Feat: Use BluePyParallel (#42)

emodel_generalisation/adaptation.py

@@ -29,6 +29,7 @@
 import numpy as np
 import pandas as pd
 import seaborn as sns
+from bluepyparallel import evaluate
 from matplotlib.backends.backend_pdf import PdfPages
 from numpy.polynomial import Polynomial
 from scipy.signal import cspline2d
@@ -41,7 +42,6 @@
 from emodel_generalisation.model.evaluation import rin_evaluation
 from emodel_generalisation.model.modifiers import remove_axon
 from emodel_generalisation.model.modifiers import remove_soma
-from emodel_generalisation.parallel import evaluate
 from emodel_generalisation.utils import FEATURE_FILTER
 from emodel_generalisation.utils import get_scores
 

emodel_generalisation/bluecellulab_evaluator.py

@@ -6,9 +6,8 @@
 
 import bluecellulab
 import efel
-
-from emodel_generalisation.parallel.evaluator import evaluate
-from emodel_generalisation.parallel.parallel import NestedPool
+from bluepyparallel.evaluator import evaluate
+from bluepyparallel.parallel import NestedPool
 
 logger = logging.getLogger(__name__)
 AXON_LOC = "self.axonal[1](0.5)._ref_v"

emodel_generalisation/cli.py

@@ -13,6 +13,7 @@
 import pandas as pd
 import seaborn as sns
 import yaml
+from bluepyparallel import init_parallel_factory
 from datareuse import Reuse
 from matplotlib.backends.backend_pdf import PdfPages
 from morphio import Morphology
@@ -32,7 +33,6 @@
 from emodel_generalisation.model.evaluation import evaluate_rho_axon
 from emodel_generalisation.model.evaluation import feature_evaluation
 from emodel_generalisation.model.modifiers import get_replace_axon_hoc
-from emodel_generalisation.parallel import init_parallel_factory
 from emodel_generalisation.utils import FEATURE_FILTER
 from emodel_generalisation.utils import get_feature_df
 from emodel_generalisation.utils import get_score_df

emodel_generalisation/mcmc.py

@@ -31,6 +31,8 @@
 import numpy as np
 import pandas as pd
 import seaborn as sns
+from bluepyparallel import evaluate
+from bluepyparallel import init_parallel_factory
 from matplotlib.backends.backend_pdf import PdfPages
 from mpl_toolkits import axisartist
 from scipy.spatial import distance_matrix
@@ -45,8 +47,6 @@
 from emodel_generalisation.information import rsi_gaussian
 from emodel_generalisation.model.access_point import AccessPoint
 from emodel_generalisation.model.evaluation import get_evaluator_from_access_point
-from emodel_generalisation.parallel import evaluate
-from emodel_generalisation.parallel import init_parallel_factory
 from emodel_generalisation.utils import cluster_matrix
 
 # pylint: disable=too-many-lines,too-many-locals

emodel_generalisation/model/evaluation.py

@@ -42,12 +42,12 @@
 from bluepyopt.ephys.objectives import SingletonObjective
 from bluepyopt.ephys.objectivescalculators import ObjectivesCalculator
 from bluepyopt.ephys.simulators import NrnSimulator
+from bluepyparallel import evaluate
+from bluepyparallel.parallel import NestedPool
 
 from emodel_generalisation.model import bpopt
 from emodel_generalisation.model import modifiers
 from emodel_generalisation.model.ecodes import eCodes
-from emodel_generalisation.parallel import evaluate
-from emodel_generalisation.parallel.parallel import NestedPool
 
 # pylint: disable=too-many-lines
 

emodel_generalisation/morph_utils.py

@@ -27,6 +27,7 @@
 import numpy as np
 import pandas as pd
 import yaml
+from bluepyparallel.evaluator import evaluate
 from diameter_synthesis import build_diameters
 from diameter_synthesis import build_models
 from diameter_synthesis.main import plot_models
@@ -38,8 +39,6 @@
 from neurom import view
 from tqdm import tqdm
 
-from emodel_generalisation.parallel.evaluator import evaluate
-
 
 def create_combos_df(
     morphology_dataset_path, generalisation_rule_path, emodel, n_min_per_mtype, n_morphs