fix tests

Author: Jaquier Aurélien Tristan

bluepyopt/ephys/models.py

@@ -686,7 +686,9 @@ def instantiate(self, sim=None):
             nsegs_method=None,
         )
 
-        self.lfpy_electrode = RecExtElectrode(self.lfpy_cell, probe=self.electrode)
+        self.lfpy_electrode = RecExtElectrode(
+            self.lfpy_cell, probe=self.electrode
+        )
 
         if self.mechanisms is not None:
             for mechanism in self.mechanisms:

bluepyopt/ephys/protocols.py

@@ -206,7 +206,9 @@ def _run_func(self, cell_model, param_values, sim=None):
                         tstop=self.total_duration,
                         cvode_active=self.cvode_active)
                 else:
-                    sim.run(tstop=self.total_duration, cvode_active=self.cvode_active)
+                    sim.run(
+                        self.total_duration, cvode_active=self.cvode_active
+                    )
             except (RuntimeError, simulators.NrnSimulatorException):
                 logger.debug(
                     'SweepProtocol: Running of parameter set {%s} generated '
@@ -293,7 +295,8 @@ def instantiate(self, sim=None, cell_model=None):
         for recording in self.recordings:
             try:
                 if isinstance(recording, LFPRecording):
-                    recording.instantiate(sim=sim, lfpy_cell=cell_model.lfpy_cell,
+                    recording.instantiate(sim=sim,
+                                          lfpy_cell=cell_model.lfpy_cell,
                                           electrode=cell_model.lfpy_electrode)
                 else:
                     recording.instantiate(sim=sim, icell=cell_model.icell)

bluepyopt/ephys/simulators.py

@@ -229,7 +229,7 @@ def run(
         lfpy_cell.tstop = tstop
 
         if dt is not None:
-            lfpy_cell.LFPyCell.dt = dt
+            lfpy_cell.dt = dt
 
         if cvode_active and dt is not None:
             raise ValueError(
@@ -281,4 +281,4 @@ def __init__(self, message, original):
         """Constructor"""
 
         super(LFPySimulatorException, self).__init__(message)
-        self.original = original
+        self.original = original

bluepyopt/tests/test_ephys/test_protocols.py

@@ -424,7 +424,7 @@ def test_sweepprotocol_instantiate_with_LFPyCellModel():
     import LFPy
 
     dummy_cell = dummycells.DummyLFPyCellModel1()
-    nrn_sim = ephys.simulators.LFPySimulator(LFPyCellModel=dummy_cell)
+    nrn_sim = ephys.simulators.LFPySimulator()
 
     soma_loc = ephys.locations.NrnSeclistCompLocation(
         name='soma_loc',
@@ -450,8 +450,8 @@ def test_sweepprotocol_instantiate_with_LFPyCellModel():
         stimuli=[stim],
         recordings=[rec])
 
-    icell, lfpy_cell = dummy_cell.instantiate(sim=nrn_sim)
-    protocol.instantiate(sim=nrn_sim, icell=icell, LFPyCell=lfpy_cell)
+    dummy_cell.instantiate(sim=nrn_sim)
+    protocol.instantiate(sim=nrn_sim, cell_model=dummy_cell)
 
     # check that recording and stimuli have been instantiated with LFPy
     assert rec.instantiated

bluepyopt/tests/test_ephys/test_recordings.py

@@ -103,11 +103,11 @@ def test_lfprecording_instantiate():
     lfpy_cell = ephys.models.LFPyCellModel(
         name="lfpy_cell", morph=test_morph, mechs=[]
     )
-    neuron_sim = ephys.simulators.LFPySimulator(LFPyCellModel=lfpy_cell)
+    neuron_sim = ephys.simulators.LFPySimulator()
     lfpy_cell.instantiate(sim=neuron_sim)
 
     recording.instantiate(
-        sim=neuron_sim, icell=lfpy_cell.icell, LFPyCell=lfpy_cell.LFPyCell
+        sim=neuron_sim, lfpy_cell=lfpy_cell.lfpy_cell
     )
 
     assert recording.instantiated

bluepyopt/tests/test_ephys/test_simulators.py

@@ -146,7 +146,7 @@ def test_lfpysimulator_init():
     """ephys.simulators: test if LFPySimulator constructor works"""
 
     empty_cell = ephys.models.LFPyCellModel(name="empty_cell")
-    neuron_sim = ephys.simulators.LFPySimulator(LFPyCellModel=empty_cell)
+    neuron_sim = ephys.simulators.LFPySimulator()
     assert isinstance(neuron_sim, ephys.simulators.LFPySimulator)
 
 
@@ -156,7 +156,7 @@ def test_lfpyimulator_init_windows():
 
     with mock.patch('platform.system', mock.MagicMock(return_value="Windows")):
         empty_cell = ephys.models.LFPyCellModel(name="empty_cell")
-        neuron_sim = ephys.simulators.LFPySimulator(LFPyCellModel=empty_cell)
+        neuron_sim = ephys.simulators.LFPySimulator()
         assert isinstance(neuron_sim, ephys.simulators.LFPySimulator)
         assert not neuron_sim.disable_banner
         assert not neuron_sim.banner_disabled
@@ -172,7 +172,7 @@ def test__lfpysimulator_neuron_import():
     """ephys.simulators: test neuron import from LFPySimulator"""
     from bluepyopt import ephys  # NOQA
     empty_cell = ephys.models.LFPyCellModel(name="empty_cell")
-    neuron_sim = ephys.simulators.LFPySimulator(LFPyCellModel=empty_cell)
+    neuron_sim = ephys.simulators.LFPySimulator()
     assert isinstance(neuron_sim.neuron, types.ModuleType)
 
 
@@ -190,7 +190,7 @@ def test_lfpysim_run_cvodeactive_dt_exception():
     lfpy_cell = ephys.models.LFPyCellModel(
         name="lfpy_cell", morph=test_morph, mechs=[]
     )
-    neuron_sim = ephys.simulators.LFPySimulator(LFPyCellModel=lfpy_cell)
+    neuron_sim = ephys.simulators.LFPySimulator()
     lfpy_cell.instantiate(sim=neuron_sim)
 
     with pytest.raises(
@@ -201,7 +201,13 @@ def test_lfpysim_run_cvodeactive_dt_exception():
             'cvode_active is True in the NrnSimulator run method'
         ),
     ):
-        neuron_sim.run(10, dt=0.1, cvode_active=True)
+        neuron_sim.run(
+            tstop=10,
+            dt=0.1,
+            cvode_active=True,
+            lfpy_cell=lfpy_cell.lfpy_cell,
+            lfpy_electrode=lfpy_cell.lfpy_electrode
+        )
 
     lfpy_cell.destroy(sim=neuron_sim)
 

bluepyopt/tests/test_ephys/test_stimuli.py

@@ -250,7 +250,7 @@ def test_LFPySquarePulse_instantiate():
 
     nrn_sim = ephys.simulators.NrnSimulator()
     dummy_cell = dummycells.DummyLFPyCellModel1()
-    icell, lfpycell = dummy_cell.instantiate(sim=nrn_sim)
+    _, lfpycell = dummy_cell.instantiate(sim=nrn_sim)
 
     soma_loc = ephys.locations.NrnSeclistCompLocation(
         name=None,
@@ -266,7 +266,7 @@ def test_LFPySquarePulse_instantiate():
         total_duration=300
     )
 
-    stim.instantiate(sim=nrn_sim, icell=icell, LFPyCell=lfpycell)
+    stim.instantiate(lfpy_cell=lfpycell)
     nrn_sim.run(stim.total_duration)
 
     stim.destroy(sim=nrn_sim)

bluepyopt/tests/test_ephys/testmodels/dummycells.py

@@ -70,7 +70,9 @@ def __init__(self, name=None):
         super(DummyLFPyCellModel1, self).__init__(name)
         self.persistent = []
         self.icell = None
-        self.LFPyCell = None
+        self.lfpy_cell = None
+        self.electrode = None
+        self.lfpy_electrode = None
 
     def freeze(self, param_values):
         """Freeze model"""
@@ -111,7 +113,7 @@ def __init__(self):
         self.persistent.append(self.icell)
         self.persistent.append(self.icell.soma[0])
 
-        self.LFPyCell = LFPy.Cell(
+        self.lfpy_cell = LFPy.Cell(
             morphology=sim.neuron.h.allsec(),
             dt=0.025,
             v_init=-65,
@@ -120,7 +122,7 @@ def __init__(self):
             nsegs_method=None,
         )
 
-        return self.icell, self.LFPyCell
+        return self.icell, self.lfpy_cell
 
     def destroy(self, sim=None):
         """Destroy cell from simulator"""