bluecellulab 2.6.69__tar.gz → 2.6.71__tar.gz

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.69
+Version: 2.6.71
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/bluecellulab/cell/core.py

@@ -840,7 +840,18 @@ class Cell(InjectableMixin, PlottableMixin):
         connected to that cell."""
         if self.sonata_proxy is None:
             raise BluecellulabError("Cell: add_synapse_replay requires a sonata proxy.")
-        synapse_spikes: dict = get_synapse_replay_spikes(stimulus.spike_file)
+
+        file_path = Path(stimulus.spike_file).expanduser()
+        if not file_path.is_absolute():
+            config_dir = stimulus.config_dir
+            if config_dir is not None:
+                file_path = Path(config_dir) / file_path
+
+        file_path = file_path.resolve()
+
+        if not file_path.exists():
+            raise FileNotFoundError(f"Spike file not found: {str(file_path)}")
+        synapse_spikes: dict = get_synapse_replay_spikes(str(file_path))
         for synapse_id, synapse in self.synapses.items():
             source_population = synapse.syn_description["source_population_name"]
             pre_gid = CellId(

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/bluecellulab/circuit/config/sonata_simulation_config.py

@@ -55,8 +55,9 @@ class SonataSimulationConfig:
         inputs = self.impl.config.get("inputs")
         if inputs is None:
             return result
+        config_dir = self._get_config_dir()
         for value in inputs.values():
-            stimulus = Stimulus.from_sonata(value)
+            stimulus = Stimulus.from_sonata(value, config_dir=config_dir)
             if stimulus:
                 result.append(stimulus)
         return result
@@ -84,7 +85,11 @@ class SonataSimulationConfig:
         filepath = self.impl.config.get("compartment_sets_file")
         if not filepath:
             raise ValueError("No 'compartment_sets_file' entry found in SONATA config.")
-        with open(filepath, 'r') as f:
+        config_dir = self._get_config_dir()
+        full_path = Path(filepath)
+        if config_dir is not None and not full_path.is_absolute():
+            full_path = Path(config_dir) / filepath
+        with open(full_path, 'r') as f:
             return json.load(f)
 
     @lru_cache(maxsize=1)
@@ -214,3 +219,12 @@ class SonataSimulationConfig:
         connection_override: ConnectionOverrides
     ) -> None:
         self._connection_overrides.append(connection_override)
+
+    def _get_config_dir(self):
+        # Prefer config_path, fallback to _simulation_config_path
+        config_path = getattr(self.impl, "config_path", None)
+        if config_path is None:
+            sim_config_path = getattr(self.impl, "_simulation_config_path", None)
+            if sim_config_path is not None:
+                config_path = Path(sim_config_path)
+        return str(config_path.parent) if config_path is not None else None

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -19,7 +19,6 @@ Run-time validates the data via Pydantic.
 from __future__ import annotations
 
 from enum import Enum
-from pathlib import Path
 from typing import Optional
 import warnings
 
@@ -212,7 +211,7 @@ class Stimulus:
             raise ValueError(f"Unknown pattern {pattern}")
 
     @classmethod
-    def from_sonata(cls, stimulus_entry: dict) -> Optional[Stimulus]:
+    def from_sonata(cls, stimulus_entry: dict, config_dir: Optional[str] = None) -> Optional[Stimulus]:
         pattern = Pattern.from_sonata(stimulus_entry["module"])
         if pattern == Pattern.NOISE:
             return Noise(
@@ -259,6 +258,7 @@ class Stimulus:
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 spike_file=stimulus_entry["spike_file"],
+                config_dir=config_dir,
             )
         elif pattern == Pattern.SHOT_NOISE:
             return ShotNoise(
@@ -361,13 +361,7 @@ class RelativeLinear(Stimulus):
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class SynapseReplay(Stimulus):
     spike_file: str
-
-    @field_validator("spike_file")
-    @classmethod
-    def spike_file_exists(cls, v):
-        if not Path(v).exists():
-            raise ValueError(f"spike_file {v} does not exist")
-        return v
+    config_dir: Optional[str] = None
 
 
 @dataclass(frozen=True, config=dict(extra="forbid"))

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/bluecellulab/tools.py

@@ -127,7 +127,7 @@ def calculate_SS_voltage_subprocess(
     simulation.run(1000, cvode=template_accepts_cvode(template_path))
     time = cell.get_time()
     voltage = cell.get_voltage_recording(section=neuron_section, segx=segx)
-    SS_voltage = np.mean(voltage[np.where((time < 1000) & (time > 800))])
+    SS_voltage = np.mean(voltage[np.where((time <= 1000) & (time > 800))])
     cell.delete()
 
     if check_for_spiking:

{bluecellulab-2.6.69 → bluecellulab-2.6.71}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.69
+Version: 2.6.71
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0