Somatic validation evaluator (#9)

* add initial evaluator validation scripts

* remove unused stimuli in stimuli.py

* use NrnHDPulse from local stimuli file

* format somatic val evaluator scripts

* rename evaluator_validation -> evaluator

* use "step" key to access stimulus definition instead of "stimuli"

* provide start stop times of idthresh protocol

* add mechanisms to somatic_validation

* adapt evaluator.py to bpe2 output format

* add initial somatic validation script

* simplify protocol_name comparison

* remove bAP checks from evaluator

* arrange imports in model.py

* correct etype name L5PC->L5TPC

* update feature extraction tests after handling noisy current data

* remove unused variables from write_corrected_protocols

* create a function to get_model_threshold

* add protocol's amplitude correction

* beautify  models_thresh_all_pyr.json

* add somatic validation feature extraction output

* don't extract per-cell in somatic val

* create objectives in validation

* update .gitignore

* move model_thresh and opt_thresh inside write_corrected prots

* add main function to validation.py

* add initial somatic validation notebook

* use long_amp for depol and amp for step_amplitude

* compute stimulus duration by toff-ton, don't read from file

* evaluator compute duration_of_depol2

* update protocols & features to be used in som_val

* add test_somatic_validation

* remove duplication between IDhyperpol and sAHP

* rename requirements.txt -> somatic-val-requirements.txt

* ci compile mechanisms before somatic val

* compare validation results feature by feature

Author: anilbey

.github/workflows/python-app.yml

@@ -94,7 +94,8 @@ jobs:
       run: |
         pip install -r test-requirements.txt
         cd somatic_validation
-        pip install -r requirements.txt
+        pip install -r somatic-val-requirements.txt
+        nrnivmodl mechanisms
         pytest -sx tests
 
   code-style:

.gitignore

@@ -16,6 +16,6 @@ model_management/mm_run_minimal/output_select
 model_management/mm_run_minimal/tests/tmp
 model_management/mm_run_minimal/tests/output
 model_management/mm_run_minimal/tests/output_select
-somatic_validation/L5PC
-somatic_validation/test_L5PC
+somatic_validation/L5TPC/*.pdf
+somatic_validation/test_L5TPC
 *.DS_Store