Merge pull request #86 from darshanmandge/cvode_update

Disable CVODE if neuron_dt is None

bluepyemodel/evaluation/evaluation.py

@@ -241,7 +241,8 @@ def get_evaluator_from_access_point(
             and validation efeatures be added to the evaluator.
         timeout (float): duration (in second) after which the evaluation of a
             protocol will be interrupted.
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
+        use_fixed_dt_recordings (bool): used for legacy currentscape
+            to record at a fixed dt of 0.1 ms.
         record_ions_and_currents (bool): whether to add the ion and non-specific currents
             and the ionic concentration to the recordings.
 

bluepyemodel/evaluation/evaluator.py

@@ -108,7 +108,8 @@ def define_recording(recording_conf, use_fixed_dt_recordings=False):
         recording_conf (dict): configuration of the recording. Must contain the type of the
             recording as well as information about the location of the recording (see function
             define_location).
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
+        use_fixed_dt_recordings (bool): used for legacy currentscape
+            to record at a fixed dt of 0.1 ms.
 
     Returns:
         FixedDtRecordingCustom or LooseDtRecordingCustom
@@ -125,19 +126,23 @@ def define_recording(recording_conf, use_fixed_dt_recordings=False):
     return rec_class(name=recording_conf["name"], location=location, variable=variable)
 
 
-def define_protocol(protocol_configuration, stochasticity=False, use_fixed_dt_recordings=False):
+def define_protocol(
+    protocol_configuration, stochasticity=False, use_fixed_dt_recordings=False, dt=None
+):
     """Create a protocol.
 
     Args:
         protocol_configuration (ProtocolConfiguration): configuration of the protocol
         stochasticity (bool): Should the stochastic channels be stochastic or
             deterministic
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
-
+        use_fixed_dt_recordings (bool): used for legacy currentscape to record at a fixed dt
+            of 0.1 ms. However, Simulations will be run based on dt.
+        dt (float): NEURON dt for fixed time step simulation. If None, variable
+            dt will be used.
     Returns:
         Protocol
     """
-    cvode_active = True
+    cvode_active = not dt
 
     recordings = []
     for rec_conf in protocol_configuration.recordings:
@@ -393,6 +398,7 @@ def define_protocols(
     include_validation_protocols,
     stochasticity,
     use_fixed_dt_recordings,
+    dt,
 ):
     """Instantiate several efeatures"""
 
@@ -401,7 +407,7 @@ def define_protocols(
         if not include_validation_protocols and protocols_def.validation:
             continue
         protocols[protocols_def.name] = define_protocol(
-            protocols_def, stochasticity, use_fixed_dt_recordings
+            protocols_def, stochasticity, use_fixed_dt_recordings, dt
         )
 
     return protocols
@@ -440,6 +446,7 @@ def define_optimisation_protocol(
     stochasticity=True,
     efel_settings=None,
     use_fixed_dt_recordings=False,
+    dt=None,
 ):
     """Create a meta protocol in charge of running the other protocols.
 
@@ -451,14 +458,17 @@ def define_optimisation_protocol(
         stochasticity (bool): Should the stochastic channels be stochastic or
             deterministic
         efel_settings (dict): eFEl settings.
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
+        use_fixed_dt_recordings (bool): used for legacy currentscape
+            to record at a fixed dt of 0.1 ms.
+        dt (float): NEURON dt for fixed time step simulation. If None, variable dt will be used.
     """
 
     protocols = define_protocols(
         fitness_calculator_configuration,
         include_validation_protocols,
         stochasticity,
         use_fixed_dt_recordings,
+        dt,
     )
 
     efeatures = define_efeatures(
@@ -482,6 +492,7 @@ def define_threshold_based_optimisation_protocol(
     max_depth_holding_search=7,
     max_depth_threshold_search=10,
     spikecount_timeout=50,
+    dt=None,
 ):
     """Create a meta protocol in charge of running the other protocols.
 
@@ -501,20 +512,23 @@ def define_threshold_based_optimisation_protocol(
             will search for the rheobase.
         strict_holding_bounds (bool): to adaptively enlarge bounds if holding current is outside
             when set to False
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
+        use_fixed_dt_recordings (bool): used for legacy currentscape
+            to record at a fixed dt of 0.1 ms.
         max_depth_holding_search (int): maximum depth for the binary search for the
             holding current
         max_depth_threshold_search (int): maximum depth for the binary search for the
             threshold current
         spikecount_timeout (float): timeout for spikecount computation, if timeout is reached,
             we set spikecount=2 as if many spikes were present, to speed up bisection search.
+        dt (float): NEURON dt for fixed time step simulation. If None, variable dt will be used.
     """
 
     protocols = define_protocols(
         fitness_calculator_configuration,
         include_validation_protocols,
         stochasticity,
         use_fixed_dt_recordings,
+        dt,
     )
 
     efeatures = define_efeatures(
@@ -581,7 +595,7 @@ def get_simulator(stochasticity, cell_model, dt=None, mechanisms_directory=None,
     Args:
         stochasticity (bool): allow the use of simulator for stochastic channels
         cell_model (CellModel): used to check if any stochastic channels are present
-        dt (float): if not None, cvode will be disabled and fixed timesteps used.
+        dt (float): NEURON dt for fixed time step simulation. If None, variable dt will be used.
         mechanisms_directory (str or Path): path to the directory containing the mechanisms
         cvode_minstep (float): minimum time step allowed for a CVODE step.
     """
@@ -639,7 +653,8 @@ def create_evaluator(
         include_validation_protocols (bool): should the validation protocols
             and validation efeatures be added to the evaluator.
         mechanisms_directory (str or Path): path to the directory containing the mechanisms.
-        use_fixed_dt_recordings (bool): whether to record at a fixed dt of 0.1 ms.
+        use_fixed_dt_recordings (bool): used for legacy currentscape
+            to record at a fixed dt of 0.1 ms.
 
     Returns:
         CellEvaluator
@@ -673,6 +688,7 @@ def create_evaluator(
             max_depth_holding_search=pipeline_settings.max_depth_holding_search,
             max_depth_threshold_search=pipeline_settings.max_depth_threshold_search,
             spikecount_timeout=pipeline_settings.spikecount_timeout,
+            dt=pipeline_settings.neuron_dt,
         )
     else:
         main_protocol, features = define_optimisation_protocol(
@@ -681,6 +697,7 @@ def create_evaluator(
             stochasticity=stochasticity,
             efel_settings=pipeline_settings.efel_settings,
             use_fixed_dt_recordings=use_fixed_dt_recordings,
+            dt=pipeline_settings.neuron_dt,
         )
 
     fitness_calculator = define_fitness_calculator(features)