Added smoke tests and refactored test code

hnn_core/tests/test_network.py

@@ -21,34 +21,39 @@
 @pytest.mark.parametrize("network_model",
                          ["law_2021", "calcium", "jones_2009"])
 def test_network_io(tmpdir, network_model):
+    # Instantiating network along with drives
     if network_model == "jones_2009":
         net = jones_2009_model(add_drives_from_params=True)
     elif network_model == "law_2021":
         net = law_2021_model(add_drives_from_params=True)
     elif network_model == "calcium":
         net = calcium_model(add_drives_from_params=True)
-    # add_erp_drives_to_model(net)
+
+    # Adding bias
     net.add_tonic_bias(cell_type='L2_pyramidal', amplitude=1.0)
+
     # Test __eq__ method
     net_copy = net.copy()
     assert net_copy == net
+
+    # Adding electrode arrays
     electrode_pos = (1, 2, 3)
     net.add_electrode_array('el1', electrode_pos)
     electrode_pos = [(1, 2, 3), (-1, -2, -3)]
     net.add_electrode_array('arr1', electrode_pos)
+
     # Writing network
     net.write(tmpdir.join('net.hdf5'))
+
     # Testing when overwrite is False and same filename is used
     with pytest.raises(FileExistsError,
                        match="File already exists at path "):
         net.write(tmpdir.join('net.hdf5'), overwrite=False)
+
     # Reading network
     net_read = read_network(tmpdir.join('net.hdf5'))
     assert net == net_read
 
-    # Add test to check weights are equal in connections and drives (todo)
-    # Run simulation and simulation output should be same (dipole) (Done)
-
     # Simulating network
     dpls1 = simulate_dipole(net, tstop=2, n_trials=1)
     dpls2 = simulate_dipole(net_read, tstop=2, n_trials=1)
@@ -57,29 +62,50 @@ def test_network_io(tmpdir, network_model):
         for dpl_key in dpl1.data.keys():
             assert_allclose(dpl1.data[dpl_key],
                             dpl2.data[dpl_key], rtol=0.000051, atol=0)
-    # Writing network
+    # Writing simulated network and reading it
     net.write(tmpdir.join('net_sim.hdf5'))
-    # Reading network
     net_sim = read_network(tmpdir.join('net_sim.hdf5'))
     assert net == net_sim
-    # For cell response vsec isec bug
+
+    # For cell response vsec isec bug (Not checked by __eq__)
     assert net.cell_response.vsec == net_sim.cell_response.vsec
 
+    # Smoke test
+    net_sim.plot_cells(show=False)
+
     # Checking Saving unsimulated network
     net.write(tmpdir.join('net_unsim.hdf5'), save_unsimulated=True)
-    net_unsim = read_network(tmpdir.join('net_unsim.hdf5'))
+    net_unsim_read = read_network(tmpdir.join('net_unsim.hdf5'))
     net_unsim = net.copy()
     net_unsim.cell_response = None
-    assert net_unsim == net_unsim
-    # Run simulation on the read unsimulated network and check it against the
+    assert net_unsim_read == net_unsim
+
+    # Running simulation on the read unsimulated network and check it against
     # previous simulation
+    dpls3 = simulate_dipole(net_unsim_read, tstop=2, n_trials=1)
+    for dpl1, dpl3 in zip(dpls1, dpls3):
+        assert_allclose(dpl1.times, dpl3.times, rtol=0.00051, atol=0)
+        for dpl_key in dpl1.data.keys():
+            assert_allclose(dpl1.data[dpl_key],
+                            dpl3.data[dpl_key], rtol=0.000051, atol=0)
+
+    # Smoke test
+    net_unsim_read.plot_cells(show=False)
 
     # Checking reading of raw network
     net_raw = read_network(tmpdir.join('net_sim.hdf5'),
                            read_raw=True)
     assert net_raw == net_unsim
-    # Add smoke tests for plotting
-    # Use pytest.parametrize to run through different networks
+    # Checking simulation correctness of read raw network
+    dpls4 = simulate_dipole(net_raw, tstop=2, n_trials=1)
+    for dpl1, dpl4 in zip(dpls1, dpls4):
+        assert_allclose(dpl1.times, dpl4.times, rtol=0.00051, atol=0)
+        for dpl_key in dpl1.data.keys():
+            assert_allclose(dpl1.data[dpl_key],
+                            dpl4.data[dpl_key], rtol=0.000051, atol=0)
+
+    # Smoke test
+    net_raw.plot_cells(show=False)
 
     # Checking object type field not exists error
     dummy_data = dict()
@@ -88,13 +114,16 @@ def test_network_io(tmpdir, network_model):
     with pytest.raises(NameError,
                        match="The given file is not compatible."):
         read_network(tmpdir.join('not_net.hdf5'))
+
     # Checking wrong object type error
     dummy_data['object_type'] = "net"
     write_hdf5(tmpdir.join('not_net.hdf5'), dummy_data, overwrite=True)
     with pytest.raises(ValueError,
                        match="The object should be of type Network."):
         read_network(tmpdir.join('not_net.hdf5'))
 
+    # Add test to check weights are equal in connections and drives (todo)
+
 
 def test_network_models():
     """"Test instantiations of the network object"""