bluecellulab 2.6.16__py3-none-any.whl → 2.6.18__py3-none-any.whl

bluecellulab/analysis/inject_sequence.py

@@ -37,6 +37,7 @@ def run_stimulus(
     stimulus: Stimulus,
     section: str,
     segment: float,
+    cvode: bool = True,
 ) -> Recording:
     """Creates a cell and stimulates it with a given stimulus.
 
@@ -45,6 +46,7 @@ def run_stimulus(
         stimulus: The input stimulus to inject into the cell.
         section: Name of the section of cell where the stimulus is to be injected.
         segment: The segment of the section where the stimulus is to be injected.
+        cvode: True to use variable time-steps. False for fixed time-steps.
 
     Returns:
         The voltage-time recording at the specified location.
@@ -61,7 +63,7 @@ def run_stimulus(
     current_vector = neuron.h.Vector()
     current_vector.record(iclamp._ref_i)
     simulation = Simulation(cell)
-    simulation.run(stimulus.stimulus_time)
+    simulation.run(stimulus.stimulus_time, cvode=cvode)
     current = np.array(current_vector.to_python())
     voltage = cell.get_voltage_recording(neuron_section, segment)
     time = cell.get_time()
@@ -78,6 +80,7 @@ def apply_multiple_stimuli(
     section_name: str | None = None,
     segment: float = 0.5,
     n_processes: int | None = None,
+    cvode: bool = True,
 ) -> StimulusRecordings:
     """Apply multiple stimuli to the cell on isolated processes.
 
@@ -91,6 +94,7 @@ def apply_multiple_stimuli(
           If None, the stimuli are applied at the soma[0] of the cell.
         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.
 
     Returns:
         A dictionary where the keys are the names of the stimuli and the values
@@ -140,7 +144,7 @@ def apply_multiple_stimuli(
         else:
             raise ValueError("Unknown stimulus name.")
 
-        task_args.append((cell.template_params, stimulus, section_name, segment))
+        task_args.append((cell.template_params, stimulus, section_name, segment, cvode))
 
     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-2.6.16.dist-info → bluecellulab-2.6.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.16
+Version: 2.6.18
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.16.dist-info → bluecellulab-2.6.18.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=K3166jDTikEMMfRPJvuqfC6VPdUfyK7Ua7_M9Tr6uZg,5738
+bluecellulab/analysis/inject_sequence.py,sha256=6_OuUtUjmSvhCj5_mX-8ZnUpv5jXUHHYDYPUcV2m0eE,5958
 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-2.6.16.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.16.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.16.dist-info/METADATA,sha256=MQKPZ5_GTCnARQeb7CjYBHAOGsJ--Cv_n-vTzjbDcKE,7054
-bluecellulab-2.6.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.6.16.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.16.dist-info/RECORD,,
+bluecellulab-2.6.18.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.18.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.18.dist-info/METADATA,sha256=qRtydITfTVimJQmOLizHxMlxNIteEBD1-W9FWWXMr74,7054
+bluecellulab-2.6.18.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+bluecellulab-2.6.18.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.18.dist-info/RECORD,,

{bluecellulab-2.6.16.dist-info → bluecellulab-2.6.18.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any