bluecellulab 2.5.10__py3-none-any.whl → 2.5.11__py3-none-any.whl

bluecellulab/__init__.py

@@ -7,7 +7,7 @@ try:
 except ImportError:
     BLUEPY_AVAILABLE = False
 
-from .importer import *  # NOQA
+from bluecellulab.importer import import_hoc
 from .verbosity import *
 from .cell import Cell, create_ball_stick  # NOQA
 from .circuit import EmodelProperties
@@ -19,7 +19,7 @@ from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
 from .circuit_simulation import CircuitSimulation, CircuitSimulation  # NOQA
-
+import neuron
 
 from .simulation.neuron_globals import NeuronGlobals
 

bluecellulab/analysis/inject_sequence.py

@@ -7,9 +7,9 @@ import neuron
 import numpy as np
 from bluecellulab.cell.core import Cell
 from bluecellulab.cell.template import TemplateParams
+from bluecellulab.simulation.parallel import IsolatedProcess
 from bluecellulab.simulation.simulation import Simulation
 from bluecellulab.stimulus.factory import Stimulus, StimulusFactory
-from bluecellulab.utils import IsolatedProcess
 
 
 class StimulusName(Enum):

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -19,8 +19,9 @@ import os
 from pathlib import Path
 from typing import Optional
 
+import neuron
 import pandas as pd
-from bluecellulab import circuit, neuron
+from bluecellulab import circuit
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.circuit.config import BluepySimulationConfig
 from bluecellulab.circuit.config.definition import SimulationConfig

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -22,8 +22,9 @@ from bluepysnap.bbp import Cell as SnapCell
 from bluepysnap.circuit_ids import CircuitNodeId, CircuitEdgeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap import Circuit as SnapCircuit
+import neuron
 import pandas as pd
-from bluecellulab import circuit, neuron
+from bluecellulab import circuit
 from bluecellulab.circuit.circuit_access.definition import EmodelProperties
 from bluecellulab.circuit import CellId, SynapseProperty
 from bluecellulab.circuit.config import SimulationConfig

bluecellulab/simulation/neuron_globals.py

@@ -13,6 +13,7 @@
 # limitations under the License.
 """Module that handles the global NEURON parameters."""
 
+from typing import NamedTuple
 import neuron
 from bluecellulab.circuit.config.sections import Conditions, MechanismConditions
 from bluecellulab.exceptions import error_context
@@ -62,6 +63,11 @@ def set_minis_single_vesicle_values(mech_conditions: MechanismConditions) -> Non
             )
 
 
+class NeuronGlobalParams(NamedTuple):
+    temperature: float
+    v_init: float
+
+
 class NeuronGlobals:
     _instance = None
 
@@ -96,3 +102,10 @@ class NeuronGlobals:
     def v_init(self, value):
         self._v_init = value
         neuron.h.v_init = value
+
+    def export_params(self) -> NeuronGlobalParams:
+        return NeuronGlobalParams(self.temperature, self.v_init)
+
+    def load_params(self, params: NeuronGlobalParams) -> None:
+        self.temperature = params.temperature
+        self.v_init = params.v_init

bluecellulab/simulation/parallel.py

@@ -0,0 +1,36 @@
+"""Controlled simulations in parallel."""
+
+from __future__ import annotations
+from multiprocessing.pool import Pool
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
+
+
+class IsolatedProcess(Pool):
+    """Multiprocessing Pool that restricts a worker to run max 1 process.
+
+    Use this when running isolated NEURON simulations. Running 2 NEURON
+    simulations on a single process is to be avoided. Required global
+    NEURON simulation parameters will automatically be passed to each
+    worker.
+    """
+
+    def __init__(self, processes: int | None = 1):
+        """Initialize the IsolatedProcess pool.
+
+        Args:
+            processes: The number of processes to use for running the simulations.
+                       If set to None, then the number returned by os.cpu_count() is used.
+        """
+        neuron_global_params = NeuronGlobals.get_instance().export_params()
+        super().__init__(
+            processes=processes,
+            initializer=self.init_worker,
+            initargs=(neuron_global_params,),
+            maxtasksperchild=1,
+        )
+
+    @staticmethod
+    def init_worker(neuron_global_params):
+        """Load global parameters for the NEURON environment in each worker
+        process."""
+        NeuronGlobals.get_instance().load_params(neuron_global_params)

bluecellulab/tools.py

@@ -25,7 +25,8 @@ import numpy as np
 import bluecellulab
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
-from bluecellulab.utils import CaptureOutput, IsolatedProcess
+from bluecellulab.simulation.parallel import IsolatedProcess
+from bluecellulab.utils import CaptureOutput
 
 logger = logging.getLogger(__name__)
 

bluecellulab/utils.py

@@ -1,19 +1,21 @@
 """Utility functions used within BlueCellulab."""
+
 from __future__ import annotations
 import contextlib
 import io
 import json
-from multiprocessing.pool import Pool
 
 import numpy as np
 
 
 def run_once(func):
     """A decorator to ensure a function is only called once."""
+
     def wrapper(*args, **kwargs):
         if not wrapper.has_run:
             wrapper.has_run = True
             return func(*args, **kwargs)
+
     wrapper.has_run = False
     return wrapper
 
@@ -32,29 +34,25 @@ class CaptureOutput(list):
 
 class NumpyEncoder(json.JSONEncoder):
     def default(self, obj):
-        if isinstance(obj, (np.int_, np.intc, np.intp, np.int8,
-                            np.int16, np.int32, np.int64, np.uint8,
-                            np.uint16, np.uint32, np.uint64)):
+        if isinstance(
+            obj,
+            (
+                np.int_,
+                np.intc,
+                np.intp,
+                np.int8,
+                np.int16,
+                np.int32,
+                np.int64,
+                np.uint8,
+                np.uint16,
+                np.uint32,
+                np.uint64,
+            ),
+        ):
             return int(obj)
-        elif isinstance(obj, (np.float_, np.float16, np.float32,
-                              np.float64)):
+        elif isinstance(obj, (np.float_, np.float16, np.float32, np.float64)):
             return float(obj)
         elif isinstance(obj, np.ndarray):
             return obj.tolist()
         return json.JSONEncoder.default(self, obj)
-
-
-class IsolatedProcess(Pool):
-    """Multiprocessing Pool that restricts a worker to run max 1 process.
-
-    Use this when running isolated NEURON simulations. Running 2 NEURON
-    simulations on a single process is to be avoided.
-    """
-    def __init__(self, processes: int | None = 1):
-        """Initialize the IsolatedProcess pool.
-
-        Args:
-            processes: The number of processes to use for running the stimuli.
-            If set to None, then the number returned by os.cpu_count() is used.
-        """
-        super().__init__(processes=processes, maxtasksperchild=1)

{bluecellulab-2.5.10.dist-info → bluecellulab-2.5.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.10
+Version: 2.5.11
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.10.dist-info → bluecellulab-2.5.11.dist-info}/RECORD

@@ -1,4 +1,4 @@
-bluecellulab/__init__.py,sha256=-DopR1_1ji4NQlsRi4fLSUETM358o6UCdJtnhQ8wrQA,873
+bluecellulab/__init__.py,sha256=JvigOm_7WDjVAodm4R_TyRzj7vd9hmEbvLJDUVtgeqo,899
 bluecellulab/circuit_simulation.py,sha256=GLy_O5onhiSa-RajorDHlgP1rkFxjUONB4G6B4upyg0,33672
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
@@ -10,12 +10,12 @@ bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,27
 bluecellulab/psection.py,sha256=SYI2mGUIp8UiuMkyp9ITChHVLbJ0fDsEmen1pAbgNJQ,6174
 bluecellulab/psegment.py,sha256=02DkvazPGjnwjfjn1K8CZqdcVWnUhYpgrjqjoHNz6jM,3133
 bluecellulab/rngsettings.py,sha256=Dlt34dc4AoWyxCCzUK3Jlui90VCK20xHg6gD_OJzPIw,4237
-bluecellulab/tools.py,sha256=JrAfMVozfucwcyGklweMvEM7uGnTnWIDmk4eqI-43Es,11169
+bluecellulab/tools.py,sha256=Bg6F0allDJrQrvxfvPdMdFe47a_CF7Q-KmF2TWNDE44,11213
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
-bluecellulab/utils.py,sha256=fgqjgy3xzyL0zu-qjCPJdHp6PEAHADCzlr2FqyBmzHI,2012
+bluecellulab/utils.py,sha256=SbOOkzw1YGjCKV3qOw0zpabNEy7V9BRtgMLsQJiFRq4,1526
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bluecellulab/analysis/inject_sequence.py,sha256=jfEESRAUKAWgjceNWfx3Rwe1gDNWhxwZL4PfnJZCzrg,4930
+bluecellulab/analysis/inject_sequence.py,sha256=sL8G01uYzPohLkh1BT_8op2vHbSFx1_MlRgj2dY1cWs,4944
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
 bluecellulab/cell/core.py,sha256=MtrVQAxT82dc9uQuWZyTQfc6Oczrnc_y_9hcyBqUT7w,31467
@@ -39,9 +39,9 @@ bluecellulab/circuit/simulation_access.py,sha256=QHVEN-sEZbCCvblhBHEShGX0-NEXCD1
 bluecellulab/circuit/synapse_properties.py,sha256=6PpMWeothomR2c-mx63yVIISJc4eSL9xMnaIM2nryNM,5494
 bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
-bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=msAbAKH7XEPn77lTPA7-ntRiY-fCIxvLuA250gjo__Q,14681
+bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=HxQaRTz1HaeOVV87fiptJBXRNWCitT-5YHn71WtSsLg,14687
 bluecellulab/circuit/circuit_access/definition.py,sha256=SnKBFEgdXFG-QexYRrGSzVAd7bSj7NwN0IuTsjDOrDY,4435
-bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=P1ElK_VA10_JyyKbAnqzuAlduEYE2c_NSec2TZuix1U,10345
+bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=c0MMJuoT6_dRW8O5HSRS5hHv1zDKdW0sBR-DaP0F1bk,10351
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
 bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=tUyHvzlxFWRxh8rBNvU0FdUqGqJR2G8OXifATQ9W7yw,6974
 bluecellulab/circuit/config/definition.py,sha256=o0751Dd83f8TWGw95EAQ8coJrYGasdshrIrXViF5lzg,2774
@@ -53,7 +53,8 @@ bluecellulab/hoc/TDistFunc.hoc,sha256=WKX-anvL83xGuGPH9g1oIORB17UM4Pi3-iIXzKO-pU
 bluecellulab/hoc/TStim.hoc,sha256=noBJbM_ZqF6T6MEgBeowNzz21I9QeYZ5brGgUvCSm4k,8473
 bluecellulab/hoc/fileUtils.hoc,sha256=LSM7BgyjYVqo2DGSOKvg4W8IIusbsL45JVYK0vgwitU,2539
 bluecellulab/simulation/__init__.py,sha256=P2ebt0SFw-08J3ihN-LeRn95HeF79tzA-Q0ReLm32dM,214
-bluecellulab/simulation/neuron_globals.py,sha256=uxgceZ7zzbVEtITrQv8oOK900zhh7w29cScFwjLWo4I,4134
+bluecellulab/simulation/neuron_globals.py,sha256=_8xmJPQMfCyhVn6KppK7i3jaUZaALMLgyxyHMKi02yo,4508
+bluecellulab/simulation/parallel.py,sha256=xmlIelxYNct-vGhPip7_vF9gwyehdpomYB8kf9xV-S8,1314
 bluecellulab/simulation/simulation.py,sha256=I__cZwV_A8I7XSefn6aJDBA_jXCI3E35-pCNCLUsnvo,6206
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
 bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=uij_s44uNdmMwMLGmTHSRgmp9K9B_vvHHshX6YPJNJU,15686
@@ -61,9 +62,9 @@ bluecellulab/stimulus/factory.py,sha256=AOby3Sp2g8BJsRccz3afazfCyysyWIgLtcliWlye
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=YkvxbdGF-u-vxYdbRNTlX-9AtSC_3t_FQRFhybwzgrk,6805
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.5.10.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.5.10.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.5.10.dist-info/METADATA,sha256=MEgGgaV3rXDUcTU5EntzGyw3GinZSWicJnC0cQuPrXo,7026
-bluecellulab-2.5.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.5.10.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.5.10.dist-info/RECORD,,
+bluecellulab-2.5.11.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.5.11.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.5.11.dist-info/METADATA,sha256=rE7_kRYFnhuy1_9tiArH9zPRCYt2F5SmiIXbnO3GOZo,7026
+bluecellulab-2.5.11.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.5.11.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.5.11.dist-info/RECORD,,