bluecellulab 2.6.59__py3-none-any.whl → 2.6.61__py3-none-any.whl

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/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/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.dist-info → bluecellulab-2.6.61.dist-info}/METADATA

@@ -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.dist-info → bluecellulab-2.6.61.dist-info}/RECORD

@@ -49,7 +49,7 @@ bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1m
 bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=V3eqOzskX7VrMDpl-nMQVEhDg8QWgRmRduyJBii5sgI,6974
 bluecellulab/circuit/config/definition.py,sha256=I1jd4KUX21mw03FEv1aYNsT0UFbDANY3YEPwwKXqe4k,2774
 bluecellulab/circuit/config/sections.py,sha256=QRnU44-OFvHxcF1LX4bAEP9dk3I6UKsuPNBbWkdfmRE,7151
-bluecellulab/circuit/config/sonata_simulation_config.py,sha256=eRI5x1AEg0NetTsuUZhWiHNhW8zIPYul-QqX_clHQLg,6533
+bluecellulab/circuit/config/sonata_simulation_config.py,sha256=BlezWJ3dRNIu0Xs6gocscX5X69u45FSrqBtYWRTdhi4,6936
 bluecellulab/hoc/Cell.hoc,sha256=z77qRQG_-afj-RLX0xN6V-K6Duq3bR7vmlDrGWPdh4E,16435
 bluecellulab/hoc/RNGSettings.hoc,sha256=okJBdqlPXET8BrpG1Q31GdaxHfpe3CE0L5P7MAhfQTE,1227
 bluecellulab/hoc/TDistFunc.hoc,sha256=WKX-anvL83xGuGPH9g1oIORB17UM4Pi3-iIXzKO-pUQ,2663
@@ -61,16 +61,16 @@ bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQ
 bluecellulab/simulation/report.py,sha256=i_VjwIkDnHHAUk4Tx2F5LhaeBVBctcOzchK_8nG6NFw,10474
 bluecellulab/simulation/simulation.py,sha256=VhftOMYU1Rfrphvud6f0U4kvbUivSviQ5TlVljuTb88,6486
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
-bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=dTpwfRxH4c4yJDYyKrO6X-2Nqdy-QT3GxGQjfsRhNVY,17158
+bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=h_SqjJ-L3yNxiEO8I6Cy7i-lhfZXjrdCc92dl8bjOog,17229
 bluecellulab/stimulus/factory.py,sha256=4fvVFFjOGHSqBidLe_W1zQozfMEeePXWO6yYCs30-SM,30780
 bluecellulab/stimulus/stimulus.py,sha256=a_hKJUtZmIgjiFjbJf6RzUPokELqn0IHCgIWGw5XLm8,30322
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=NHwRMYMrnRVm_sHmyKTJ1bdoNmWZNU4UPOGu7FCi-PE,6987
 bluecellulab/synapse/synapse_types.py,sha256=zs_yBvGTH4QrbQF3nEViidyq1WM_ZcTSFdjUxB3khW0,16871
-bluecellulab/validation/validation.py,sha256=X8Pwj2oCPiMjBdMMWj2SwRSbnyZcUjqFo3PGT-6lWho,18465
-bluecellulab-2.6.59.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.59.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.59.dist-info/METADATA,sha256=rGUXgmt24dbIO3juu7j9qBOfk4KDaEkC2UQbeeNG3Uw,8259
-bluecellulab-2.6.59.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.59.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.59.dist-info/RECORD,,
+bluecellulab/validation/validation.py,sha256=vLaOAyCO1qwwQ5Ud9X9NDX3iSsh_2S5tUA9xRmoDHiA,18465
+bluecellulab-2.6.61.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.61.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.61.dist-info/METADATA,sha256=DiUIlPkw6xJkCmmFK2tCHbfeaoY3VdsUAMFsK-iN6BE,8259
+bluecellulab-2.6.61.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.61.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.61.dist-info/RECORD,,