bluecellulab 2.6.53__tar.gz → 2.6.54__tar.gz

{bluecellulab-2.6.53 → bluecellulab-2.6.54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.53
+Version: 2.6.54
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.53 → bluecellulab-2.6.54}/bluecellulab/analysis/analysis.py

@@ -4,11 +4,9 @@ try:
 except ImportError:
     efel = None
 from itertools import islice
-from itertools import repeat
 import logging
 from matplotlib.collections import LineCollection
 import matplotlib.pyplot as plt
-from multiprocessing import Pool
 import neuron
 import numpy as np
 import pathlib
@@ -97,20 +95,15 @@ def compute_plot_iv_curve(cell,
         for amp in list_amp
     ]
 
-    with Pool(len(steps)) as p:
-        recordings = p.starmap(
-            run_stimulus,
-            zip(
-                repeat(cell.template_params),
-                steps,
-                repeat(injecting_section),
-                repeat(injecting_segment),
-                repeat(True),  # cvode
-                repeat(True),  # add_hypamp
-                repeat(recording_section),
-                repeat(recording_segment),
-            )
-        )
+    recordings = []
+    for step in steps:
+        recording = run_stimulus(cell.template_params,
+                                 step,
+                                 section=injecting_section,
+                                 segment=injecting_segment,
+                                 recording_section=recording_section,
+                                 recording_segment=recording_segment)
+        recordings.append(recording)
 
     steady_states = []
     # compute steady state response
@@ -208,24 +201,19 @@ def compute_plot_fi_curve(cell,
         for amp in list_amp
     ]
 
-    with Pool(len(steps)) as p:
-        recordings = p.starmap(
-            run_stimulus,
-            zip(
-                repeat(cell.template_params),
-                steps,
-                repeat(injecting_section),
-                repeat(injecting_segment),
-                repeat(True),  # cvode
-                repeat(True),  # add_hypamp
-                repeat(recording_section),
-                repeat(recording_segment),
-                repeat(True),  # enable_spike_detection
-                repeat(threshold_voltage),  # threshold_spike_detection
-            )
-        )
-
-    spike_count = [len(recording.spike) for recording in recordings]
+    spikes = []
+    for step in steps:
+        recording = run_stimulus(cell.template_params,
+                                 step,
+                                 section=injecting_section,
+                                 segment=injecting_segment,
+                                 recording_section=recording_section,
+                                 recording_segment=recording_segment,
+                                 enable_spike_detection=True,
+                                 threshold_spike_detection=threshold_voltage)
+        spikes.append(recording.spike)
+
+    spike_count = [len(spike) for spike in spikes]
 
     plot_fi_curve(list_amp,
                   spike_count,

{bluecellulab-2.6.53 → bluecellulab-2.6.54}/bluecellulab/validation/validation.py

@@ -438,68 +438,38 @@ def run_validations(
     )
 
     logger.debug("Running validations...")
-    from bluecellulab.utils import NestedPool
-    with NestedPool(processes=8) as pool:
-        # Validation 1: Spiking Test
-        spiking_test_result_future = pool.apply_async(
-            spiking_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
-
-        # Validation 2: Depolarization Block Test
-        depolarization_block_result_future = pool.apply_async(
-            depolarization_block_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 1: Spiking Test
+    spiking_test_result = spiking_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage
+    )
 
-        # Validation 3: Backpropagating AP Test
-        bpap_result_future = pool.apply_async(
-            bpap_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 2: Depolarization Block Test
+    depolarization_block_result = depolarization_block_test(
+        cell.template_params, rheobase, out_dir
+    )
 
-        # Validation 4: Postsynaptic Potential Test
-        # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
+    # Validation 3: Backpropagating AP Test
+    bpap_result = bpap_test(cell.template_params, rheobase, out_dir)
 
-        # Validation 5: AIS Spiking Test
-        ais_spiking_test_result_future = pool.apply_async(
-            ais_spiking_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 4: Postsynaptic Potential Test
+    # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
 
-        # Validation 6: Hyperpolarization Test
-        hyperpolarization_result_future = pool.apply_async(
-            hyperpolarization_test,
-            (cell.template_params, rheobase, out_dir)
-        )
+    # Validation 5: AIS Spiking Test
+    ais_spiking_test_result = ais_spiking_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage
+    )
 
-        # Validation 7: Rin Test
-        rin_result_future = pool.apply_async(
-            rin_test,
-            (rin,)
-        )
+    # Validation 6: Hyperpolarization Test
+    hyperpolarization_result = hyperpolarization_test(cell.template_params, rheobase, out_dir)
 
-        # # Validation 8: IV Test
-        iv_test_result_future = pool.apply_async(
-            iv_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 7: Rin Test
+    rin_result = rin_test(rin)
 
-        # # Validation 9: FI Test
-        fi_test_result_future = pool.apply_async(
-            fi_test,
-            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-        )
+    # Validation 8: IV Test
+    iv_test_result = iv_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
 
-        # Wait for all validations to complete
-        spiking_test_result = spiking_test_result_future.get()
-        depolarization_block_result = depolarization_block_result_future.get()
-        bpap_result = bpap_result_future.get()
-        ais_spiking_test_result = ais_spiking_test_result_future.get()
-        hyperpolarization_result = hyperpolarization_result_future.get()
-        rin_result = rin_result_future.get()
-        iv_test_result = iv_test_result_future.get()
-        fi_test_result = fi_test_result_future.get()
+    # Validation 9: FI Test
+    fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
 
     return {
         "memodel_properties": {

{bluecellulab-2.6.53 → bluecellulab-2.6.54}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.53
+Version: 2.6.54
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0