting variables with explicit values should not change anything
G.v = np.arange(10)+1
G.w = 2
G.y = 5
G.z = 7
assert_allclose(G.v, np.arange(10)+1)
assert_allclose(G.w, 2)
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
# But setting with code should invalidate them
G.x = 'i*2'
assert_raises(NotImplementedError, lambda: G.x[:])
# Make sure that the array cache does not allow to use incorrectly sized
# values to pass
assert_raises(ValueError, lambda: setattr(G, 'w', [0, 2]))
assert_raises(ValueError, lambda: G.w.__setitem__(slice(0, 4), [0, 2]))
run(10*ms)
# v is now no longer known without running the network
assert_raises(NotImplementedError, lambda: G.v[:])
# Neither is w, it is updated in the synapse
assert_raises(NotImplementedError, lambda: G.w[:])
# However, no code touches y or z
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
# i is read-only anyway
assert_allclose(G.i, np.arange(10))
# After actually running the network, everything should be accessible
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir, run=True, compile=True,
with_output=with_output)
assert all(G.v > 0)
assert all(G.w > 0)
assert_allclose(G.x, np.arange(10)*2)
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
assert_allclose(G.i, np.arange(10))
assert_allclose(S.weight, 7)
reset_device()
def test_openmp_consistency():
previous_device = get_device()
n_cells = 100
n_recorded = 10
numpy.random.seed(42)
taum = 20 * ms
taus = 5 * ms
Vt = -50 * mV
Vr = -60 * mV
El = -49 * mV
fac = (60 * 0.27 / 10)
gmax = 20 * fac
dApre = .01
taupre = 20 * ms
taupost = taupre
dApost = -dApre * taupre / taupost * 1.05
dApost *= 0.1 * gmax
dApre *= 0.1 * gmax
connectivity = numpy.random.randn(n_cells, n_cells)
sources = numpy.random.randint(0, n_cells - 1, 10 * n_cells)
# Only use one spike per time step (to rule out that a single source neuron
# has more than one spike in a time step)
times = numpy.random.choice(
numpy.arange(10 * n_cells), 10 * n_cells, replace=False) * ms
v_init = Vr + numpy.random.rand(n_cells) * (Vt - Vr)
eqs = Equations('''
dv/dt = (g-(v-El))/taum : volt
dg/dt = -g/taus : volt
''')
results = {}
for (n_threads,
devicename) in [(0, 'runtime'), (0, 'cpp_standalone'),
(1, 'cpp_standalone'), (2, 'cpp_standalone'),
(3, 'cpp_standalone'), (4, 'cpp_standalone')]:
set_device(devicename, build_on_run=False, with_output=False)
Synapses.__instances__().clear()
if devicename == 'cpp_standalone':
reinit_and_delete()
prefs.devices.cpp_standalone.openmp_threads = n_threads
P = NeuronGroup(n_cells,
model=eqs,
threshold='v>Vt',
reset='v=Vr',
refractory=5 * ms)
Q = SpikeGeneratorGroup(n_cells, sources, times)
P.v = v_init
P.g = 0 * mV
S = Synapses(P,
P,
model='''dApre/dt=-Apre/taupre : 1 (event-driven)
dApost/dt=-Apost/taupost : 1 (event-driven)
w : 1''',
pre='''g += w*mV
Apre += dApre
w = w + Apost''',
post='''Apost += dApost
w = w + Apre''')
S.connect()
S.w = fac * connectivity.flatten()
T = Synapses(Q, P, model="w : 1", on_pre="g += w*mV")
T.connect(j='i')
T.w = 10 * fac
spike_mon = SpikeMonitor(P)
rate_mon = PopulationRateMonitor(P)
state_mon = StateMonitor(S,
'w',
record=np.arange(n_recorded),
dt=0.1 * second)
v_mon = StateMonitor(P, 'v', record=np.arange(n_recorded))
run(0.2 * second, report='text')
if devicename == 'cpp_standalone':
device.build(directory=None, with_output=False)
results[n_threads, devicename] = {}
results[n_threads, devicename]['w'] = state_mon.w
results[n_threads, devicename]['v'] = v_mon.v
results[n_threads, devicename]['s'] = spike_mon.num_spikes
results[n_threads, devicename]['r'] = rate_mon.rate[:]
for key1, key2 in [((0, 'runtime'), (0, 'cpp_standalone')),
((1, 'cpp_standalone'), (0, 'cpp_standalone')),
((2, 'cpp_standalone'), (0, 'cpp_standalone')),
((3, 'cpp_standalone'), (0, 'cpp_standalone')),
((4, 'cpp_standalone'), (0, 'cpp_standalone'))]:
assert_allclose(results[key1]['w'], results[key2]['w'])
assert_allclose(results[key1]['v'], results[key2]['v'])
assert_allclose(results[key1]['r'], results[key2]['r'])
assert_allclose(results[key1]['s'], results[key2]['s'])
reset_device(previous_device)
def run(codegen_targets=None, long_tests=False, test_codegen_independent=True,
test_standalone=None, test_openmp=False,
test_in_parallel=['codegen_independent', 'numpy', 'cython', 'cpp_standalone'],
reset_preferences=True, fail_for_not_implemented=True):
'''
Run brian's test suite. Needs an installation of the nose testing tool.
For testing, the preferences will be reset to the default preferences.
After testing, the user preferences will be restored.
Parameters
----------
codegen_targets : list of str or str
A list of codegeneration targets or a single target, e.g.
``['numpy', 'weave']`` to test. The whole test suite will be repeatedly
run with `codegen.target` set to the respective value. If not
specified, all available code generation targets will be tested.
long_tests : bool, optional
Whether to run tests that take a long time. Defaults to ``False``.
test_codegen_independent : bool, optional
Whether to run tests that are independent of code generation. Defaults
to ``True``.
test_standalone : str, optional
Whether to run tests for a standalone mode. Should be the name of a
standalone mode (e.g. ``'cpp_standalone'``) and expects that a device
of that name and an accordingly named "simple" device (e.g.
``'cpp_standalone_simple'`` exists that can be used for testing (see
`CPPStandaloneSimpleDevice` for details. Defaults to ``None``, meaning
that no standalone device is tested.
test_openmp : bool, optional
Whether to test standalone test with multiple threads and OpenMP. Will
be ignored if ``cpp_standalone`` is not tested. Defaults to ``False``.
reset_preferences : bool, optional
Whether to reset all preferences to the default preferences before
running the test suite. Defaults to ``True`` to get test results
independent of the user's preference settings but can be switched off
when the preferences are actually necessary to pass the tests (e.g. for
device-specific settings).
fail_for_not_implemented : bool, optional
Whether to fail for tests raising a `NotImplementedError`. Defaults to
``True``, but can be switched off for devices known to not implement
all of Brian's features.
'''
if nose is None:
raise ImportError('Running the test suite requires the "nose" package.')
if os.name == 'nt':
test_in_parallel = []
multiprocess_arguments = ['--processes=-1',
'--process-timeout=3600', # we don't want them to time out
'--process-restartworker']
if codegen_targets is None:
codegen_targets = ['numpy']
try:
import scipy.weave
codegen_targets.append('weave')
except ImportError:
try:
import weave
codegen_targets.append('weave')
except ImportError:
pass
try:
import Cython
codegen_targets.append('cython')
except ImportError:
pass
elif isinstance(codegen_targets, basestring): # allow to give a single target
codegen_targets = [codegen_targets]
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
# We write to stderr since nose does all of its output on stderr as well
sys.stderr.write('Running tests in "%s" ' % dirname)
if codegen_targets:
sys.stderr.write('for targets %s' % (', '.join(codegen_targets)))
ex_in = 'including' if long_tests else 'excluding'
sys.stderr.write(' (%s long tests)\n' % ex_in)
all_targets = set(codegen_targets)
if test_standalone:
if not isinstance(test_standalone, basestring):
raise ValueError('test_standalone argument has to be the name of a '
'standalone device (e.g. "cpp_standalone")')
if test_standalone not in all_devices:
raise ValueError('test_standalone argument "%s" is not a known '
'device. Known devices are: '
'%s' % (test_standalone,
', '.join(repr(d) for d in all_devices)))
sys.stderr.write('Testing standalone \n')
all_targets.add(test_standalone)
if test_codegen_independent:
sys.stderr.write('Testing codegen-independent code \n')
all_targets.add('codegen_independent')
parallel_tests = all_targets.intersection(set(test_in_parallel))
if parallel_tests:
sys.stderr.write('Testing with multiple processes for %s\n' % ', '.join(parallel_tests))
if reset_preferences:
sys.stderr.write('Resetting to default preferences\n')
sys.stderr.write('\n')
if reset_preferences:
# Store the currently set preferences and reset to default preferences
stored_prefs = prefs.as_file
prefs.read_preference_file(StringIO(prefs.defaults_as_file))
# Suppress INFO log messages during testing
from brian2.utils.logger import BrianLogger, LOG_LEVELS
log_level = BrianLogger.console_handler.level
BrianLogger.console_handler.setLevel(LOG_LEVELS['WARNING'])
# Switch off code optimization to get faster compilation times
prefs['codegen.cpp.extra_compile_args_gcc'].extend(['-w', '-O0'])
prefs['codegen.cpp.extra_compile_args_msvc'].extend(['/Od'])
if fail_for_not_implemented:
not_implemented_plugin = NotImplementedPlugin
else:
not_implemented_plugin = NotImplementedNoFailurePlugin
# This hack is needed to get the NotImplementedPlugin working for multiprocessing
import nose.plugins.multiprocess as multiprocess
multiprocess._instantiate_plugins = [not_implemented_plugin]
plugins = [not_implemented_plugin()]
try:
success = []
if test_codegen_independent:
sys.stderr.write('Running tests that do not use code generation\n')
# Some doctests do actually use code generation, use numpy for that
prefs.codegen.target = 'numpy'
prefs._backup()
argv = ['nosetests', dirname,
'-c=', # no config file loading
'-I', '^hears\.py$',
'-I', '^\.',
'-I', '^_',
'--with-doctest',
"-a", "codegen-independent",
'--nologcapture',
'--exe']
if 'codegen_independent' in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
for target in codegen_targets:
sys.stderr.write('Running tests for target %s:\n' % target)
prefs.codegen.target = target
# Also set the target for string-expressions -- otherwise we'd only
# ever test numpy for those
prefs.codegen.string_expression_target = target
prefs._backup()
exclude_str = "!standalone-only,!codegen-independent"
if not long_tests:
exclude_str += ',!long'
# explicitly ignore the brian2.hears file for testing, otherwise the
# doctest search will import it, failing on Python 3
argv = ['nosetests', dirname,
'-c=', # no config file loading
'-I', '^hears\.py$',
'-I', '^\.',
'-I', '^_',
# Do not run standalone or
# codegen-independent tests
"-a", exclude_str,
'--nologcapture',
'--exe']
if target in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
if test_standalone:
from brian2.devices.device import get_device, set_device
set_device(test_standalone, directory=None, # use temp directory
with_output=False)
sys.stderr.write('Testing standalone device "%s"\n' % test_standalone)
sys.stderr.write('Running standalone-compatible standard tests\n')
exclude_str = ',!long' if not long_tests else ''
argv = ['nosetests', dirname,
'-c=', # no config file loading
'-I', '^hears\.py$',
'-I', '^\.',
'-I', '^_',
# Only run standalone tests
'-a', 'standalone-compatible'+exclude_str,
'--nologcapture',
'--exe']
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
if test_openmp and test_standalone == 'cpp_standalone':
# Run all the standalone compatible tests again with 4 threads
prefs.devices.cpp_standalone.openmp_threads = 4
prefs._backup()
sys.stderr.write('Running standalone-compatible standard tests with OpenMP\n')
exclude_str = ',!long' if not long_tests else ''
argv = ['nosetests', dirname,
'-c=', # no config file loading
'-I', '^hears\.py$',
'-I', '^\.',
'-I', '^_',
# Only run standalone tests
'-a', 'standalone-compatible'+exclude_str,
'--nologcapture',
'--exe']
success.append(nose.run(argv=argv,
addplugins=plugins))
prefs.devices.cpp_standalone.openmp_threads = 0
prefs._backup()
reset_device()
sys.stderr.write('Running standalone-specific tests\n')
exclude_openmp = ',!openmp' if not test_openmp else ''
argv = ['nosetests', dirname,
'-c=', # no config file loading
'-I', '^hears\.py$',
'-I', '^\.',
'-I', '^_',
# Only run standalone tests
'-a', test_standalone+exclude_openmp,
'--nologcapture',
'--exe']
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
all_success = all(success)
if not all_success:
sys.stderr.write(('ERROR: %d/%d test suite(s) did not complete '
'successfully (see above).\n') % (len(success) - sum(success),
len(success)))
else:
sys.stderr.write(('OK: %d/%d test suite(s) did complete '
'successfully.\n') % (len(success), len(success)))
return all_success
finally:
BrianLogger.console_handler.setLevel(log_level)
if reset_preferences:
# Restore the user preferences
prefs.read_preference_file(StringIO(stored_prefs))
prefs._backup()
def run(codegen_targets=None, long_tests=False, test_codegen_independent=True,
test_standalone=None, test_openmp=False,
test_in_parallel=['codegen_independent', 'numpy', 'cython', 'cpp_standalone'],
reset_preferences=True, fail_for_not_implemented=True,
build_options=None, extra_test_dirs=None, float_dtype=None):
'''
Run brian's test suite. Needs an installation of the nose testing tool.
For testing, the preferences will be reset to the default preferences.
After testing, the user preferences will be restored.
Parameters
----------
codegen_targets : list of str or str
A list of codegeneration targets or a single target, e.g.
``['numpy', 'weave']`` to test. The whole test suite will be repeatedly
run with `codegen.target` set to the respective value. If not
specified, all available code generation targets will be tested.
long_tests : bool, optional
Whether to run tests that take a long time. Defaults to ``False``.
test_codegen_independent : bool, optional
Whether to run tests that are independent of code generation. Defaults
to ``True``.
test_standalone : str, optional
Whether to run tests for a standalone mode. Should be the name of a
standalone mode (e.g. ``'cpp_standalone'``) and expects that a device
of that name and an accordingly named "simple" device (e.g.
``'cpp_standalone_simple'`` exists that can be used for testing (see
`CPPStandaloneSimpleDevice` for details. Defaults to ``None``, meaning
that no standalone device is tested.
test_openmp : bool, optional
Whether to test standalone test with multiple threads and OpenMP. Will
be ignored if ``cpp_standalone`` is not tested. Defaults to ``False``.
reset_preferences : bool, optional
Whether to reset all preferences to the default preferences before
running the test suite. Defaults to ``True`` to get test results
independent of the user's preference settings but can be switched off
when the preferences are actually necessary to pass the tests (e.g. for
device-specific settings).
fail_for_not_implemented : bool, optional
Whether to fail for tests raising a `NotImplementedError`. Defaults to
``True``, but can be switched off for devices known to not implement
all of Brian's features.
build_options : dict, optional
Non-default build options that will be passed as arguments to the
`set_device` call for the device specified in ``test_standalone``.
extra_test_dirs : list of str or str, optional
Additional directories as a list of strings (or a single directory as
a string) that will be searched for additional tests.
float_dtype : np.dtype, optional
Set the dtype to use for floating point variables to a value different
from the default `core.default_float_dtype` setting.
'''
if nose is None:
raise ImportError('Running the test suite requires the "nose" package.')
if build_options is None:
build_options = {}
if os.name == 'nt':
test_in_parallel = []
if extra_test_dirs is None:
extra_test_dirs = []
elif isinstance(extra_test_dirs, basestring):
extra_test_dirs = [extra_test_dirs]
multiprocess_arguments = ['--processes=-1',
'--process-timeout=3600', # we don't want them to time out
'--process-restartworker']
if codegen_targets is None:
codegen_targets = ['numpy']
try:
import scipy.weave
codegen_targets.append('weave')
except ImportError:
try:
import weave
codegen_targets.append('weave')
except ImportError:
pass
try:
import Cython
codegen_targets.append('cython')
except ImportError:
pass
elif isinstance(codegen_targets, basestring): # allow to give a single target
codegen_targets = [codegen_targets]
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
dirnames = [dirname] + extra_test_dirs
# We write to stderr since nose does all of its output on stderr as well
sys.stderr.write('Running tests in %s ' % (', '.join(dirnames)))
if codegen_targets:
sys.stderr.write('for targets %s' % (', '.join(codegen_targets)))
ex_in = 'including' if long_tests else 'excluding'
sys.stderr.write(' (%s long tests)\n' % ex_in)
all_targets = set(codegen_targets)
if test_standalone:
if not isinstance(test_standalone, basestring):
raise ValueError('test_standalone argument has to be the name of a '
'standalone device (e.g. "cpp_standalone")')
if test_standalone not in all_devices:
raise ValueError('test_standalone argument "%s" is not a known '
'device. Known devices are: '
'%s' % (test_standalone,
', '.join(repr(d) for d in all_devices)))
sys.stderr.write('Testing standalone \n')
all_targets.add(test_standalone)
if test_codegen_independent:
sys.stderr.write('Testing codegen-independent code \n')
all_targets.add('codegen_independent')
parallel_tests = all_targets.intersection(set(test_in_parallel))
if parallel_tests:
sys.stderr.write('Testing with multiple processes for %s\n' % ', '.join(parallel_tests))
if reset_preferences:
sys.stderr.write('Resetting to default preferences\n')
if reset_preferences:
# Store the currently set preferences and reset to default preferences
stored_prefs = prefs.as_file
prefs.read_preference_file(StringIO(prefs.defaults_as_file))
# Avoid failures in the tests for user-registered units
import copy
import brian2.units.fundamentalunits as fundamentalunits
old_unit_registry = copy.copy(fundamentalunits.user_unit_register)
fundamentalunits.user_unit_register = fundamentalunits.UnitRegistry()
if float_dtype is not None:
sys.stderr.write('Setting dtype for floating point variables to: '
'{}\n'.format(float_dtype.__name__))
prefs['core.default_float_dtype'] = float_dtype
prefs._backup()
sys.stderr.write('\n')
# Suppress INFO log messages during testing
from brian2.utils.logger import BrianLogger, LOG_LEVELS
log_level = BrianLogger.console_handler.level
BrianLogger.console_handler.setLevel(LOG_LEVELS['WARNING'])
# Switch off code optimization to get faster compilation times
prefs['codegen.cpp.extra_compile_args_gcc'].extend(['-w', '-O0'])
prefs['codegen.cpp.extra_compile_args_msvc'].extend(['/Od'])
if fail_for_not_implemented:
not_implemented_plugin = NotImplementedPlugin
else:
not_implemented_plugin = NotImplementedNoFailurePlugin
# This hack is needed to get the NotImplementedPlugin working for multiprocessing
import nose.plugins.multiprocess as multiprocess
multiprocess._instantiate_plugins = [not_implemented_plugin]
plugins = [not_implemented_plugin()]
from brian2.devices import set_device
set_device('runtime')
try:
success = []
if test_codegen_independent:
sys.stderr.write('Running tests that do not use code generation\n')
# Some doctests do actually use code generation, use numpy for that
prefs.codegen.target = 'numpy'
prefs._backup()
# Print output changed in numpy 1.14, stick with the old format to
# avoid doctest failures
import numpy as np
try:
np.set_printoptions(legacy='1.13')
except TypeError:
pass # using a numpy version < 1.14
argv = make_argv(dirnames, "codegen-independent", doctests=True)
if 'codegen_independent' in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
for target in codegen_targets:
sys.stderr.write('Running tests for target %s:\n' % target)
prefs.codegen.target = target
# Also set the target for string-expressions -- otherwise we'd only
# ever test numpy for those
prefs.codegen.string_expression_target = target
prefs._backup()
exclude_str = "!standalone-only,!codegen-independent"
if not long_tests:
exclude_str += ',!long'
# explicitly ignore the brian2.hears file for testing, otherwise the
# doctest search will import it, failing on Python 3
argv = make_argv(dirnames, exclude_str)
if target in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
if test_standalone:
from brian2.devices.device import get_device, set_device
set_device(test_standalone, directory=None, # use temp directory
with_output=False, **build_options)
sys.stderr.write('Testing standalone device "%s"\n' % test_standalone)
sys.stderr.write('Running standalone-compatible standard tests (single run statement)\n')
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',!multiple-runs'
argv = make_argv(dirnames, 'standalone-compatible'+exclude_str)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
reset_device()
sys.stderr.write('Running standalone-compatible standard tests (multiple run statements)\n')
set_device(test_standalone, directory=None, # use temp directory
with_output=False, build_on_run=False, **build_options)
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',multiple-runs'
argv = make_argv(dirnames, 'standalone-compatible'+exclude_str)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
reset_device()
if test_openmp and test_standalone == 'cpp_standalone':
# Run all the standalone compatible tests again with 4 threads
set_device(test_standalone, directory=None, # use temp directory
with_output=False, **build_options)
prefs.devices.cpp_standalone.openmp_threads = 4
prefs._backup()
sys.stderr.write('Running standalone-compatible standard tests with OpenMP (single run statements)\n')
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',!multiple-runs'
argv = make_argv(dirnames,
'standalone-compatible' + exclude_str)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
reset_device()
set_device(test_standalone, directory=None, # use temp directory
with_output=False, build_on_run=False, **build_options)
sys.stderr.write('Running standalone-compatible standard tests with OpenMP (multiple run statements)\n')
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',multiple-runs'
argv = make_argv(dirnames,
'standalone-compatible' + exclude_str)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
prefs.devices.cpp_standalone.openmp_threads = 0
prefs._backup()
reset_device()
sys.stderr.write('Running standalone-specific tests\n')
exclude_openmp = ',!openmp' if not test_openmp else ''
argv = make_argv(dirnames, test_standalone+exclude_openmp)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv,
addplugins=plugins))
clear_caches()
all_success = all(success)
if not all_success:
sys.stderr.write(('ERROR: %d/%d test suite(s) did not complete '
'successfully (see above).\n') % (len(success) - sum(success),
len(success)))
else:
sys.stderr.write(('OK: %d/%d test suite(s) did complete '
'successfully.\n') % (len(success), len(success)))
return all_success
finally:
BrianLogger.console_handler.setLevel(log_level)
if reset_preferences:
# Restore the user preferences
prefs.read_preference_file(StringIO(stored_prefs))
prefs._backup()
fundamentalunits.user_unit_register = old_unit_registry
def run(codegen_targets=None,
long_tests=False,
test_codegen_independent=True,
test_standalone=None,
test_openmp=False,
test_in_parallel=[
'codegen_independent', 'numpy', 'cython', 'cpp_standalone'
],
reset_preferences=True,
fail_for_not_implemented=True,
build_options=None,
extra_test_dirs=None,
float_dtype=None):
'''
Run brian's test suite. Needs an installation of the nose testing tool.
For testing, the preferences will be reset to the default preferences.
After testing, the user preferences will be restored.
Parameters
----------
codegen_targets : list of str or str
A list of codegeneration targets or a single target, e.g.
``['numpy', 'weave']`` to test. The whole test suite will be repeatedly
run with `codegen.target` set to the respective value. If not
specified, all available code generation targets will be tested.
long_tests : bool, optional
Whether to run tests that take a long time. Defaults to ``False``.
test_codegen_independent : bool, optional
Whether to run tests that are independent of code generation. Defaults
to ``True``.
test_standalone : str, optional
Whether to run tests for a standalone mode. Should be the name of a
standalone mode (e.g. ``'cpp_standalone'``) and expects that a device
of that name and an accordingly named "simple" device (e.g.
``'cpp_standalone_simple'`` exists that can be used for testing (see
`CPPStandaloneSimpleDevice` for details. Defaults to ``None``, meaning
that no standalone device is tested.
test_openmp : bool, optional
Whether to test standalone test with multiple threads and OpenMP. Will
be ignored if ``cpp_standalone`` is not tested. Defaults to ``False``.
reset_preferences : bool, optional
Whether to reset all preferences to the default preferences before
running the test suite. Defaults to ``True`` to get test results
independent of the user's preference settings but can be switched off
when the preferences are actually necessary to pass the tests (e.g. for
device-specific settings).
fail_for_not_implemented : bool, optional
Whether to fail for tests raising a `NotImplementedError`. Defaults to
``True``, but can be switched off for devices known to not implement
all of Brian's features.
build_options : dict, optional
Non-default build options that will be passed as arguments to the
`set_device` call for the device specified in ``test_standalone``.
extra_test_dirs : list of str or str, optional
Additional directories as a list of strings (or a single directory as
a string) that will be searched for additional tests.
float_dtype : np.dtype, optional
Set the dtype to use for floating point variables to a value different
from the default `core.default_float_dtype` setting.
'''
if nose is None:
raise ImportError(
'Running the test suite requires the "nose" package.')
if build_options is None:
build_options = {}
if os.name == 'nt':
test_in_parallel = []
if extra_test_dirs is None:
extra_test_dirs = []
elif isinstance(extra_test_dirs, basestring):
extra_test_dirs = [extra_test_dirs]
multiprocess_arguments = [
'--processes=-1',
'--process-timeout=3600', # we don't want them to time out
'--process-restartworker'
]
if codegen_targets is None:
codegen_targets = ['numpy']
try:
import scipy.weave
codegen_targets.append('weave')
except ImportError:
try:
import weave
codegen_targets.append('weave')
except ImportError:
pass
try:
import Cython
codegen_targets.append('cython')
except ImportError:
pass
elif isinstance(codegen_targets,
basestring): # allow to give a single target
codegen_targets = [codegen_targets]
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
dirnames = [dirname] + extra_test_dirs
# We write to stderr since nose does all of its output on stderr as well
sys.stderr.write('Running tests in %s ' % (', '.join(dirnames)))
if codegen_targets:
sys.stderr.write('for targets %s' % (', '.join(codegen_targets)))
ex_in = 'including' if long_tests else 'excluding'
sys.stderr.write(' (%s long tests)\n' % ex_in)
all_targets = set(codegen_targets)
if test_standalone:
if not isinstance(test_standalone, basestring):
raise ValueError(
'test_standalone argument has to be the name of a '
'standalone device (e.g. "cpp_standalone")')
if test_standalone not in all_devices:
raise ValueError(
'test_standalone argument "%s" is not a known '
'device. Known devices are: '
'%s' %
(test_standalone, ', '.join(repr(d) for d in all_devices)))
sys.stderr.write('Testing standalone \n')
all_targets.add(test_standalone)
if test_codegen_independent:
sys.stderr.write('Testing codegen-independent code \n')
all_targets.add('codegen_independent')
parallel_tests = all_targets.intersection(set(test_in_parallel))
if parallel_tests:
sys.stderr.write('Testing with multiple processes for %s\n' %
', '.join(parallel_tests))
if reset_preferences:
sys.stderr.write('Resetting to default preferences\n')
if reset_preferences:
# Store the currently set preferences and reset to default preferences
stored_prefs = prefs.as_file
prefs.read_preference_file(StringIO(prefs.defaults_as_file))
# Avoid failures in the tests for user-registered units
import copy
import brian2.units.fundamentalunits as fundamentalunits
old_unit_registry = copy.copy(fundamentalunits.user_unit_register)
fundamentalunits.user_unit_register = fundamentalunits.UnitRegistry()
if float_dtype is not None:
sys.stderr.write('Setting dtype for floating point variables to: '
'{}\n'.format(float_dtype.__name__))
prefs['core.default_float_dtype'] = float_dtype
prefs._backup()
sys.stderr.write('\n')
# Suppress INFO log messages during testing
from brian2.utils.logger import BrianLogger, LOG_LEVELS
log_level = BrianLogger.console_handler.level
BrianLogger.console_handler.setLevel(LOG_LEVELS['WARNING'])
# Switch off code optimization to get faster compilation times
prefs['codegen.cpp.extra_compile_args_gcc'].extend(['-w', '-O0'])
prefs['codegen.cpp.extra_compile_args_msvc'].extend(['/Od'])
if fail_for_not_implemented:
not_implemented_plugin = NotImplementedPlugin
else:
not_implemented_plugin = NotImplementedNoFailurePlugin
# This hack is needed to get the NotImplementedPlugin working for multiprocessing
import nose.plugins.multiprocess as multiprocess
multiprocess._instantiate_plugins = [not_implemented_plugin]
plugins = [not_implemented_plugin()]
from brian2.devices import set_device
set_device('runtime')
try:
success = []
if test_codegen_independent:
sys.stderr.write('Running tests that do not use code generation\n')
# Some doctests do actually use code generation, use numpy for that
prefs.codegen.target = 'numpy'
prefs._backup()
# Print output changed in numpy 1.14, stick with the old format to
# avoid doctest failures
import numpy as np
try:
np.set_printoptions(legacy='1.13')
except TypeError:
pass # using a numpy version < 1.14
argv = make_argv(dirnames, "codegen-independent", doctests=True)
if 'codegen_independent' in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
for target in codegen_targets:
sys.stderr.write('Running tests for target %s:\n' % target)
prefs.codegen.target = target
# Also set the target for string-expressions -- otherwise we'd only
# ever test numpy for those
prefs.codegen.string_expression_target = target
prefs._backup()
exclude_str = "!standalone-only,!codegen-independent"
if not long_tests:
exclude_str += ',!long'
# explicitly ignore the brian2.hears file for testing, otherwise the
# doctest search will import it, failing on Python 3
argv = make_argv(dirnames, exclude_str)
if target in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
if test_standalone:
from brian2.devices.device import get_device, set_device
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
**build_options)
sys.stderr.write('Testing standalone device "%s"\n' %
test_standalone)
sys.stderr.write(
'Running standalone-compatible standard tests (single run statement)\n'
)
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',!multiple-runs'
argv = make_argv(dirnames, 'standalone-compatible' + exclude_str)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
reset_device()
sys.stderr.write(
'Running standalone-compatible standard tests (multiple run statements)\n'
)
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
build_on_run=False,
**build_options)
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',multiple-runs'
argv = make_argv(dirnames, 'standalone-compatible' + exclude_str)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
reset_device()
if test_openmp and test_standalone == 'cpp_standalone':
# Run all the standalone compatible tests again with 4 threads
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
**build_options)
prefs.devices.cpp_standalone.openmp_threads = 4
prefs._backup()
sys.stderr.write(
'Running standalone-compatible standard tests with OpenMP (single run statements)\n'
)
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',!multiple-runs'
argv = make_argv(dirnames,
'standalone-compatible' + exclude_str)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
reset_device()
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
build_on_run=False,
**build_options)
sys.stderr.write(
'Running standalone-compatible standard tests with OpenMP (multiple run statements)\n'
)
exclude_str = ',!long' if not long_tests else ''
exclude_str += ',multiple-runs'
argv = make_argv(dirnames,
'standalone-compatible' + exclude_str)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
prefs.devices.cpp_standalone.openmp_threads = 0
prefs._backup()
reset_device()
sys.stderr.write('Running standalone-specific tests\n')
exclude_openmp = ',!openmp' if not test_openmp else ''
argv = make_argv(dirnames, test_standalone + exclude_openmp)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(nose.run(argv=argv, addplugins=plugins))
clear_caches()
all_success = all(success)
if not all_success:
sys.stderr.write(('ERROR: %d/%d test suite(s) did not complete '
'successfully (see above).\n') %
(len(success) - sum(success), len(success)))
else:
sys.stderr.write(
('OK: %d/%d test suite(s) did complete '
'successfully.\n') % (len(success), len(success)))
return all_success
finally:
BrianLogger.console_handler.setLevel(log_level)
if reset_preferences:
# Restore the user preferences
prefs.read_preference_file(StringIO(stored_prefs))
prefs._backup()
fundamentalunits.user_unit_register = old_unit_registry
def simple_model(N,
params,
record=None,
update_progress=None,
fm=None,
minimum_initial_time=100 * ms,
use_standalone_openmp=False):
if use_standalone_openmp:
prefs.devices.cpp_standalone.openmp_threads = multiprocessing.cpu_count(
) / 2 # assume hyperthreading
set_device('cpp_standalone', with_output=True)
seed(3402348923) # for reproducibility
if fm is None:
fm = dietz_fm
orig_fm = fm
min_tauihc = 0.1 * ms
eqs = '''
carrier = clip(cos(2*pi*fc*t), 0, Inf) : 1
A_raw = (carrier*gain*0.5*(1-cos(2*pi*fm*t)))**gamma : 1
dA_filt/dt = (A_raw-A)/(int(tauihc<min_tauihc)*1*second+tauihc) : 1
A = A_raw*int(tauihc<min_tauihc)+A_filt*int(tauihc>=min_tauihc) : 1
dQ/dt = -k*Q*A+R*(1-Q) : 1
AQ = A*Q : 1
dAe/dt = (AQ-Ae)/taue : 1
dAi/dt = (AQ-Ai)/taui : 1
out = clip(Ae-beta*Ai, 0, Inf) : 1
gain = 10**(level/20.) : 1
R = (1-alpha)/taua : Hz
k = alpha/taua : Hz
fc = fc_Hz*Hz : Hz
fc_Hz : 1
fm : Hz
tauihc = tauihc_ms*ms : second
taue = taue_ms*ms : second
taui = taui_ms*ms : second
taua = taua_ms*ms : second
tauihc_ms : 1
taue_ms : 1
taui_ms : 1
taua_ms : 1
alpha : 1
beta : 1
gamma : 1
level : 1
# Accumulation variables
start_time : second
end_time : second
do_accumulate = 1.0*int(t>=start_time and t<end_time) : 1
accum_sum_out : 1
accum_sum_out_rising : 1
accum_sum_out_falling : 1
accum_argmax_out : second
accum_max_out : 1
accum_weighted_sum_cos_phase : 1
accum_weighted_sum_sin_phase : 1
'''
G = NeuronGroup(N * len(fm), eqs, method='euler', dt=0.1 * ms)
rr = G.run_regularly('''
accum_sum_out += out*do_accumulate
phase = (2*pi*fm*t)%(2*pi)
accum_sum_out_rising += out*int(phase<pi)*do_accumulate
accum_sum_out_falling += out*int(phase>=pi)*do_accumulate
accum_weighted_sum_cos_phase += out*cos(phase)*do_accumulate
accum_weighted_sum_sin_phase += out*sin(phase)*do_accumulate
is_larger = out>accum_max_out and do_accumulate>0
accum_max_out = int(not is_larger)*accum_max_out+int(is_larger)*out
accum_argmax_out = int(not is_larger)*accum_argmax_out+int(is_larger)*t
''',
when='end')
params = params.copy()
for k, v in params.items():
if isinstance(v, tuple) and len(v) == 2:
low, high = v
params[k] = v = rand(N) * (high - low) + low
params2d = params.copy()
for k, v in params2d.items():
if isinstance(v, ndarray) and v.size > 1:
v = reshape(v, v.size)
fm, v = meshgrid(orig_fm,
v) # fm and v have shape (N, len(dietz_fm))
fm.shape = fm.size
v.shape = v.size
params2d[k] = v
params2d['fm'] = fm
G.set_states(params2d)
G.tauihc_ms['tauihc_ms<min_tauihc/ms'] = 0
G.Q = 1
net = Network(G, rr)
# Calculate how long to run the simulation
period = 1 / fm
num_initial_cycles = ceil(
minimum_initial_time /
period) # at least one period and at least that time
start_time = num_initial_cycles * period
end_time = (num_initial_cycles + 1) * period
duration = amax(end_time)
G.start_time = start_time
G.end_time = end_time
# Run the simulation
if isinstance(update_progress, basestring):
report_period = 10 * second
else:
report_period = 1 * second
if record:
M = StateMonitor(G, record, record=True)
net.add(M)
net.run(duration, report=update_progress, report_period=report_period)
G.accum_sum_out['accum_sum_out<1e-10'] = 1
for name in [
'accum_sum_out_rising', 'accum_sum_out_falling',
'accum_argmax_out', 'accum_max_out',
'accum_weighted_sum_cos_phase', 'accum_weighted_sum_sin_phase'
]:
if name == 'accum_argmax_out':
u = second
else:
u = 1
getattr(G, name)['accum_sum_out>1e10'] = 0 * u
G.accum_sum_out['accum_sum_out>1e10'] = 1
c = G.accum_weighted_sum_cos_phase[:]
s = G.accum_weighted_sum_sin_phase[:]
weighted_phase = (angle(c + 1j * s) + 2 * pi) % (2 * pi)
vs = sqrt(c**2 + s**2) / G.accum_sum_out[:]
mean_fr = G.accum_sum_out[:] / ((end_time - start_time) / G.dt)
onsettiness = 0.5 * (1 + (G.accum_sum_out_rising[:] -
G.accum_sum_out_falling[:]) / G.accum_sum_out[:])
res = Results(
accum_argmax_out=G.accum_argmax_out[:],
accum_max_out=G.accum_max_out[:],
weighted_phase=weighted_phase,
vs=vs,
mean_fr=mean_fr,
onsettiness=onsettiness,
params=params,
start_time=start_time,
end_time=end_time,
)
if record:
for name in record:
v = getattr(M, name)[:, :]
v.shape = (N, len(dietz_fm), -1)
setattr(res, name, v)
res.t = M.t[:]
if use_standalone_openmp:
reset_device()
reinit_devices()
return res
def run(codegen_targets=None,
long_tests=False,
test_codegen_independent=True,
test_standalone=None,
test_openmp=False,
test_in_parallel=[
'codegen_independent', 'numpy', 'cython', 'cpp_standalone'
],
reset_preferences=True,
fail_for_not_implemented=True,
build_options=None,
extra_test_dirs=None,
float_dtype=None,
additional_args=None):
'''
Run brian's test suite. Needs an installation of the pytest testing tool.
For testing, the preferences will be reset to the default preferences.
After testing, the user preferences will be restored.
Parameters
----------
codegen_targets : list of str or str
A list of codegeneration targets or a single target, e.g.
``['numpy', 'weave']`` to test. The whole test suite will be repeatedly
run with `codegen.target` set to the respective value. If not
specified, all available code generation targets will be tested.
long_tests : bool, optional
Whether to run tests that take a long time. Defaults to ``False``.
test_codegen_independent : bool, optional
Whether to run tests that are independent of code generation. Defaults
to ``True``.
test_standalone : str, optional
Whether to run tests for a standalone mode. Should be the name of a
standalone mode (e.g. ``'cpp_standalone'``) and expects that a device
of that name and an accordingly named "simple" device (e.g.
``'cpp_standalone_simple'`` exists that can be used for testing (see
`CPPStandaloneSimpleDevice` for details. Defaults to ``None``, meaning
that no standalone device is tested.
test_openmp : bool, optional
Whether to test standalone test with multiple threads and OpenMP. Will
be ignored if ``cpp_standalone`` is not tested. Defaults to ``False``.
reset_preferences : bool, optional
Whether to reset all preferences to the default preferences before
running the test suite. Defaults to ``True`` to get test results
independent of the user's preference settings but can be switched off
when the preferences are actually necessary to pass the tests (e.g. for
device-specific settings).
fail_for_not_implemented : bool, optional
Whether to fail for tests raising a `NotImplementedError`. Defaults to
``True``, but can be switched off for devices known to not implement
all of Brian's features.
build_options : dict, optional
Non-default build options that will be passed as arguments to the
`set_device` call for the device specified in ``test_standalone``.
extra_test_dirs : list of str or str, optional
Additional directories as a list of strings (or a single directory as
a string) that will be searched for additional tests.
float_dtype : np.dtype, optional
Set the dtype to use for floating point variables to a value different
from the default `core.default_float_dtype` setting.
additional_args : list of str, optional
Optional command line arguments to pass to ``pytest``
'''
if pytest is None:
raise ImportError(
'Running the test suite requires the "pytest" package.')
if build_options is None:
build_options = {}
if os.name == 'nt':
test_in_parallel = []
if extra_test_dirs is None:
extra_test_dirs = []
elif isinstance(extra_test_dirs, basestring):
extra_test_dirs = [extra_test_dirs]
if additional_args is None:
additional_args = []
multiprocess_arguments = ['-n', 'auto']
if codegen_targets is None:
codegen_targets = ['numpy']
try:
import scipy.weave
codegen_targets.append('weave')
except ImportError:
try:
import weave
codegen_targets.append('weave')
except ImportError:
pass
try:
import Cython
codegen_targets.append('cython')
except ImportError:
pass
elif isinstance(codegen_targets,
basestring): # allow to give a single target
codegen_targets = [codegen_targets]
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
dirnames = [dirname] + extra_test_dirs
print('Running tests in %s ' % (', '.join(dirnames)), end='')
if codegen_targets:
print('for targets %s' % (', '.join(codegen_targets)), end='')
ex_in = 'including' if long_tests else 'excluding'
print(' (%s long tests)' % ex_in)
print("Running Brian version {} "
"from '{}'".format(brian2.__version__,
os.path.dirname(brian2.__file__)))
all_targets = set(codegen_targets)
if test_standalone:
if not isinstance(test_standalone, basestring):
raise ValueError(
'test_standalone argument has to be the name of a '
'standalone device (e.g. "cpp_standalone")')
if test_standalone not in all_devices:
raise ValueError(
'test_standalone argument "%s" is not a known '
'device. Known devices are: '
'%s' %
(test_standalone, ', '.join(repr(d) for d in all_devices)))
print('Testing standalone')
all_targets.add(test_standalone)
if test_codegen_independent:
print('Testing codegen-independent code')
all_targets.add('codegen_independent')
parallel_tests = all_targets.intersection(set(test_in_parallel))
if parallel_tests:
try:
import xdist
print('Testing with multiple processes for %s' %
', '.join(parallel_tests))
except ImportError:
test_in_parallel = []
if reset_preferences:
print('Resetting to default preferences')
if reset_preferences:
stored_prefs = prefs.as_file
prefs.read_preference_file(StringIO(prefs.defaults_as_file))
# Avoid failures in the tests for user-registered units
import copy
import brian2.units.fundamentalunits as fundamentalunits
old_unit_registry = copy.copy(fundamentalunits.user_unit_register)
fundamentalunits.user_unit_register = fundamentalunits.UnitRegistry()
if float_dtype is not None:
print('Setting dtype for floating point variables to: '
'{}'.format(float_dtype.__name__))
prefs['core.default_float_dtype'] = float_dtype
print()
# Suppress INFO log messages during testing
from brian2.utils.logger import BrianLogger, LOG_LEVELS
log_level = BrianLogger.console_handler.level
BrianLogger.console_handler.setLevel(LOG_LEVELS['WARNING'])
# Switch off code optimization to get faster compilation times
prefs['codegen.cpp.extra_compile_args_gcc'].extend(['-w', '-O0'])
prefs['codegen.cpp.extra_compile_args_msvc'].extend(['-w', '-O0'])
from brian2.devices import set_device
set_device('runtime')
pref_plugin = PreferencePlugin(prefs, fail_for_not_implemented)
try:
success = []
if test_codegen_independent:
print('Running doctests')
# Some doctests do actually use code generation, use numpy for that
prefs['codegen.target'] = 'numpy'
# Always test doctests with 64 bit, to avoid differences in print output
if float_dtype is not None:
prefs['core.default_float_dtype'] = np.float64
sphinx_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..',
'docs_sphinx'))
if os.path.exists(sphinx_dir):
sphinx_doc_dir = [sphinx_dir]
else:
# When running on travis, the source directory is in the SRCDIR
# environment variable
if 'SRCDIR' in os.environ:
sphinx_dir = os.path.abspath(
os.path.join(os.environ['SRCDIR'], 'docs_sphinx'))
if os.path.exists(sphinx_dir):
sphinx_doc_dir = [sphinx_dir]
else:
sphinx_doc_dir = []
else:
sphinx_doc_dir = []
argv = make_argv(dirnames + sphinx_doc_dir, doctests=True)
if 'codegen_independent' in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
# Set float_dtype back again if necessary
if float_dtype is not None:
prefs['core.default_float_dtype'] = float_dtype
print('Running tests that do not use code generation')
argv = make_argv(dirnames, "codegen_independent")
if 'codegen_independent' in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
for target in codegen_targets:
print('Running tests for target %s:' % target)
# Also set the target for string-expressions -- otherwise we'd only
# ever test numpy for those
prefs['codegen.target'] = target
markers = "not standalone_only and not codegen_independent"
if not long_tests:
markers += ' and not long'
# explicitly ignore the brian2.hears file for testing, otherwise the
# doctest search will import it, failing on Python 3
argv = make_argv(dirnames, markers)
if target in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
if test_standalone:
from brian2.devices.device import get_device, set_device
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
**build_options)
print('Testing standalone device "%s"' % test_standalone)
print(
'Running standalone-compatible standard tests (single run statement)'
)
markers = 'and not long' if not long_tests else ''
markers += ' and not multiple_runs'
argv = make_argv(dirnames, 'standalone_compatible ' + markers)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
reset_device()
print(
'Running standalone-compatible standard tests (multiple run statements)'
)
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
build_on_run=False,
**build_options)
markers = ' and not long' if not long_tests else ''
markers += ' and multiple_runs'
argv = make_argv(dirnames, 'standalone_compatible' + markers)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
reset_device()
if test_openmp and test_standalone == 'cpp_standalone':
# Run all the standalone compatible tests again with 4 threads
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
**build_options)
prefs['devices.cpp_standalone.openmp_threads'] = 4
print(
'Running standalone-compatible standard tests with OpenMP (single run statements)'
)
markers = ' and not long' if not long_tests else ''
markers += ' and not multiple_runs'
argv = make_argv(dirnames, 'standalone_compatible' + markers)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
reset_device()
set_device(
test_standalone,
directory=None, # use temp directory
with_output=False,
build_on_run=False,
**build_options)
print(
'Running standalone-compatible standard tests with OpenMP (multiple run statements)'
)
markers = ' and not long' if not long_tests else ''
markers += ' and multiple_runs'
argv = make_argv(dirnames, 'standalone_compatible' + markers)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
prefs['devices.cpp_standalone.openmp_threads'] = 0
reset_device()
print('Running standalone-specific tests')
exclude_openmp = ' and not openmp' if not test_openmp else ''
argv = make_argv(dirnames, test_standalone + exclude_openmp)
if test_standalone in test_in_parallel:
argv.extend(multiprocess_arguments)
success.append(
pytest.main(argv +
additional_args, plugins=[pref_plugin]) == 0)
clear_caches()
all_success = all(success)
if not all_success:
print(('ERROR: %d/%d test suite(s) did not complete '
'successfully (see above).') %
(len(success) - sum(success), len(success)))
else:
print(('OK: %d/%d test suite(s) did complete '
'successfully.') % (len(success), len(success)))
return all_success
finally:
BrianLogger.console_handler.setLevel(log_level)
if reset_preferences:
# Restore the user preferences
prefs.read_preference_file(StringIO(stored_prefs))
prefs._backup()
fundamentalunits.user_unit_register = old_unit_registry
def test_array_cache(with_output=False):
# Check that variables are only accessible from Python when they should be
set_device('cpp_standalone', build_on_run=False)
G = NeuronGroup(10,
'''dv/dt = -v / (10*ms) : 1
w : 1
x : 1
y : 1
z : 1 (shared)''',
threshold='v>1')
S = Synapses(G, G, 'weight: 1', on_pre='w += weight')
S.connect(p=0.2)
S.weight = 7
# All neurongroup values should be known
assert_allclose(G.v, 0)
assert_allclose(G.w, 0)
assert_allclose(G.x, 0)
assert_allclose(G.y, 0)
assert_allclose(G.z, 0)
assert_allclose(G.i, np.arange(10))
# But the synaptic variable is not -- we don't know the number of synapses
assert_raises(NotImplementedError, lambda: S.weight[:])
# Setting variables with explicit values should not change anything
G.v = np.arange(10) + 1
G.w = 2
G.y = 5
G.z = 7
assert_allclose(G.v, np.arange(10) + 1)
assert_allclose(G.w, 2)
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
# But setting with code should invalidate them
G.x = 'i*2'
assert_raises(NotImplementedError, lambda: G.x[:])
# Make sure that the array cache does not allow to use incorrectly sized
# values to pass
assert_raises(ValueError, lambda: setattr(G, 'w', [0, 2]))
assert_raises(ValueError, lambda: G.w.__setitem__(slice(0, 4), [0, 2]))
run(10 * ms)
# v is now no longer known without running the network
assert_raises(NotImplementedError, lambda: G.v[:])
# Neither is w, it is updated in the synapse
assert_raises(NotImplementedError, lambda: G.w[:])
# However, no code touches y or z
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
# i is read-only anyway
assert_allclose(G.i, np.arange(10))
# After actually running the network, everything should be accessible
tempdir = tempfile.mkdtemp()
if with_output:
print tempdir
device.build(directory=tempdir,
run=True,
compile=True,
with_output=with_output)
assert all(G.v > 0)
assert all(G.w > 0)
assert_allclose(G.x, np.arange(10) * 2)
assert_allclose(G.y, 5)
assert_allclose(G.z, 7)
assert_allclose(G.i, np.arange(10))
assert_allclose(S.weight, 7)
reset_device()
