diff --git a/emodel_generalisation/bluecellulab_evaluator.py b/emodel_generalisation/bluecellulab_evaluator.py index 4fbe8e8..31fe557 100644 --- a/emodel_generalisation/bluecellulab_evaluator.py +++ b/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), ) diff --git a/emodel_generalisation/model/bpopt.py b/emodel_generalisation/model/bpopt.py index a12ed61..93a9513 100644 --- a/emodel_generalisation/model/bpopt.py +++ b/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): diff --git a/emodel_generalisation/model/evaluation.py b/emodel_generalisation/model/evaluation.py index dfa3481..d52af38 100644 --- a/emodel_generalisation/model/evaluation.py +++ b/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), ) diff --git a/setup.py b/setup.py index 21bd3a2..b4e5f84 100644 --- a/setup.py +++ b/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",