Handle non-availability of certain simulators

(e.g. NEST on Windows)

test/system/scenarios/fixtures.py

@@ -0,0 +1,29 @@
+
+import pytest
+
+available_modules = {}
+
+try:
+    import pyNN.neuron
+    available_modules["neuron"] = pyNN.neuron
+except ImportError:
+    pass
+
+try:
+    import pyNN.nest
+    available_modules["nest"] = pyNN.nest
+except ImportError:
+    pass
+
+try:
+    import pyNN.brian2
+    available_modules["brian2"] = pyNN.brian2
+except ImportError:
+    pass
+
+
+def get_simulator(sim_name):
+    if sim_name in available_modules:
+        return available_modules[sim_name]
+    else:
+        pytest.skip(f"{sim_name} not available")

test/system/scenarios/test_cell_types.py

@@ -9,14 +9,13 @@
 import quantities as pq
 from pyNN.parameters import Sequence
 from pyNN.errors import InvalidParameterValueError
-import pyNN.nest
-import pyNN.neuron
-import pyNN.brian2
+from .fixtures import get_simulator
 import pytest
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_EIF_cond_alpha_isfa_ista(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_EIF_cond_alpha_isfa_ista(sim_name, plot_figure=False):
+    sim = get_simulator(sim_name)
     sim.setup(timestep=0.01, min_delay=0.1, max_delay=4.0)
     ifcell = sim.create(sim.EIF_cond_alpha_isfa_ista(
         i_offset=1.0, tau_refrac=2.0, v_spike=-40))
@@ -39,8 +38,9 @@ def test_EIF_cond_alpha_isfa_ista(sim, plot_figure=False):
     return data
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_HH_cond_exp(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_HH_cond_exp(sim_name, plot_figure=False):
+    sim = get_simulator(sim_name)
     sim.setup(timestep=0.001, min_delay=0.1)
     cellparams = {
         'gbar_Na': 20.0,
@@ -72,8 +72,9 @@ def test_HH_cond_exp(sim, plot_figure=False):
 
 
 # exclude brian2 - see issue 370
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron))
-def issue367(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron"))
+def issue367(sim_name, plot_figure=False):
+    sim = get_simulator(sim_name)
     # AdEx dynamics for delta_T=0
     sim.setup(timestep=0.001, min_delay=0.1, max_delay=4.0)
     v_thresh = -50
@@ -103,8 +104,9 @@ def issue367(sim, plot_figure=False):
     return data
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_SpikeSourcePoisson(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_SpikeSourcePoisson(sim_name, plot_figure=False):
+    sim = get_simulator(sim_name)
     try:
         from scipy.stats import kstest
     except ImportError:
@@ -152,12 +154,13 @@ def test_SpikeSourcePoisson(sim, plot_figure=False):
     return data
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron))
-def test_SpikeSourceGamma(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron"))
+def test_SpikeSourceGamma(sim_name, plot_figure=False):
     try:
         from scipy.stats import kstest
     except ImportError:
         pytest.skip("scipy not available")
+    sim = get_simulator(sim_name)
     sim.setup()
     params = {
         "beta": [100.0, 200.0, 1000.0],
@@ -208,12 +211,13 @@ def test_SpikeSourceGamma(sim, plot_figure=False):
     return data
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron))
-def test_SpikeSourcePoissonRefractory(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron"))
+def test_SpikeSourcePoissonRefractory(sim_name, plot_figure=False):
     try:
         from scipy.stats import kstest
     except ImportError:
         pytest.skip("scipy not available")
+    sim = get_simulator(sim_name)
     sim.setup()
     params = {
         "rate": [100, 100, 50.0],
@@ -266,17 +270,19 @@ def test_SpikeSourcePoissonRefractory(sim, plot_figure=False):
     return data
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_issue511(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_issue511(sim_name):
     """Giving SpikeSourceArray an array of non-ordered spike times should produce an InvalidParameterValueError error"""
+    sim = get_simulator(sim_name)
     sim.setup()
     celltype = sim.SpikeSourceArray(spike_times=[[2.4, 4.8, 6.6, 9.4], [3.5, 6.8, 9.6, 8.3]])
     with pytest.raises(InvalidParameterValueError):
         sim.Population(2, celltype)
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_update_SpikeSourceArray(sim, plot_figure=False):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_update_SpikeSourceArray(sim_name, plot_figure=False):
+    sim = get_simulator(sim_name)
     sim.setup()
     sources = sim.Population(2, sim.SpikeSourceArray(spike_times=[]))
     sources.record('spikes')

test/system/scenarios/test_connection_handling.py

@@ -2,18 +2,16 @@
 Tests of the fine-grained connection API
 
 """
-
 from numpy.testing import assert_array_equal
 import numpy as np
 from pyNN import common
-import pyNN.nest
-import pyNN.neuron
-import pyNN.brian2
+from .fixtures import get_simulator
 import pytest
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_connections_attribute(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_connections_attribute(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(4, sim.SpikeSourceArray())
     p2 = sim.Population(3, sim.IF_cond_exp())
@@ -25,8 +23,9 @@ def test_connections_attribute(sim):
     assert isinstance(connections[0], common.Connection)
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_connection_access_weight_and_delay(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_connection_access_weight_and_delay(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(4, sim.SpikeSourceArray())
     p2 = sim.Population(3, sim.IF_cond_exp())
@@ -47,11 +46,12 @@ def test_connection_access_weight_and_delay(sim):
                        target)
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_issue672(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_issue672(sim_name):
     """
     Check that creating new Projections does not mess up existing ones.
     """
+    sim = get_simulator(sim_name)
     sim.setup(verbosity="error")
 
     p1 = sim.Population(5, sim.IF_curr_exp())
@@ -70,8 +70,9 @@ def test_issue672(sim):
     assert_array_equal(wA, wB)
 
 
-# @pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-# def test_update_synaptic_plasticity_parameters(sim):
+# @pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+# def test_update_synaptic_plasticity_parameters(sim_name):
+#     sim = get_simulator(sim_name)
 #     sim.setup()
 #     p1 = sim.Population(3, sim.IF_cond_exp(), label="presynaptic")
 #     p2 = sim.Population(2, sim.IF_cond_exp(), label="postsynaptic")
@@ -92,9 +93,10 @@ def test_issue672(sim):
 #                        np.array([[0.01, 0.011], [0.012, 0.013], [0.014, 0.015]]))
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron))
-def test_issue652(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron"))
+def test_issue652(sim_name):
     """Correctly handle A_plus = 0 in SpikePairRule."""
+    sim = get_simulator(sim_name)
     sim.setup()
 
     neural_population1 = sim.Population(10, sim.IF_cond_exp())

test/system/scenarios/test_connectors.py

@@ -3,9 +3,7 @@
 from numpy.testing import assert_array_equal, assert_allclose
 from pyNN.random import NumpyRNG, RandomDistribution
 from pyNN.utility import connection_plot, init_logging
-import pyNN.nest
-import pyNN.neuron
-import pyNN.brian2
+from .fixtures import get_simulator
 import pytest
 
 
@@ -15,8 +13,9 @@
 # TODO: add some tests with projections between Assemblies and PopulationViews
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_all_to_all_static_no_self(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_all_to_all_static_no_self(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p = sim.Population(5, sim.IF_cond_exp())
     synapse_type = sim.StaticSynapse(weight=RandomDistribution('gamma', k=2.0, theta=0.5), delay="0.2+0.3*d")
@@ -30,8 +29,9 @@ def test_all_to_all_static_no_self(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_all_to_all_tsodyksmarkram(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_all_to_all_tsodyksmarkram(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -48,8 +48,9 @@ def test_all_to_all_tsodyksmarkram(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_pre_no_replacement(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_pre_no_replacement(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -79,8 +80,9 @@ def test_fixed_number_pre_no_replacement(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_pre_with_replacement(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_pre_with_replacement(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -96,8 +98,9 @@ def test_fixed_number_pre_with_replacement(sim):
         assert column.sum() == 1.5
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_pre_with_replacement_heterogeneous_parameters(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_pre_with_replacement_heterogeneous_parameters(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -116,8 +119,9 @@ def test_fixed_number_pre_with_replacement_heterogeneous_parameters(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_post_no_replacement(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_post_no_replacement(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -146,8 +150,9 @@ def test_fixed_number_post_no_replacement(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_post_with_replacement(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_post_with_replacement(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -169,8 +174,9 @@ def test_fixed_number_post_with_replacement(sim):
         assert row.sum() == (row.size - n_nan)*0.5
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_fixed_number_post_with_replacement_heterogeneous_parameters(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_fixed_number_post_with_replacement_heterogeneous_parameters(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     p1 = sim.Population(5, sim.IF_cond_exp())
     p2 = sim.Population(7, sim.IF_cond_exp())
@@ -189,9 +195,10 @@ def test_fixed_number_post_with_replacement_heterogeneous_parameters(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron, pyNN.brian2))
-def test_issue309(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron", "brian2"))
+def test_issue309(sim_name):
     # check that FixedProbability(1) gives the same results as AllToAll
+    sim = get_simulator(sim_name)
     sim.setup()
     p = sim.Population(5, sim.IF_cond_exp())
     synapse_type = sim.StaticSynapse(weight=0.1, delay="0.2+0.3*d")
@@ -205,8 +212,9 @@ def test_issue309(sim):
     sim.end()
 
 
-@pytest.mark.parametrize("sim", (pyNN.nest, pyNN.neuron))
-def test_issue622(sim):
+@pytest.mark.parametrize("sim_name", ("nest", "neuron"))
+def test_issue622(sim_name):
+    sim = get_simulator(sim_name)
     sim.setup()
     pop = sim.Population(10, sim.IF_cond_exp, {}, label="pop")