Merge branch 'lfpy' of https://github.com/alejoe91/BluePyOpt into small-changes

Author: Jaquier Aurélien Tristan

bluepyopt/ephys/protocols.py

@@ -288,7 +288,7 @@ def instantiate(self, sim=None, cell_model=None):
 
         for stimulus in self.stimuli:
             if isinstance(stimulus, LFPStimulus):
-                stimulus.instantiate(lfpy_cell=cell_model.lfpy_cell)
+                stimulus.instantiate(sim=sim, lfpy_cell=cell_model.lfpy_cell)
             else:
                 stimulus.instantiate(sim=sim, icell=cell_model.icell)
 

bluepyopt/ephys/stimuli.py

@@ -36,7 +36,7 @@ class LFPStimulus(Stimulus):
 
     """Base class for stimulus supporting LFPy cells."""
 
-    def instantiate(self, lfpy_cell=None):
+    def instantiate(self, sim=None, lfpy_cell=None):
         """Run stimulus"""
         raise NotImplementedError
 
@@ -366,7 +366,7 @@ def __init__(self,
         self.total_duration = total_duration
         self.iclamp = None
 
-    def instantiate(self, lfpy_cell=None):
+    def instantiate(self, sim=None, lfpy_cell=None):
         """Run stimulus"""
         import LFPy
         from .locations import NrnSomaDistanceCompLocation

bluepyopt/tests/test_ephys/test_stimuli.py

@@ -248,9 +248,9 @@ def test_LFPySquarePulse_init():
 def test_LFPySquarePulse_instantiate():
     """ephys.stimuli: test if LFPySquarePulse instantiate works"""
 
-    nrn_sim = ephys.simulators.NrnSimulator()
+    lfpy_sim = ephys.simulators.LFPySimulator()
     dummy_cell = dummycells.DummyLFPyCellModel1()
-    _, lfpycell = dummy_cell.instantiate(sim=nrn_sim)
+    _, lfpycell = dummy_cell.instantiate(sim=lfpy_sim)
 
     soma_loc = ephys.locations.NrnSeclistCompLocation(
         name=None,
@@ -266,8 +266,8 @@ def test_LFPySquarePulse_instantiate():
         total_duration=300
     )
 
-    stim.instantiate(lfpy_cell=lfpycell)
-    nrn_sim.run(stim.total_duration)
+    stim.instantiate(sim=lfpy_sim, lfpy_cell=lfpycell)
+    lfpy_sim.run(stim.total_duration)
 
-    stim.destroy(sim=nrn_sim)
-    dummy_cell.destroy(sim=nrn_sim)
+    stim.destroy(sim=lfpy_sim)
+    dummy_cell.destroy(sim=lfpy_sim)