bluecellulab 2.4.1__py3-none-any.whl → 2.5.3__py3-none-any.whl

bluecellulab/__init__.py

@@ -8,9 +8,9 @@ except ImportError:
     BLUEPY_AVAILABLE = False
 
 from .importer import *  # NOQA
-from .tools import *  # NOQA
 from .verbosity import *
 from .cell import Cell, create_ball_stick  # NOQA
+from .circuit import EmodelProperties
 from .connection import Connection  # NOQA
 from .plotwindow import PlotWindow  # NOQA
 from .dendrogram import Dendrogram  # NOQA
@@ -19,3 +19,10 @@ from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
 from .ssim import SSim  # NOQA
+
+
+from .simulation.neuron_globals import NeuronGlobals
+
+logger.debug("Loading the hoc files.")
+import_hoc(neuron)
+_ = NeuronGlobals.get_instance()  # initiate the singleton

bluecellulab/cell/core.py

@@ -39,7 +39,7 @@ from bluecellulab.circuit import EmodelProperties, SynapseProperty
 from bluecellulab.circuit.node_id import CellId
 from bluecellulab.circuit.simulation_access import get_synapse_replay_spikes
 from bluecellulab.exceptions import BluecellulabError
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 from bluecellulab.neuron_interpreter import eval_neuron
 from bluecellulab.rngsettings import RNGSettings
 from bluecellulab.stimulus.circuit_stimulus_definitions import SynapseReplay
@@ -73,7 +73,7 @@ class Cell(InjectableMixin, PlottableMixin):
             emodel_properties=template_params.emodel_properties,
         )
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(self,
                  template_path: str | Path,
                  morphology_path: str | Path,
@@ -191,29 +191,10 @@ class Cell(InjectableMixin, PlottableMixin):
         """Connect this cell to a circuit via sonata proxy."""
         self.sonata_proxy = sonata_proxy
 
-    def re_init_rng(self, use_random123_stochkv: bool = False) -> None:
+    def re_init_rng(self) -> None:
         """Reinitialize the random number generator for stochastic channels."""
-
         if not self.is_made_passive:
-            if use_random123_stochkv:
-                channel_id = 0
-                for section in self.somatic:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-                for section in self.basal:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-                for section in self.apical:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-            else:
-                self.cell.re_init_rng()
+            self.cell.re_init_rng()
 
     def get_psection(self, section_id: int | str) -> PSection:
         """Return a python section with the specified section id."""

bluecellulab/importer.py

@@ -52,8 +52,8 @@ def import_mod_lib(neuron: ModuleType) -> str:
     return res
 
 
-def import_neurodamus(neuron: ModuleType) -> None:
-    """Import neurodamus."""
+def import_hoc(neuron: ModuleType) -> None:
+    """Import hoc dependencies."""
     neuron.h.load_file("stdrun.hoc")  # nrn
     hoc_files = [
         "Cell.hoc",  # ND
@@ -75,17 +75,15 @@ def print_header(neuron: ModuleType, mod_lib_path: str) -> None:
 
 
 @run_once
-def _load_hoc_and_mod_files() -> None:
+def _load_mod_files() -> None:
     """Import hoc and mod files."""
     logger.debug("Loading the mod files.")
     mod_lib_paths = import_mod_lib(neuron)
-    logger.debug("Loading the hoc files.")
-    import_neurodamus(neuron)
     print_header(neuron, mod_lib_paths)
 
 
-def load_hoc_and_mod_files(func):
+def load_mod_files(func):
     def wrapper(*args, **kwargs):
-        _load_hoc_and_mod_files()
+        _load_mod_files()
         return func(*args, **kwargs)
     return wrapper

bluecellulab/rngsettings.py

@@ -20,7 +20,7 @@ from typing import Optional
 import neuron
 from bluecellulab.circuit.config.definition import SimulationConfig
 from bluecellulab.exceptions import UndefinedRNGException
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 
 logger = logging.getLogger(__name__)
 
@@ -37,7 +37,7 @@ class RNGSettings:
             cls._instance = cls()
         return cls._instance
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(
         self,
         mode="Random123",

bluecellulab/simulation/__init__.py

@@ -3,4 +3,3 @@
 from .simulation import Simulation
 from .neuron_globals import set_global_condition_parameters
 from .neuron_globals import set_minis_single_vesicle_values
-from .neuron_globals import set_tstop_value

bluecellulab/simulation/neuron_globals.py

@@ -62,6 +62,37 @@ def set_minis_single_vesicle_values(mech_conditions: MechanismConditions) -> Non
             )
 
 
-def set_tstop_value(tstop: float) -> None:
-    """Set the tstop value required by Tstim noise stimuli."""
-    neuron.h.tstop = tstop
+class NeuronGlobals:
+    _instance = None
+
+    def __init__(self):
+        raise RuntimeError('Call get_instance() instead')
+
+    @classmethod
+    def get_instance(cls):
+        if cls._instance is None:
+            cls._instance = cls.__new__(cls)
+            # Initialize default values
+            cls._instance._temperature = 34.0  # Default temperature
+            cls._instance.v_init = neuron.h.v_init
+            # Set the default values in NEURON
+            neuron.h.celsius = cls._instance._temperature
+        return cls._instance
+
+    @property
+    def temperature(self):
+        return self._temperature
+
+    @temperature.setter
+    def temperature(self, value):
+        self._temperature = value
+        neuron.h.celsius = value
+
+    @property
+    def v_init(self):
+        return self._v_init
+
+    @v_init.setter
+    def v_init(self, value):
+        self._v_init = value
+        neuron.h.v_init = value

bluecellulab/simulation/simulation.py

@@ -88,13 +88,11 @@ class Simulation:
             cvode=True,
             cvode_minstep=None,
             cvode_maxstep=None,
-            celsius=34,
-            v_init=-65,
             dt=0.025,
             forward_skip=None,
             forward_skip_value=False,
-            show_progress=None,
-            use_random123_stochkv=False):
+            show_progress=None
+    ):
         """Run the simulation."""
         # if maxtime <= neuron.h.t:
         #     raise Exception("Simulation: need to provide a maxtime (=%f) "
@@ -108,7 +106,6 @@ class Simulation:
             self.progress_dt = maxtime / 100
             self.init_progress_callback()
 
-        neuron.h.celsius = celsius
         neuron.h.tstop = maxtime
 
         cvode_old_status = neuron.h.cvode_active()
@@ -125,11 +122,9 @@ class Simulation:
                                "was set")
             neuron.h.cvode_active(0)
 
-        neuron.h.v_init = v_init
-
         for cell in self.cells:
             with contextlib.suppress(AttributeError):
-                cell.re_init_rng(use_random123_stochkv=use_random123_stochkv)
+                cell.re_init_rng()
         neuron.h.dt = dt
         neuron.h.steps_per_ms = 1.0 / dt
 
@@ -176,6 +171,3 @@ class Simulation:
             neuron.h.cvode_active(cvode_old_status)
 
         logger.debug("Finished simulation.")
-
-    def __del__(self):
-        pass

bluecellulab/ssim.py

@@ -39,14 +39,14 @@ from bluecellulab.circuit.config import SimulationConfig
 from bluecellulab.circuit.format import determine_circuit_format, CircuitFormat
 from bluecellulab.circuit.node_id import create_cell_id, create_cell_ids
 from bluecellulab.circuit.simulation_access import BluepySimulationAccess, SimulationAccess, SonataSimulationAccess, _sample_array
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 from bluecellulab.rngsettings import RNGSettings
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
 from bluecellulab.stimulus.circuit_stimulus_definitions import Noise, OrnsteinUhlenbeck, RelativeOrnsteinUhlenbeck, RelativeShotNoise, ShotNoise
 import bluecellulab.stimulus.circuit_stimulus_definitions as circuit_stimulus_definitions
 from bluecellulab.exceptions import BluecellulabError
 from bluecellulab.simulation import (
     set_global_condition_parameters,
-    set_tstop_value
 )
 from bluecellulab.synapse.synapse_types import SynapseID
 
@@ -56,7 +56,7 @@ logger = logging.getLogger(__name__)
 class SSim:
     """Class that loads a circuit simulation to do cell simulations."""
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(
         self,
         simulation_config: str | Path | SimulationConfig,
@@ -106,11 +106,6 @@ class SSim:
 
         self.gids_instantiated = False
 
-        # Make sure tstop is set correctly, because it is used by the
-        # TStim noise stimulus
-        if self.circuit_access.config.duration is not None:
-            set_tstop_value(self.circuit_access.config.duration)
-
         self.spike_threshold = self.circuit_access.config.spike_threshold
         self.spike_location = self.circuit_access.config.spike_location
 
@@ -596,8 +591,10 @@ class SSim:
             forward_skip_value = self.circuit_access.config.forward_skip
         if celsius is None:
             celsius = self.circuit_access.config.celsius
+            NeuronGlobals.get_instance().temperature = celsius
         if v_init is None:
             v_init = self.circuit_access.config.v_init
+            NeuronGlobals.get_instance().v_init = v_init
 
         sim = bluecellulab.Simulation(self.pc)
         for cell_id in self.cells:
@@ -612,8 +609,6 @@ class SSim:
             t_stop,
             cvode=cvode,
             dt=dt,
-            celsius=celsius,
-            v_init=v_init,
             forward_skip=forward_skip,
             forward_skip_value=forward_skip_value,
             show_progress=show_progress)

bluecellulab/tools.py

@@ -60,6 +60,8 @@ def calculate_SS_voltage(
     template_format: str,
     emodel_properties: EmodelProperties | None,
     step_level: float,
+    check_for_spiking=False,
+    spike_threshold=-20.0,
 ) -> float:
     """Calculate the steady state voltage at a certain current step."""
     with IsolatedProcess() as runner:
@@ -71,6 +73,8 @@ def calculate_SS_voltage(
                 template_format,
                 emodel_properties,
                 step_level,
+                check_for_spiking,
+                spike_threshold,
             ],
         )
     return SS_voltage
@@ -82,8 +86,8 @@ def calculate_SS_voltage_subprocess(
     template_format: str,
     emodel_properties: EmodelProperties | None,
     step_level: float,
-    check_for_spiking=False,
-    spike_threshold=-20.0,
+    check_for_spiking: bool,
+    spike_threshold: float,
 ) -> float:
     """Subprocess wrapper of calculate_SS_voltage.
 

{bluecellulab-2.4.1.dist-info → bluecellulab-2.5.3.dist-info}/METADATA

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.4.1
+Version: 2.5.3
 Summary: The Pythonic Blue Brain simulator access
-Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
 License: Apache2.0
-Keywords: computational neuroscience,simulation,analysis,parameters,Blue Brain Project
+Project-URL: Homepage, https://github.com/BlueBrain/BlueCelluLab
+Project-URL: Documentation, https://bluecellulab.readthedocs.io/
+Keywords: computational neuroscience,simulation,analysis,SONATA,neural networks,neuron,Blue Brain Project
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: License :: OSI Approved :: Apache Software License

{bluecellulab-2.4.1.dist-info → bluecellulab-2.5.3.dist-info}/RECORD

@@ -1,16 +1,16 @@
-bluecellulab/__init__.py,sha256=lYxUZtN_mLNUPJgBnKd4GbwDIVScDPD6ouC7OvWQxS0,645
+bluecellulab/__init__.py,sha256=yC97iFnCVDtwqspxdpt4C-qq9vQF7AMJOWe1h_cB0Wc,827
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
 bluecellulab/graph.py,sha256=ODiQy4xjRVxtNITXeXpYnqHas0wR7gZ_aXuDAF7jMq4,3419
-bluecellulab/importer.py,sha256=l5nvD0y41-AheqoDNBGAX5qFTCG6_UFlLmqyFbUo77E,2998
+bluecellulab/importer.py,sha256=zwVi1Nx2f8xzFfzxzYoXa7gfi7DQapqkRJII5sBbRyY,2900
 bluecellulab/neuron_interpreter.py,sha256=hXig_u3T6JmEHbkV8ZblEZtX0kY80ate4VpRtANNFrM,2185
 bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,2721
 bluecellulab/psection.py,sha256=EgAS8IS9DcYv2xOkNISgfg_CfRc0nDfRFjvgQhyi9eY,6328
 bluecellulab/psegment.py,sha256=rBryDYHC_uDK9itfXXrFZ0DL9F6WgRICL0j5EHN56QM,3125
-bluecellulab/rngsettings.py,sha256=qjwnzAEdbRt66DKd_NTD2OZnlu4hDH7UUOXxd0G9c_Q,4244
-bluecellulab/ssim.py,sha256=U8HFKso4lQkKowts_x2DQfG3ihR56KcN0ITeTlGu3hI,33533
-bluecellulab/tools.py,sha256=tS9a9VDMQOVw6zIllT3FxPIzQk4xheNlGf8lpIg01FY,10931
+bluecellulab/rngsettings.py,sha256=KACk4ujPXhlHL9iAoTdAjjLuFEcUoG6aes92ZClSoQQ,4228
+bluecellulab/ssim.py,sha256=radFcT2lWRfb1C0zKlqw0JQ6JY4b9LJiDP9JDPeQIqs,33399
+bluecellulab/tools.py,sha256=8QMNdmh9lRDOWT4kz9cI_MYNVh4ulxgY8CtHZbaMbkA,11056
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=fgqjgy3xzyL0zu-qjCPJdHp6PEAHADCzlr2FqyBmzHI,2012
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
@@ -18,7 +18,7 @@ bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 bluecellulab/analysis/inject_sequence.py,sha256=jfEESRAUKAWgjceNWfx3Rwe1gDNWhxwZL4PfnJZCzrg,4930
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
-bluecellulab/cell/core.py,sha256=r_9nq9MBm-VM-oZQc2KN3a4GxFRYgWy9AF-XpjMIDAE,32156
+bluecellulab/cell/core.py,sha256=uxAWAZ6NpODJ3O77p0JWL6AVey3lOyetU3SVZxP4a9Q,31201
 bluecellulab/cell/injector.py,sha256=XC49VSHw78xCHzLJKO_-unnnVZAZXsYg5qbmZPx01AA,18091
 bluecellulab/cell/plotting.py,sha256=_hZs5oYG4vmJBVf05cJ2O_cVazi5Eap8OkL9BtIwjW8,4001
 bluecellulab/cell/random.py,sha256=FDby9BN4eJT27COwHP59bhDE2v-c6rdOKNFj3cYZTVY,1773
@@ -52,18 +52,18 @@ bluecellulab/hoc/RNGSettings.hoc,sha256=okJBdqlPXET8BrpG1Q31GdaxHfpe3CE0L5P7MAhf
 bluecellulab/hoc/TDistFunc.hoc,sha256=WKX-anvL83xGuGPH9g1oIORB17UM4Pi3-iIXzKO-pUQ,2663
 bluecellulab/hoc/TStim.hoc,sha256=noBJbM_ZqF6T6MEgBeowNzz21I9QeYZ5brGgUvCSm4k,8473
 bluecellulab/hoc/fileUtils.hoc,sha256=LSM7BgyjYVqo2DGSOKvg4W8IIusbsL45JVYK0vgwitU,2539
-bluecellulab/simulation/__init__.py,sha256=G1md-6mqaYQkfZT8pmzqRi3WW1fMQCgkeaela2kX3OM,258
-bluecellulab/simulation/neuron_globals.py,sha256=PuAxrXbr734RP-5q6YkHpnOgzTVyo_8SYZux9HABlaI,3348
-bluecellulab/simulation/simulation.py,sha256=tM5Psl-w25CHA4hp2fqs3GcZ2HSjIbu_6iyOcs-1jd8,6439
+bluecellulab/simulation/__init__.py,sha256=P2ebt0SFw-08J3ihN-LeRn95HeF79tzA-Q0ReLm32dM,214
+bluecellulab/simulation/neuron_globals.py,sha256=uxgceZ7zzbVEtITrQv8oOK900zhh7w29cScFwjLWo4I,4134
+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
 bluecellulab/stimulus/factory.py,sha256=AOby3Sp2g8BJsRccz3afazfCyysyWIgLtcliWlyeiu0,8097
 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-2.4.1.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.4.1.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.4.1.dist-info/METADATA,sha256=7Ug3ADUg1_1XIbqRyQ07KaSb512jch3wiaxRKsxkXPY,6907
-bluecellulab-2.4.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.4.1.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.4.1.dist-info/RECORD,,
+bluecellulab-2.5.3.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.5.3.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.5.3.dist-info/METADATA,sha256=rYhJTsxGMFuS6MWaiwkByBjBpVxemuA3GoybjU0PgSM,7003
+bluecellulab-2.5.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.5.3.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.5.3.dist-info/RECORD,,