partial fix

emodel_generalisation/bluecellulab_evaluator.py

@@ -9,6 +9,7 @@
 import efel
 from bluecellulab.simulation.neuron_globals import NeuronGlobals
 from bluepyparallel.evaluator import evaluate
+
 from emodel_generalisation.utils import isolate
 
 logger = logging.getLogger(__name__)

emodel_generalisation/model/bpopt.py

@@ -902,7 +902,7 @@ def __init__(
             name=f"{name}.spike_count_stimint",
             efel_feature_name="spike_count_stimint",
             recording_names={"": f"{name}.{location.name}.v"},
-            stim_start=500,  # discard begining to allow for a couple of initial APs
+            stim_start=500,  # discard beginning to allow for a couple of initial APs
             stim_end=2000,
             exp_mean=1,
             exp_std=0.1,

emodel_generalisation/utils.py

@@ -25,14 +25,14 @@
 from functools import partial
 from hashlib import sha256
 from itertools import cycle
-from pathlib import Path
 from multiprocessing.context import TimeoutError  # pylint: disable=redefined-builtin
-from bluepyparallel.parallel import NestedPool
+from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 from bluepyopt.ephys.responses import TimeVoltageResponse
+from bluepyparallel.parallel import NestedPool
 from matplotlib.backends.backend_pdf import PdfPages
 from scipy.cluster.hierarchy import dendrogram
 from scipy.cluster.hierarchy import linkage

tests/data/adapt_df.csv

@@ -1,7 +1,7 @@
-Unnamed: 0,mtype,layer,morphology,synapse_class,morph_class,hemisphere,etype,model_template,region,x,y,z,orientation,emodel,ais_scaler,soma_scaler,ais_model,soma_model
-1,L5_TPC:A,5,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,EXC,PYR,right,generic,hoc:generic_model,MOs@right,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
+Unnamed: 0,morph_class,mtype,morphology,model_template,region,synapse_class,layer,hemisphere,etype,x,y,z,orientation,emodel,ais_scaler,soma_scaler,ais_model,soma_model
+1,PYR,L5_TPC:A,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,hoc:generic_model,MOs@right,EXC,5,right,generic,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,1.0,1.0,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_surface"": 1167.714655051592, ""soma_radius"": 10.0}"
-2,L5_TPC:A,5,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,EXC,PYR,right,generic,hoc:generic_model,MOp@right,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
+ [0. 0. 1.]]",generic_model,1.1,1.1,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_surface"": 1167.714655051592, ""soma_radius"": 10.0}"
+2,PYR,L5_TPC:A,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,hoc:generic_model,MOp@right,EXC,5,right,generic,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,1.0,1.0,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_surface"": 1167.714655051592, ""soma_radius"": 10.0}"
+ [0. 0. 1.]]",generic_model,1.1,1.1,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_surface"": 1167.714655051592, ""soma_radius"": 10.0}"

tests/data/adapted_evaluation_df.csv

@@ -1,7 +1,7 @@
-etype,region,morph_class,mtype,morphology,synapse_class,hemisphere,model_template,layer,ais_scaler,soma_scaler,x,y,z,orientation,emodel,ais_model,soma_model,exception,features,scores,trace_data
-generic,MOs@right,PYR,L5_TPC:A,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,EXC,right,hoc:generic_model,5,1.0,1.0,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
+morph_class,mtype,morphology,model_template,region,synapse_class,layer,hemisphere,etype,ais_scaler,soma_scaler,x,y,z,orientation,emodel,ais_model,soma_model,exception,features,scores,trace_data
+PYR,L5_TPC:A,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,hoc:generic_model,MOs@right,EXC,5,right,generic,1.1,1.1,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 20.828084320123192, ""IDRest_150.soma.v.AP_amplitude"": 53.56395753781952, ""IDRest_200.soma.v.mean_frequency"": 27.934388253898348, ""IDRest_200.soma.v.AP_amplitude"": 53.779478010796346, ""IDRest_280.soma.v.mean_frequency"": 36.7291061470728, ""IDRest_280.soma.v.AP_amplitude"": 53.85104717835058, ""RMPProtocol.soma.v.voltage_base"": -69.31069436808355, ""RMPProtocol.soma.v.Spikecount"": 5.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.053125000000000006, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.0598896226535, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 171.29380609396492, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.052856673215615144}","{""IDRest_150.soma.v.mean_frequency"": 2.914042160061596, ""IDRest_150.soma.v.AP_amplitude"": 8.218021231090244, ""IDRest_200.soma.v.mean_frequency"": 3.967194126949174, ""IDRest_200.soma.v.AP_amplitude"": 8.110260994601823, ""IDRest_280.soma.v.mean_frequency"": 5.864553073536399, ""IDRest_280.soma.v.AP_amplitude"": 8.07447641082471, ""RMPProtocol.soma.v.voltage_base"": 1.5378611263832909, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.09375, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.059889622653500396, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.287061939060351, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.8571334643123028}",
-generic,MOp@right,PYR,L5_TPC:A,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,EXC,right,hoc:generic_model,5,1.0,1.0,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
+ [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 17.570535563419252, ""IDRest_150.soma.v.AP_amplitude"": 55.39737419147699, ""IDRest_200.soma.v.mean_frequency"": 24.347355606626557, ""IDRest_200.soma.v.AP_amplitude"": 55.783184825944716, ""IDRest_280.soma.v.mean_frequency"": 32.55285600443829, ""IDRest_280.soma.v.AP_amplitude"": 55.9149320756509, ""RMPProtocol.soma.v.voltage_base"": -70.28549140927481, ""RMPProtocol.soma.v.Spikecount"": 5.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.053125000000000006, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.00777720496266, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 169.91847638730917, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.046635434877685934}","{""IDRest_150.soma.v.mean_frequency"": 1.285267781709626, ""IDRest_150.soma.v.AP_amplitude"": 7.301312904261504, ""IDRest_200.soma.v.mean_frequency"": 2.1736778033132786, ""IDRest_200.soma.v.AP_amplitude"": 7.108407587027645, ""IDRest_280.soma.v.mean_frequency"": 3.776428002219145, ""IDRest_280.soma.v.AP_amplitude"": 7.0425339621745495, ""RMPProtocol.soma.v.voltage_base"": 1.3429017181450376, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.09375, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.007777204962664541, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.3008152361269083, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.7327086975537186}",
+PYR,L5_TPC:A,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,hoc:generic_model,MOp@right,EXC,5,right,generic,1.1,1.1,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 18.211250505846717, ""IDRest_150.soma.v.AP_amplitude"": 51.5181063546671, ""IDRest_200.soma.v.mean_frequency"": 25.946536478752243, ""IDRest_200.soma.v.AP_amplitude"": 51.814606368747036, ""IDRest_280.soma.v.mean_frequency"": 35.25901817191464, ""IDRest_280.soma.v.AP_amplitude"": 51.92412071915578, ""RMPProtocol.soma.v.voltage_base"": -76.82035872240675, ""RMPProtocol.soma.v.Spikecount"": 6.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.06796875000000001, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.01598241401135, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 149.80419034227666, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.05688690378340191}","{""IDRest_150.soma.v.mean_frequency"": 1.6056252529233586, ""IDRest_150.soma.v.AP_amplitude"": 9.240946822666452, ""IDRest_200.soma.v.mean_frequency"": 2.9732682393761216, ""IDRest_200.soma.v.AP_amplitude"": 9.092696815626486, ""IDRest_280.soma.v.mean_frequency"": 5.12950908595732, ""IDRest_280.soma.v.AP_amplitude"": 9.037939640422106, ""RMPProtocol.soma.v.voltage_base"": 0.030766, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.0640625, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.015982414011347146, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.501958096577233, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.9377380756680381}",
+ [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 19.51974691636182, ""IDRest_150.soma.v.AP_amplitude"": 53.64663901095507, ""IDRest_200.soma.v.mean_frequency"": 26.99191929412969, ""IDRest_200.soma.v.AP_amplitude"": 53.955235597646244, ""IDRest_280.soma.v.mean_frequency"": 36.01800900445903, ""IDRest_280.soma.v.AP_amplitude"": 54.06750345591785, ""RMPProtocol.soma.v.voltage_base"": -78.16946608707919, ""RMPProtocol.soma.v.Spikecount"": 6.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.06875, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.09902934622046, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 147.51245669415312, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.060956196156172524}","{""IDRest_150.soma.v.mean_frequency"": 2.259873458180911, ""IDRest_150.soma.v.AP_amplitude"": 8.176680494522463, ""IDRest_200.soma.v.mean_frequency"": 3.4959596470648453, ""IDRest_200.soma.v.AP_amplitude"": 8.022382201176882, ""IDRest_280.soma.v.mean_frequency"": 5.509004502229516, ""IDRest_280.soma.v.AP_amplitude"": 7.96624827204107, ""RMPProtocol.soma.v.voltage_base"": 0.2338932174158373, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.0625, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.09902934622046189, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.524875433058469, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 1.0191239231234503}",

tests/data/evaluation_df.csv

@@ -1,7 +1,7 @@
-mtype,etype,model_template,morph_class,synapse_class,layer,region,hemisphere,morphology,x,y,z,orientation,emodel,ais_model,soma_model,exception,features,scores,trace_data
-L5_TPC:A,generic,hoc:generic_model,PYR,EXC,5,MOs@right,right,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
+morph_class,mtype,morphology,model_template,region,synapse_class,layer,hemisphere,etype,x,y,z,orientation,emodel,exception,features,scores,trace_data
+PYR,L5_TPC:A,hashed/be/fb/befbcea89657fdd07ae181b977b9e320,hoc:generic_model,MOs@right,EXC,5,right,generic,3887.062211566772,1924.0204607290975,6775.602532718369,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 17.01809022989483, ""IDRest_150.soma.v.AP_amplitude"": 57.74731715766996, ""IDRest_200.soma.v.mean_frequency"": 24.038862828210206, ""IDRest_200.soma.v.AP_amplitude"": 58.078713635979184, ""IDRest_280.soma.v.mean_frequency"": 32.58766421123901, ""IDRest_280.soma.v.AP_amplitude"": 58.245488451959865, ""RMPProtocol.soma.v.voltage_base"": -66.35232862203746, ""RMPProtocol.soma.v.Spikecount"": 5.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.051562500000000004, ""SearchHoldingCurrent.soma.v.voltage_base"": -82.94181734045071, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 179.45614761441178, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.043736971847982836}","{""IDRest_150.soma.v.mean_frequency"": 1.0090451149474156, ""IDRest_150.soma.v.AP_amplitude"": 6.126341421165019, ""IDRest_200.soma.v.mean_frequency"": 2.019431414105103, ""IDRest_200.soma.v.AP_amplitude"": 5.960643182010407, ""IDRest_280.soma.v.mean_frequency"": 3.7938321056195043, ""IDRest_280.soma.v.AP_amplitude"": 5.877255774020064, ""RMPProtocol.soma.v.voltage_base"": 2.1295342755925075, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.096875, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.058182659549288473, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.2054385238558827, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.6747394369596567}",
-L5_TPC:A,generic,hoc:generic_model,PYR,EXC,5,MOp@right,right,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
+ [0. 0. 1.]]",generic_model,,"{""IDRest_150.soma.v.mean_frequency"": 17.01809022989483, ""IDRest_150.soma.v.AP_amplitude"": 57.74731715766996, ""IDRest_200.soma.v.mean_frequency"": 24.038862828210206, ""IDRest_200.soma.v.AP_amplitude"": 58.078713635979184, ""IDRest_280.soma.v.mean_frequency"": 32.58766421123901, ""IDRest_280.soma.v.AP_amplitude"": 58.245488451959865, ""RMPProtocol.soma.v.voltage_base"": -66.35232862203746, ""RMPProtocol.soma.v.Spikecount"": 5.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.051562500000000004, ""SearchHoldingCurrent.soma.v.voltage_base"": -82.94169679712304, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 179.45614761441178, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.043736971847982836}","{""IDRest_150.soma.v.mean_frequency"": 1.0090451149474156, ""IDRest_150.soma.v.AP_amplitude"": 6.126341421165019, ""IDRest_200.soma.v.mean_frequency"": 2.019431414105103, ""IDRest_200.soma.v.AP_amplitude"": 5.960643182010407, ""IDRest_280.soma.v.mean_frequency"": 3.7938321056195043, ""IDRest_280.soma.v.AP_amplitude"": 5.877255774020064, ""RMPProtocol.soma.v.voltage_base"": 2.1295342755925075, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.096875, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.05830320287695656, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.2054385238558827, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.6747394369596567}",
+PYR,L5_TPC:A,hashed/d6/a9/d6a9976c7588ae0111f17f28e39a1e6d,hoc:generic_model,MOp@right,EXC,5,right,generic,6291.256509715739,1139.1852640664094,6812.970413610967,"[[1. 0. 0.]
  [0. 1. 0.]
- [0. 0. 1.]]",generic_model,"{""popt"": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}","{""soma_radius"": 10.0, ""soma_surface"": 1167.714655051592}",,"{""IDRest_150.soma.v.mean_frequency"": 21.307672480429662, ""IDRest_150.soma.v.AP_amplitude"": 51.276480916739004, ""IDRest_200.soma.v.mean_frequency"": 30.406432649716162, ""IDRest_200.soma.v.AP_amplitude"": 51.25679986852141, ""IDRest_280.soma.v.mean_frequency"": 41.679271284949614, ""IDRest_280.soma.v.AP_amplitude"": 50.94403679026918, ""RMPProtocol.soma.v.voltage_base"": -72.26510227533872, ""RMPProtocol.soma.v.Spikecount"": 6.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.06718750000000001, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.08857871429298, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 155.80389971422335, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.059734491885581026}","{""IDRest_150.soma.v.mean_frequency"": 3.153836240214831, ""IDRest_150.soma.v.AP_amplitude"": 9.361759541630494, ""IDRest_200.soma.v.mean_frequency"": 5.203216324858081, ""IDRest_200.soma.v.AP_amplitude"": 9.37160006573929, ""IDRest_280.soma.v.mean_frequency"": 8.339635642474807, ""IDRest_280.soma.v.AP_amplitude"": 9.52798160486541, ""RMPProtocol.soma.v.voltage_base"": 0.9469795449322561, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.06562499999999999, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.08857871429297859, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.4419610028577665, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.9946898377116205}",
+ [0. 0. 1.]]",generic_model,,"{""IDRest_150.soma.v.mean_frequency"": 21.307672480429662, ""IDRest_150.soma.v.AP_amplitude"": 51.276480916739004, ""IDRest_200.soma.v.mean_frequency"": 30.406432649716162, ""IDRest_200.soma.v.AP_amplitude"": 51.25679986852141, ""IDRest_280.soma.v.mean_frequency"": 41.679271284949614, ""IDRest_280.soma.v.AP_amplitude"": 50.94403679026918, ""RMPProtocol.soma.v.voltage_base"": -72.26510227533872, ""RMPProtocol.soma.v.Spikecount"": 6.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": -0.06718750000000001, ""SearchHoldingCurrent.soma.v.voltage_base"": -83.08653117477492, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 155.80389971422335, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.059734491885581026}","{""IDRest_150.soma.v.mean_frequency"": 3.153836240214831, ""IDRest_150.soma.v.AP_amplitude"": 9.361759541630494, ""IDRest_200.soma.v.mean_frequency"": 5.203216324858081, ""IDRest_200.soma.v.AP_amplitude"": 9.37160006573929, ""IDRest_280.soma.v.mean_frequency"": 8.339635642474807, ""IDRest_280.soma.v.AP_amplitude"": 9.52798160486541, ""RMPProtocol.soma.v.voltage_base"": 0.9469795449322561, ""RMPProtocol.soma.v.Spikecount"": 250.0, ""SearchHoldingCurrent.soma.v.bpo_holding_current"": 0.06562499999999999, ""SearchHoldingCurrent.soma.v.voltage_base"": 0.0865311747749189, ""RinProtocol.soma.v.ohmic_input_resistance_vb_ssse"": 3.4419610028577665, ""SearchThresholdCurrent.soma.v.bpo_threshold_current"": 0.9946898377116205}",

tests/test_cli.py

@@ -66,7 +66,7 @@ def test_compute_currents(cli_runner, tmpdir):
 
 
 def test_evaluate(cli_runner, tmpdir):
-    """Tetst cli evaluate."""
+    """Test cli evaluate."""
     # fmt: off
     response = cli_runner.invoke(
         tested.cli,

tests/test_evaluation.py

@@ -39,8 +39,8 @@ def test_feature_evaluation(morphs_combos_df, access_point):
         "IDRest_280.soma.v.AP_amplitude": 0.4711507560288358,
         "RMPProtocol.soma.v.voltage_base": 0.33131119446020707,
         "RMPProtocol.soma.v.Spikecount": 0.0,
-        "SearchHoldingCurrent.soma.v.bpo_holding_current": 0.18281250000000002,
-        "SearchHoldingCurrent.soma.v.voltage_base": 0.043970045446585004,
+        "SearchHoldingCurrent.soma.v.bpo_holding_current": 0.1828125,
+        "SearchHoldingCurrent.soma.v.voltage_base": 0.038499,
         "RinProtocol.soma.v.ohmic_input_resistance_vb_ssse": 0.17312024013731503,
         "SearchThresholdCurrent.soma.v.bpo_threshold_current": 0.10935385147499851,
     }
@@ -84,7 +84,7 @@ def test_evaluate_soma_rin(morphs_combos_df, access_point):
 def test_evaluate_ais_rin(morphs_combos_df, access_point):
     """ """
     df = evaluation.evaluate_ais_rin(morphs_combos_df, access_point)
-    assert_allclose(df.loc[0, "rin_ais"], 90942.204436, rtol=1e-5)
+    assert_allclose(df.loc[0, "rin_ais"], 131668.995389, rtol=1e-5)
 
 
 def test_evaluate_somadend_rin(morphs_combos_df, access_point):
@@ -102,4 +102,4 @@ def test_evaluate_rho(morphs_combos_df, access_point):
 def test_evaluate_rho_axon(morphs_combos_df, access_point):
     """ """
     df = evaluation.evaluate_rho_axon(morphs_combos_df, access_point)
-    assert_allclose(df.loc[0, "rho_axon"], 168.681031, rtol=1e-5)
+    assert_allclose(df.loc[0, "rho_axon"], 244.221723, rtol=1e-5)