bluecellulab 2.6.17__py3-none-any.whl → 2.6.19__py3-none-any.whl

bluecellulab/analysis/inject_sequence.py

@@ -9,6 +9,7 @@ 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.circuit_stimulus_definitions import Hyperpolarizing
 from bluecellulab.stimulus.factory import Stimulus, StimulusFactory
 
 
@@ -38,6 +39,7 @@ def run_stimulus(
     section: str,
     segment: float,
     cvode: bool = True,
+    add_hypamp: bool = True,
 ) -> Recording:
     """Creates a cell and stimulates it with a given stimulus.
 
@@ -56,6 +58,9 @@ def run_stimulus(
     """
     cell = Cell.from_template_parameters(template_params)
     neuron_section = cell.sections[section]
+    if add_hypamp:
+        hyp_stim = Hyperpolarizing(target="", delay=0.0, duration=stimulus.stimulus_time)
+        cell.add_replay_hypamp(hyp_stim)
     cell.add_voltage_recording(neuron_section, segment)
     iclamp, _ = cell.inject_current_waveform(
         stimulus.time, stimulus.current, section=neuron_section, segx=segment
@@ -81,6 +86,7 @@ def apply_multiple_stimuli(
     segment: float = 0.5,
     n_processes: int | None = None,
     cvode: bool = True,
+    add_hypamp: bool = True,
 ) -> StimulusRecordings:
     """Apply multiple stimuli to the cell on isolated processes.
 
@@ -95,6 +101,7 @@ def apply_multiple_stimuli(
         segment: The segment of the section where the stimuli are applied.
         n_processes: The number of processes to use for running the stimuli.
         cvode: True to use variable time-steps. False for fixed time-steps.
+        add_hypamp: True to add the cell's holding current stimulus
 
     Returns:
         A dictionary where the keys are the names of the stimuli and the values
@@ -144,7 +151,7 @@ def apply_multiple_stimuli(
         else:
             raise ValueError("Unknown stimulus name.")
 
-        task_args.append((cell.template_params, stimulus, section_name, segment, cvode))
+        task_args.append((cell.template_params, stimulus, section_name, segment, cvode, add_hypamp))
 
     with IsolatedProcess(processes=n_processes) as pool:
         # Map expects a function and a list of argument tuples

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -47,7 +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"]
@@ -191,7 +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-2.6.17.dist-info → bluecellulab-2.6.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.17
+Version: 2.6.19
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.17.dist-info → bluecellulab-2.6.19.dist-info}/RECORD

@@ -15,7 +15,7 @@ bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,
 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=6_OuUtUjmSvhCj5_mX-8ZnUpv5jXUHHYDYPUcV2m0eE,5958
+bluecellulab/analysis/inject_sequence.py,sha256=Ih3wdNRn0-lM-NW8agrMUGS862CEgzn_hl54DFDXyjM,6325
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
 bluecellulab/cell/core.py,sha256=2UtXXd4FA2X5A_7ljjbN4yobpMWD2FWfux67ZFND2rI,31315
@@ -41,7 +41,7 @@ bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLU
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
 bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=pUoTw6wXMGZAqjjC3vpdZcm8ex108aEPw0L6fSypx9g,14273
 bluecellulab/circuit/circuit_access/definition.py,sha256=SnKBFEgdXFG-QexYRrGSzVAd7bSj7NwN0IuTsjDOrDY,4435
-bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=c0MMJuoT6_dRW8O5HSRS5hHv1zDKdW0sBR-DaP0F1bk,10351
+bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=N5ynUkDotAjAtJgECQoBej0wJTlsU7cJZGF-MyxQhF4,10361
 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
@@ -62,9 +62,9 @@ bluecellulab/stimulus/factory.py,sha256=XDbnqCuMCh1RdZLKvlRucMj3wkXDqy6mEda_Oh6Y
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=3y15LlaBoNJiU2KUeTkh70pyU5OYf6xQIMSBmmMPMak,6987
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.6.17.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.17.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.17.dist-info/METADATA,sha256=mk1GlOKidaxD1TWN0ESwwmh8wBtYtrrzNFj7_-iGtv0,7054
-bluecellulab-2.6.17.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-bluecellulab-2.6.17.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.17.dist-info/RECORD,,
+bluecellulab-2.6.19.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.19.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.19.dist-info/METADATA,sha256=IEr-rd-kfUVgbtQtMun0hl4zAWn7IRGySnn041OYpzQ,7054
+bluecellulab-2.6.19.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+bluecellulab-2.6.19.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.19.dist-info/RECORD,,