bluecellulab 2.6.59__tar.gz → 2.6.61__tar.gz

{bluecellulab-2.6.59 → bluecellulab-2.6.61}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.59
+Version: 2.6.61
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.59 → bluecellulab-2.6.61}/bluecellulab/circuit/config/sonata_simulation_config.py

@@ -88,11 +88,23 @@ class SonataSimulationConfig:
 
     @lru_cache(maxsize=1)
     def get_node_sets(self) -> dict[str, dict]:
-        filepath = self.impl.circuit.config.get("node_sets_file")
-        if not filepath:
-            raise ValueError("No 'node_sets_file' entry found in SONATA config.")
-        with open(filepath, 'r') as f:
-            return json.load(f)
+        circuit_filepath = self.impl.circuit.config.get("node_sets_file")
+        base_node_sets = {}
+        if circuit_filepath:
+            with open(circuit_filepath, "r") as f:
+                base_node_sets = json.load(f)
+
+        sim_filepath = self.impl.config.get("node_sets_file")
+        if sim_filepath:
+            with open(sim_filepath, "r") as f:
+                sim_node_sets = json.load(f)
+            # Overwrite/add entries
+            base_node_sets.update(sim_node_sets)
+
+        if not base_node_sets:
+            raise ValueError("No 'node_sets_file' found in simulation or circuit config.")
+
+        return base_node_sets
 
     @lru_cache(maxsize=1)
     def get_report_entries(self) -> dict[str, dict]:

{bluecellulab-2.6.59 → bluecellulab-2.6.61}/bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -243,7 +243,7 @@ class Stimulus:
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 amp_start=stimulus_entry["amp_start"],
-                amp_end=stimulus_entry["amp_end"],
+                amp_end=stimulus_entry.get("amp_end", stimulus_entry["amp_start"]),
             )
         elif pattern == Pattern.RELATIVE_LINEAR:
             return RelativeLinear(
@@ -251,7 +251,7 @@ class Stimulus:
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 percent_start=stimulus_entry["percent_start"],
-                percent_end=stimulus_entry["percent_end"],
+                percent_end=stimulus_entry.get("percent_end", stimulus_entry["percent_start"]),
             )
         elif pattern == Pattern.SYNAPSE_REPLAY:
             return SynapseReplay(
@@ -285,7 +285,7 @@ class Stimulus:
                 decay_time=stimulus_entry["decay_time"],
                 mean_percent=stimulus_entry["mean_percent"],
                 sd_percent=stimulus_entry["sd_percent"],
-                relative_skew=stimulus_entry.get("RelativeSkew", 0.5),
+                relative_skew=stimulus_entry.get("relative_skew", 0.5),
                 seed=stimulus_entry.get("random_seed", None),
                 mode=ClampMode(stimulus_entry.get("input_type", "current_clamp").lower()),
                 reversal=stimulus_entry.get("reversal", 0.0)

{bluecellulab-2.6.59 → bluecellulab-2.6.61}/bluecellulab/validation/validation.py

@@ -429,7 +429,7 @@ def thumbnail_test(template_params, rheobase, out_dir):
     outpath = plot_trace(
         recording,
         out_dir,
-        fname="thumbnail.pdf",
+        fname="thumbnail.png",
         title="",
         plot_current=False
     )

{bluecellulab-2.6.59 → bluecellulab-2.6.61}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.59
+Version: 2.6.61
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0