bluecellulab 2.6.15__py3-none-any.whl → 2.6.17__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/cell/core.py

@@ -719,27 +719,26 @@ class Cell(InjectableMixin, PlottableMixin):
             pre_gid = CellId(
                 source_population, int(synapse.syn_description[SynapseProperty.PRE_GID])
             )
-            if self.sonata_proxy.circuit_access.target_contains_cell(stimulus.source, pre_gid):
-                if pre_gid.id in synapse_spikes:
-                    spikes_of_interest = synapse_spikes[pre_gid.id]
-                    # filter spikes of interest >=stimulus.delay, <=stimulus.duration
-                    spikes_of_interest = spikes_of_interest[
-                        (spikes_of_interest >= stimulus.delay)
-                        & (spikes_of_interest <= stimulus.duration)
-                    ]
-                    connection = bluecellulab.Connection(
-                        synapse,
-                        pre_spiketrain=spikes_of_interest,
-                        pre_cell=None,
-                        stim_dt=self.record_dt,
-                        spike_threshold=spike_threshold,
-                        spike_location=spike_location,
-                    )
-                    logger.debug(
-                        f"Added synapse replay from {pre_gid} to {self.cell_id.id}, {synapse_id}"
-                    )
-
-                    self.connections[synapse_id] = connection
+            if pre_gid.id in synapse_spikes:
+                spikes_of_interest = synapse_spikes[pre_gid.id]
+                # filter spikes of interest >=stimulus.delay, <=stimulus.duration
+                spikes_of_interest = spikes_of_interest[
+                    (spikes_of_interest >= stimulus.delay)
+                    & (spikes_of_interest <= stimulus.duration)
+                ]
+                connection = bluecellulab.Connection(
+                    synapse,
+                    pre_spiketrain=spikes_of_interest,
+                    pre_cell=None,
+                    stim_dt=self.record_dt,
+                    spike_threshold=spike_threshold,
+                    spike_location=spike_location,
+                )
+                logger.debug(
+                    f"Added synapse replay from {pre_gid} to {self.cell_id.id}, {synapse_id}"
+                )
+
+                self.connections[synapse_id] = connection
 
     @property
     def info_dict(self):

bluecellulab/circuit/simulation_access.py

@@ -172,7 +172,7 @@ class SonataSimulationAccess:
 
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
-    """Read the .dat file containing the spike replays."""
+    """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'][:]

bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -243,7 +243,6 @@ class Stimulus:
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 spike_file=stimulus_entry["spike_file"],
-                source=stimulus_entry["source"],
             )
         elif pattern == Pattern.SHOT_NOISE:
             return ShotNoise(
@@ -331,7 +330,6 @@ class RelativeLinear(Stimulus):
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class SynapseReplay(Stimulus):
     spike_file: str
-    source: str
 
     @field_validator("spike_file")
     @classmethod

{bluecellulab-2.6.15.dist-info → bluecellulab-2.6.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.15
+Version: 2.6.17
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.15.dist-info → bluecellulab-2.6.17.dist-info}/RECORD

@@ -15,10 +15,10 @@ 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=ZVzy3tsA5X7OyCmnHQn0d6AlNg9rOG2ojKuojvKdsFw,31487
+bluecellulab/cell/core.py,sha256=2UtXXd4FA2X5A_7ljjbN4yobpMWD2FWfux67ZFND2rI,31315
 bluecellulab/cell/injector.py,sha256=XC49VSHw78xCHzLJKO_-unnnVZAZXsYg5qbmZPx01AA,18091
 bluecellulab/cell/plotting.py,sha256=hW5KAmaSonJ1tgR6xRrnfVe33I5mBsBUrKJQwGvAbUc,4032
 bluecellulab/cell/random.py,sha256=FDby9BN4eJT27COwHP59bhDE2v-c6rdOKNFj3cYZTVY,1773
@@ -35,7 +35,7 @@ bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGp
 bluecellulab/circuit/format.py,sha256=eYhiBIQnPnnVBmaSDymFjQprXN9QjEYKmFhb2mIS86o,1674
 bluecellulab/circuit/iotools.py,sha256=KVE7x5LNQ4RgjNh05Q-h3Swpbs3nRFtrcWNHj62aiRI,1585
 bluecellulab/circuit/node_id.py,sha256=gaRAW3UhbPOPsoXMHLjo3qH9iNod7YB8ZOcguWprrU4,1265
-bluecellulab/circuit/simulation_access.py,sha256=jrVz6pFNAuwvuvsTq9OqeDfjIZ5akE98RBMBNDwuDVQ,7062
+bluecellulab/circuit/simulation_access.py,sha256=BGstSD0nkmW4AMRCztYcM6ehWj-XuznWUuG0vjs0aZI,7061
 bluecellulab/circuit/synapse_properties.py,sha256=a4-Yw_f8JIR6i2YG8qhCW97TMSd_Z-aF6lp_a1wBwnM,6374
 bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
@@ -57,14 +57,14 @@ bluecellulab/simulation/neuron_globals.py,sha256=_8xmJPQMfCyhVn6KppK7i3jaUZaALML
 bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQkLV_U0,1514
 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/circuit_stimulus_definitions.py,sha256=QztVteUUeMZolPMVjx-S-KgpahnQlbfTziJsJ_wCmaw,15621
 bluecellulab/stimulus/factory.py,sha256=XDbnqCuMCh1RdZLKvlRucMj3wkXDqy6mEda_Oh6Yqo4,19955
 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-2.6.15.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.15.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.15.dist-info/METADATA,sha256=qDL_gdXlfPzB7pl-AowRxYMoRKfd_nfsl-61bumRdtE,7054
-bluecellulab-2.6.15.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.6.15.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.15.dist-info/RECORD,,
+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-2.6.15.dist-info → bluecellulab-2.6.17.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