bluecellulab 2.4.0__py3-none-any.whl → 2.6.37__py3-none-any.whl

bluecellulab/cell/serialized_sections.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -15,17 +15,14 @@
 index."""
 from __future__ import annotations
 import logging
-import warnings
 import neuron
 from bluecellulab.type_aliases import HocObjectType, NeuronSection
 
 
 logger = logging.getLogger(__name__)
-warnings.filterwarnings("once", category=UserWarning, module=__name__)
 
 
 class SerializedSections:
-
     def __init__(self, cell: HocObjectType) -> None:
         self.isec2sec: dict[int, NeuronSection] = {}
         n = cell.nSecAll
@@ -37,7 +34,8 @@ class SerializedSections:
                 raise ValueError("Error: failure in mk2_isec2sec()")
 
             if v_value < 0:
-                warnings.warn(
-                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}")
+                logging.debug(
+                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}"
+                )
             else:
                 self.isec2sec[int(v_value)] = neuron.h.SectionRef(sec=sec)

bluecellulab/cell/sonata_proxy.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/cell/stimuli_generator.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -114,17 +114,35 @@ def gen_shotnoise_signal(tau_D, tau_R, rate, amp_mean, amp_var,
     return tvec, P
 
 
-def get_relative_shotnoise_params(mean, var, tau_D, tau_R, cv_square):
+def get_relative_shotnoise_params(mean, sd, tau_D, tau_R, relative_skew):
     """Returns Rate, amp_mean and amp_var parameters."""
     # bi-exponential time to peak [ms]
     t_peak = math.log(tau_D / tau_R) / (1 / tau_R - 1 / tau_D)
     # bi-exponential peak height [1]
-    x_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
-
-    rate_ms = (1 + cv_square) / 2 * (mean ** 2 / var) / (tau_D + tau_R)
-    rate = rate_ms * 1000  # rate in 1 / s [Hz]
-    amp_mean = mean * x_peak / rate_ms / (tau_D - tau_R)
-    amp_var = cv_square * amp_mean ** 2
+    F_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
+
+    # utility constants
+    Xi = (tau_D - tau_R) / F_peak
+    A = 1 / (tau_D + tau_R)
+    B = 1 / ((tau_D + 2 * tau_R) * (2 * tau_D + tau_R))
+
+    # skewness
+    skew_bnd_min = (8 / 3) * (B / A ** 2) * (sd / mean)
+    skew = (1 + relative_skew) * skew_bnd_min
+    if skew < skew_bnd_min or skew > 2 * skew_bnd_min:
+        raise ValueError("skewness out of bounds")
+
+    # cumulants
+    lambda2_1 = sd ** 2 / mean                     # lambda2 over lambda1
+    lambda3_2 = sd * skew                          # lambda3 over lambda2
+    theta1pk = 2 / (A * Xi) * lambda2_1            # = (1 + k) * theta
+    theta2pk = (3 * A) / (4 * B * Xi) * lambda3_2  # = (2 + k) * theta
+
+    # derived parameters
+    amp_mean = 2 * theta1pk - theta2pk               # mean amplitude [nA or uS]
+    amp_var = amp_mean * (theta2pk - theta1pk)  # variance of amplitude [nA^2 or uS^2]
+    rate_ms = mean / (amp_mean * Xi)                 # event rate in 1 / ms
+    rate = rate_ms * 1000                            # event rate in 1 / s [Hz]
 
     return rate, amp_mean, amp_var
 

bluecellulab/cell/template.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,7 +20,8 @@ import os
 from pathlib import Path
 import re
 import string
-from typing import Optional
+from typing import NamedTuple, Optional
+import uuid
 
 import neuron
 
@@ -44,6 +45,13 @@ def public_hoc_cell(cell: HocObjectType) -> HocObjectType:
          from the hoc model. Either getCell() or CellRef needs to be provided""")
 
 
+class TemplateParams(NamedTuple):
+    template_filepath: str | Path
+    morph_filepath: str | Path
+    template_format: str
+    emodel_properties: Optional[EmodelProperties]
+
+
 class NeuronTemplate:
     """NeuronTemplate representation."""
 
@@ -119,8 +127,8 @@ class NeuronTemplate:
         # templates load outside of bluecellulab
         template_name = "%s_bluecellulab" % template_name
         template_name = get_neuron_compliant_template_name(template_name)
-        obj_address = hex(id(self))
-        template_name = f"{template_name}_{obj_address}"
+        unique_id = uuid.uuid4().hex
+        template_name = f"{template_name}_{unique_id}"
 
         template_content = re.sub(
             r"begintemplate\s*(\S*)",

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -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
@@ -57,7 +58,6 @@ class BluepyCircuitAccess:
             raise FileNotFoundError(
                 f"Circuit config file {simulation_config} not found.")
 
-        # to allow the usage of SimulationConfig outside of Ssim
         if isinstance(simulation_config, BluepySimulationConfig):
             simulation_config = simulation_config.impl
 
@@ -191,23 +191,15 @@ class BluepyCircuitAccess:
 
             if isinstance(connectome._impl, SonataConnectome):
                 logger.debug('Using sonata style synapse file, not nrn.h5')
-                # load 'afferent_section_pos' instead of '_POST_DISTANCE'
-                if 'afferent_section_pos' in connectome.available_properties:
-                    connectome_properties[
-                        connectome_properties.index(SynapseProperty.POST_SEGMENT_OFFSET)
-                    ] = 'afferent_section_pos'
-
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
-            else:
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
+                connectome_properties.remove(SynapseProperty.POST_SEGMENT_OFFSET)
+            else:  # afferent section_pos will be computed via post_segment_offset
+                connectome_properties.remove(SynapseProperty.AFFERENT_SECTION_POS)
+
+            connectome_properties = properties_to_bluepy(connectome_properties)
+            synapses = connectome.afferent_synapses(
+                gid, properties=connectome_properties
+            )
+            synapses.columns = properties_from_bluepy(synapses.columns)
 
             synapses = synapses.reset_index(drop=True)
             synapses.index = pd.MultiIndex.from_tuples(

bluecellulab/circuit/circuit_access/definition.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -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
@@ -46,7 +47,7 @@ class SonataCircuitAccess:
             raise FileNotFoundError(f"Circuit config file {simulation_config} not found.")
 
         if isinstance(simulation_config, SonataSimulationConfig):
-            self.config: SimulationConfig = simulation_config
+            self.config = simulation_config
         else:
             self.config = SonataSimulationConfig(simulation_config)
         circuit_config = self.config.impl.config["network"]
@@ -190,7 +191,7 @@ class SonataCircuitAccess:
 
     @lru_cache(maxsize=16)
     def get_target_cell_ids(self, target: str) -> set[CellId]:
-        ids = self._circuit.nodes.ids(target)
+        ids = self._circuit.nodes.ids(self.config.impl.node_sets[target])
         return {CellId(x.population, x.id) for x in ids}
 
     @lru_cache(maxsize=100)

bluecellulab/circuit/config/bluepy_simulation_config.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/definition.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/sections.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/sonata_simulation_config.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/format.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/iotools.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -32,7 +32,7 @@ def parse_outdat(path: str | Path) -> dict[CellId, np.ndarray]:
     # convert Series to DataFrame with 2 columns for `groupby` operation
     spike_df = spikes.to_frame().reset_index()
     if (spike_df["t"] < 0).any():
-        logger.warning('SSim: Found negative spike times in out.dat ! '
+        logger.warning('Found negative spike times in out.dat ! '
                        'Clipping them to 0')
         spike_df["t"].clip(lower=0., inplace=True)
 

bluecellulab/circuit/node_id.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/simulation_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -18,6 +18,7 @@ import logging
 from pathlib import Path
 from typing import Optional, Protocol
 
+import h5py
 import pandas as pd
 
 from bluecellulab.circuit.config import SimulationConfig, SonataSimulationConfig
@@ -171,13 +172,15 @@ class SonataSimulationAccess:
 
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
-    """Read the .dat file containing the spike replays."""
-    data = np.genfromtxt(f_name, skip_header=1)
-    spikes = pd.DataFrame(data=data, columns=["t", "node_id"]).astype({"node_id": int})
-    # subtract 1 from all node_ids to make them 0-based
-    # source: https://sonata-extension.readthedocs.io/
-    # en/latest/blueconfig-projection-example.html#dat-spike-files
-    spikes["node_id"] -= 1
+    """Read the .h5 file containing the spike replays."""
+    with h5py.File(f_name, 'r') as f:
+        # Access the timestamps and node_ids datasets
+        timestamps = f['/spikes/All/timestamps'][:]
+        node_ids = f['/spikes/All/node_ids'][:]
+
+        spikes = pd.DataFrame(data={'t': timestamps, 'node_id': node_ids})
+        spikes = spikes.astype({"node_id": int})
+
     if (spikes["t"] < 0).any():
         logger.warning("Found negative spike times... Clipping them to 0")
         spikes["t"].clip(lower=0., inplace=True)

bluecellulab/circuit/synapse_properties.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -40,6 +40,7 @@ class SynapseProperty(Enum):
     NRRP = "NRRP"
     U_HILL_COEFFICIENT = "u_hill_coefficient"
     CONDUCTANCE_RATIO = "conductance_scale_factor"
+    AFFERENT_SECTION_POS = "afferent_section_pos"
 
     @classmethod
     def from_bluepy(cls, prop: BLPSynapse) -> SynapseProperty:
@@ -76,6 +77,7 @@ class SynapseProperties:
         SynapseProperty.NRRP,
         SynapseProperty.U_HILL_COEFFICIENT,
         SynapseProperty.CONDUCTANCE_RATIO,
+        SynapseProperty.AFFERENT_SECTION_POS,
     )
     plasticity = (
         "volume_CR", "rho0_GB", "Use_d_TM", "Use_p_TM", "gmax_d_AMPA",
@@ -98,6 +100,7 @@ snap_to_synproperty = MappingProxyType({
     "n_rrp_vesicles": SynapseProperty.NRRP,
     "u_hill_coefficient": SynapseProperty.U_HILL_COEFFICIENT,
     "conductance_scale_factor": SynapseProperty.CONDUCTANCE_RATIO,
+    "afferent_section_pos": SynapseProperty.AFFERENT_SECTION_POS,
 })
 
 
@@ -137,23 +140,36 @@ def properties_from_bluepy(
     'str's."""
     if not BLUEPY_AVAILABLE:
         raise ExtraDependencyMissingError("bluepy")
-    return [
-        SynapseProperty.from_bluepy(prop)
-        if isinstance(prop, BLPSynapse)
-        else prop
-        for prop in props
-    ]
+    res: list[SynapseProperty | str] = []
+    for prop in props:
+        if isinstance(prop, BLPSynapse):
+            res.append(SynapseProperty.from_bluepy(prop))
+        elif prop == "afferent_section_pos":  # jira_url/project/issues/browse/NSETM-2313
+            res.append(SynapseProperty.AFFERENT_SECTION_POS)
+        else:
+            res.append(prop)
+    return res
 
 
 def properties_to_bluepy(props: list[SynapseProperty | str]) -> list[BLPSynapse | str]:
     """Convert a list of SynapseProperty to bluepy Synapse properties, spare
     'str's."""
-    return [
+    # bluepy does not have AFFERENT_SECTION_POS atm.
+    # jira_url/project/issues/browse/NSETM-2313
+    bluepy_recognised_props = props.copy()
+    removed_afferent_section_pos = False
+    if SynapseProperty.AFFERENT_SECTION_POS in bluepy_recognised_props:
+        removed_afferent_section_pos = True
+        bluepy_recognised_props.remove(SynapseProperty.AFFERENT_SECTION_POS)
+    res = [
         prop.to_bluepy()
         if isinstance(prop, SynapseProperty)
         else prop
-        for prop in props
+        for prop in bluepy_recognised_props
     ]
+    if removed_afferent_section_pos:
+        res.append("afferent_section_pos")
+    return res
 
 
 def synapse_property_encoder(dct: dict[SynapseProperty | str, Any]) -> dict[str, Any]:

bluecellulab/circuit/validate.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/{ssim.py → circuit_simulation.py}

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,6 +25,9 @@ import neuron
 import numpy as np
 import pandas as pd
 from pydantic.types import NonNegativeInt
+from typing_extensions import deprecated
+from typing import Optional
+
 import bluecellulab
 from bluecellulab.cell import CellDict
 from bluecellulab.cell.sonata_proxy import SonataProxy
@@ -39,24 +42,29 @@ 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
 
 logger = logging.getLogger(__name__)
 
 
+@deprecated("SSim will be removed, use CircuitSimulation instead.")
 class SSim:
     """Class that loads a circuit simulation to do cell simulations."""
 
-    @load_hoc_and_mod_files
+
+class CircuitSimulation:
+    """Class that loads a circuit simulation to do cell simulations."""
+
+    @load_mod_files
     def __init__(
         self,
         simulation_config: str | Path | SimulationConfig,
@@ -106,14 +114,11 @@ 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
 
+        self.projections: list[str] = []
+
         condition_parameters = self.circuit_access.config.condition_parameters()
         set_global_condition_parameters(condition_parameters)
 
@@ -224,34 +229,34 @@ class SSim:
                 }
 
         if self.gids_instantiated:
-            raise Exception("SSim: instantiate_gids() called twice on the \
-                    same SSim, this is not supported yet")
+            raise BluecellulabError(
+                "instantiate_gids() is called twice on the "
+                "same CircuitSimumation, this is not supported")
         else:
             self.gids_instantiated = True
 
         if pre_spike_trains or add_replay:
             if add_synapses is False:
-                raise Exception("SSim: you need to set add_synapses to True "
-                                "if you want to specify use add_replay or "
-                                "pre_spike_trains")
+                raise BluecellulabError("You need to set add_synapses to True "
+                                        "if you want to specify use add_replay or "
+                                        "pre_spike_trains")
 
         if add_projections is True:
-            projections = self.circuit_access.config.get_all_projection_names()
+            self.projections = self.circuit_access.config.get_all_projection_names()
         elif add_projections is False:
-            projections = []
+            self.projections = []
         else:
-            projections = add_projections
+            self.projections = add_projections
 
         self._add_cells(cell_ids)
         if add_synapses:
             self._add_synapses(
                 pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
         if add_replay or interconnect_cells or pre_spike_trains:
             if add_replay and not add_synapses:
-                raise Exception("SSim: add_replay option can not be used if "
-                                "add_synapses is False")
+                raise BluecellulabError("add_replay option can not be used if "
+                                        "add_synapses is False")
             self._add_connections(add_replay=add_replay,
                                   interconnect_cells=interconnect_cells,
                                   user_pre_spike_trains=pre_spike_trains)  # type: ignore
@@ -354,18 +359,17 @@ class SSim:
                 ornstein_uhlenbeck_stim_count += 1
 
     def _add_synapses(
-            self, pre_gids=None, add_minis=False, projections=None):
+            self, pre_gids=None, add_minis=False):
         """Instantiate all the synapses."""
         for cell_id in self.cells:
             self._add_cell_synapses(
                 cell_id, pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
 
     def _add_cell_synapses(
-        self, cell_id: CellId, pre_gids=None, add_minis=False, projections=None
+        self, cell_id: CellId, pre_gids=None, add_minis=False
     ) -> None:
-        syn_descriptions = self.get_syn_descriptions(cell_id, projections=projections)
+        syn_descriptions = self.get_syn_descriptions(cell_id)
 
         if pre_gids is not None:
             if self.circuit_format == CircuitFormat.SONATA:
@@ -420,12 +424,10 @@ class SSim:
         )
         return syn_descriptions[filtered_rows]
 
-    def get_syn_descriptions(
-        self, cell_id: int | tuple[str, int], projections=None
-    ) -> pd.DataFrame:
+    def get_syn_descriptions(self, cell_id: int | tuple[str, int]) -> pd.DataFrame:
         """Get synapse descriptions dataframe."""
         cell_id = create_cell_id(cell_id)
-        return self.circuit_access.extract_synapses(cell_id, projections=projections)
+        return self.circuit_access.extract_synapses(cell_id, projections=self.projections)
 
     @staticmethod
     def merge_pre_spike_trains(*train_dicts) -> dict[CellId, np.ndarray]:
@@ -554,7 +556,7 @@ class SSim:
         cvode: bool = False,
         show_progress: bool = False,
     ):
-        """Simulate the SSim.
+        """Simulate the Circuit.
 
         Parameters
         ----------
@@ -596,8 +598,10 @@ 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 +616,6 @@ 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)
@@ -710,7 +712,7 @@ class SSim:
         return voltage
 
     def delete(self):
-        """Delete ssim and all of its attributes.
+        """Delete CircuitSimulation and all of its attributes.
 
         NEURON objects are explicitly needed to be deleted.
         """

bluecellulab/connection.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/dendrogram.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/exceptions.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/graph.py

@@ -82,4 +82,4 @@ def plot_graph(G: nx.Graph, node_size: float = 400, edge_width: float = 0.4, nod
     # Add text at the bottom of the figure
     plt.figtext(0.5, 0.01, "Network of simulated cells", ha="center", fontsize=10, va="bottom")
 
-    plt.show()
+    return plt