code style update

model_management/mm_run_minimal/emodels_dir/singlecell-optimization/setup/__init__.py

@@ -17,8 +17,10 @@
 To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/legalcode or send a letter to Creative Commons, 171
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
+
 from neuron import h
-if hasattr(h, 'nrnunit_use_legacy'):
+
+if hasattr(h, "nrnunit_use_legacy"):
     h.nrnunit_use_legacy(True)
 from . import evaluator
 from . import template

model_management/mm_run_minimal/emodels_dir/singlecell-optimization/setup/evaluator.py

@@ -405,14 +405,16 @@ def define_protocols(
                 "type" in protocol_definition
                 and protocol_definition["type"] == "RatSSCxThresholdDetectionProtocol"
             ):
-                protocols_dict[
-                    "ThresholdDetection"
-                ] = protocols.RatSSCxThresholdDetectionProtocol(
-                    "IDRest",
-                    step_protocol_template=read_step_protocol(
-                        "Threshold", protocol_definition["step_template"], recordings
-                    ),
-                    prefix=prefix,
+                protocols_dict["ThresholdDetection"] = (
+                    protocols.RatSSCxThresholdDetectionProtocol(
+                        "IDRest",
+                        step_protocol_template=read_step_protocol(
+                            "Threshold",
+                            protocol_definition["step_template"],
+                            recordings,
+                        ),
+                        prefix=prefix,
+                    )
                 )
             else:
                 stimuli = []
@@ -488,7 +490,6 @@ def calculate_score(self, responses, trace_check=False):
 
 
 class eFELFeatureExtra(eFELFeature):
-
     """eFEL feature extra"""
 
     SERIALIZED_FIELDS = (
@@ -647,7 +648,6 @@ def calculate_score(self, responses, trace_check=False):
 
 
 class SingletonWeightObjective(EFeatureObjective):
-
     """Single EPhys feature"""
 
     def __init__(self, name, feature, weight):
@@ -775,7 +775,6 @@ def define_fitness_calculator(
 
 
 class MultiEvaluator(bpopt.evaluators.Evaluator):
-
     """Multiple cell evaluator"""
 
     def __init__(

model_management/mm_run_minimal/emodels_dir/singlecell-optimization/setup/protocols.py

@@ -38,7 +38,6 @@
 
 
 class RatSSCxMainProtocol(ephys.protocols.Protocol):
-
     """Main protocol to fit RatSSCx neuron ephys parameters.
 
     Pseudo code:
@@ -193,7 +192,6 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
 
 
 class RatSSCxRinHoldcurrentProtocol(ephys.protocols.Protocol):
-
     """IDRest protocol to fit RatSSCx neuron ephys parameters"""
 
     def __init__(
@@ -385,7 +383,6 @@ def voltage_base(self, current, cell_model, param_values, sim=None, short=False)
 
 
 class RatSSCxThresholdDetectionProtocol(ephys.protocols.Protocol):
-
     """IDRest protocol to fit RatSSCx neuron ephys parameters"""
 
     def __init__(
@@ -641,7 +638,6 @@ def search_spike_threshold(
 
 
 class StepProtocol(ephys.protocols.SweepProtocol):
-
     """Protocol consisting of step and holding current"""
 
     def __init__(
@@ -665,9 +661,11 @@ def __init__(
 
         super(StepProtocol, self).__init__(
             name,
-            stimuli=step_stimuli + [holding_stimulus]
-            if holding_stimulus is not None
-            else step_stimuli,
+            stimuli=(
+                step_stimuli + [holding_stimulus]
+                if holding_stimulus is not None
+                else step_stimuli
+            ),
             recordings=recordings,
             cvode_active=cvode_active,
         )
@@ -752,7 +750,6 @@ def step_amplitude(self):
 
 
 class StepThresholdProtocol(StepProtocol):
-
     """Step protocol based on threshold"""
 
     def __init__(

model_management/mm_run_minimal/emodels_dir/singlecell-optimization/setup/template.py

@@ -122,12 +122,12 @@ def define_parameters(params_filename, stage=None, past_params=None):
             dist_param_names = definition["parameters"]
         else:
             dist_param_names = None
-        distributions[
-            distribution
-        ] = ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
-            name=distribution,
-            distribution=definition["fun"],
-            dist_param_names=dist_param_names,
+        distributions[distribution] = (
+            ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
+                name=distribution,
+                distribution=definition["fun"],
+                dist_param_names=dist_param_names,
+            )
         )
 
     params_definitions = definitions["parameters"]

model_management/mm_run_minimal/tests/test_model_management.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 """Test to validate the model management output."""
 
 from pathlib import Path

optimization/opt_module/setup/__init__.py

@@ -17,8 +17,10 @@
 To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/legalcode or send a letter to Creative Commons, 171
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
+
 from neuron import h
-if hasattr(h, 'nrnunit_use_legacy'):
+
+if hasattr(h, "nrnunit_use_legacy"):
     h.nrnunit_use_legacy(True)
 
 from . import evaluator

optimization/opt_module/setup/evaluator.py

@@ -408,14 +408,16 @@ def define_protocols(
                 "type" in protocol_definition
                 and protocol_definition["type"] == "RatSSCxThresholdDetectionProtocol"
             ):
-                protocols_dict[
-                    "ThresholdDetection"
-                ] = protocols.RatSSCxThresholdDetectionProtocol(
-                    "IDRest",
-                    step_protocol_template=read_step_protocol(
-                        "Threshold", protocol_definition["step_template"], recordings
-                    ),
-                    prefix=prefix,
+                protocols_dict["ThresholdDetection"] = (
+                    protocols.RatSSCxThresholdDetectionProtocol(
+                        "IDRest",
+                        step_protocol_template=read_step_protocol(
+                            "Threshold",
+                            protocol_definition["step_template"],
+                            recordings,
+                        ),
+                        prefix=prefix,
+                    )
                 )
             else:
                 stimuli = []
@@ -491,7 +493,6 @@ def calculate_score(self, responses, trace_check=False):
 
 
 class eFELFeatureExtra(eFELFeature):
-
     """eFEL feature extra"""
 
     SERIALIZED_FIELDS = (
@@ -666,7 +667,6 @@ def calculate_score(self, responses, trace_check=False):
 
 
 class SingletonWeightObjective(EFeatureObjective):
-
     """Single EPhys feature"""
 
     def __init__(self, name, feature, weight):
@@ -794,7 +794,6 @@ def define_fitness_calculator(
 
 
 class MultiEvaluator(bpopt.evaluators.Evaluator):
-
     """Multiple cell evaluator"""
 
     def __init__(

optimization/opt_module/setup/protocols.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 """Protocols involved in fitting of RatSSCx neuron ephys parameters"""
 
 import numpy
@@ -45,7 +44,6 @@
 
 
 class RatSSCxMainProtocol(ephys.protocols.Protocol):
-
     """Main protocol to fit RatSSCx neuron ephys parameters.
 
     Pseudo code:
@@ -220,7 +218,6 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
 
 
 class RatSSCxRinHoldcurrentProtocol(ephys.protocols.Protocol):
-
     """IDRest protocol to fit RatSSCx neuron ephys parameters"""
 
     def __init__(
@@ -424,7 +421,6 @@ def voltage_base(self, current, cell_model, param_values, sim=None, short=False)
 
 
 class RatSSCxThresholdDetectionProtocol(ephys.protocols.Protocol):
-
     """IDRest protocol to fit RatSSCx neuron ephys parameters"""
 
     def __init__(
@@ -704,7 +700,6 @@ def search_spike_threshold(
 
 
 class StepProtocol(ephys.protocols.SweepProtocol):
-
     """Protocol consisting of step and holding current"""
 
     def __init__(
@@ -728,9 +723,11 @@ def __init__(
 
         super(StepProtocol, self).__init__(
             name,
-            stimuli=step_stimuli + [holding_stimulus]
-            if holding_stimulus is not None
-            else step_stimuli,
+            stimuli=(
+                step_stimuli + [holding_stimulus]
+                if holding_stimulus is not None
+                else step_stimuli
+            ),
             recordings=recordings,
             cvode_active=cvode_active,
         )
@@ -815,7 +812,6 @@ def step_amplitude(self):
 
 
 class StepThresholdProtocol(StepProtocol):
-
     """Step protocol based on threshold"""
 
     def __init__(

optimization/opt_module/setup/template.py

@@ -130,12 +130,12 @@ def define_parameters(params_filename, stage=None, past_params=None):
             dist_param_names = definition["parameters"]
         else:
             dist_param_names = None
-        distributions[
-            distribution
-        ] = ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
-            name=distribution,
-            distribution=definition["fun"],
-            dist_param_names=dist_param_names,
+        distributions[distribution] = (
+            ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
+                name=distribution,
+                distribution=definition["fun"],
+                dist_param_names=dist_param_names,
+            )
         )
 
     params_definitions = definitions["parameters"]

optimization/opt_module/tools/plot.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 import numpy
 import seaborn as sns
 import pandas as pd

optimization/opt_module/tools/plottools.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 import matplotlib
 import matplotlib.pyplot as plt
 

somatic_validation/model.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 import os
 import collections
 import json
@@ -110,12 +109,12 @@ def define_parameters(path_params):
             dist_param_names = definition["parameters"]
         else:
             dist_param_names = None
-        distributions[
-            distribution
-        ] = ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
-            name=distribution,
-            distribution=definition["fun"],
-            dist_param_names=dist_param_names,
+        distributions[distribution] = (
+            ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
+                name=distribution,
+                distribution=definition["fun"],
+                dist_param_names=dist_param_names,
+            )
         )
 
     params_definitions = definitions["parameters"]

somatic_validation/stimuli.py

@@ -28,14 +28,12 @@
 
 
 class Stimulus(object):
-
     """Stimulus protocol"""
 
     pass
 
 
 class NrnHDPulse(Stimulus):
-
     """Square pulse current clamp injection"""
 
     def __init__(

validation/lib/attenuation.py

@@ -826,7 +826,6 @@ def EPSP(evaluator, emodels_path, points):
 
 
 class NrnSynStim(ephys.stimuli.Stimulus):
-
     """Square pulse current clamp injection"""
 
     def __init__(

validation/lib/plottools.py

@@ -18,7 +18,6 @@
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
 
-
 import matplotlib
 import matplotlib.pyplot as plt
 

validation/lib/setup/__init__.py

@@ -17,4 +17,5 @@
 To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/legalcode or send a letter to Creative Commons, 171
 Second Street, Suite 300, San Francisco, California, 94105, USA.
 """
+
 from . import evaluator