Fix: Fix NO_PROGRESS (#47)

emodel_generalisation/bluecellulab_evaluator.py

@@ -1,5 +1,7 @@
 """Compute the threshold and holding current using bluecellulab, adapted from BluePyThresh."""
+
 import logging
+import os
 from copy import copy
 from multiprocessing.context import TimeoutError  # pylint: disable=redefined-builtin
 from pathlib import Path
@@ -325,4 +327,5 @@ def evaluate_currents(
             "timeout": timeout,
             "only_rin": only_rin,
         },
+        progress_bar=os.environ.get("NO_PROGRESS", False),
     )

emodel_generalisation/model/bpopt.py

@@ -113,7 +113,8 @@ def calculate_bpo_score(self, responses):
 
         if feature_value is None:
             return self.max_score
-
+        if self.efel_feature_name == "peak_voltage":
+            print(feature_value, self.exp_mean, self.exp_std)
         return abs(feature_value - self.exp_mean) / self.exp_std
 
     def _construct_efel_trace(self, responses):

emodel_generalisation/model/evaluation.py

@@ -1922,6 +1922,7 @@ def feature_evaluation(
             resume=resume,
             parallel_factory=parallel_factory,
             db_url=db_url,
+            progress_bar=os.environ.get("NO_PROGRESS", False),
         )
         .sort_values(by="index")
         .set_index("index")
@@ -2033,6 +2034,7 @@ def evaluate_rin_no_soma(
         resume=resume,
         parallel_factory=parallel_factory,
         db_url=db_url,
+        progress_bar=os.environ.get("NO_PROGRESS", False),
     )
 
 
@@ -2075,6 +2077,7 @@ def evaluate_soma_rin(
         resume=resume,
         parallel_factory=parallel_factory,
         db_url=db_url,
+        progress_bar=os.environ.get("NO_PROGRESS", False),
     )
 
 
@@ -2117,6 +2120,7 @@ def evaluate_ais_rin(
         resume=resume,
         parallel_factory=parallel_factory,
         db_url=db_url,
+        progress_bar=os.environ.get("NO_PROGRESS", False),
     )
 
 
@@ -2157,6 +2161,7 @@ def evaluate_somadend_rin(
         resume=resume,
         parallel_factory=parallel_factory,
         db_url=db_url,
+        progress_bar=os.environ.get("NO_PROGRESS", False),
     )
 
 

setup.py

@@ -43,7 +43,7 @@
     "xgboost>=1.7.5,<2",
     "pyyaml>=6",
     "datareuse>=0.0.3",
-    "bluepyparallel>=0.2.1",
+    "bluepyparallel>=0.2.2",
     "bluecellulab>=1.7.6,<=2.3.1",
     "voxcell>=3.1.5",
     "efel>=5.5.5",