bluecellulab 2.6.69__py3-none-any.whl → 2.6.71__py3-none-any.whl

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/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/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/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.dist-info → bluecellulab-2.6.71.dist-info}/METADATA

@@ -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.dist-info → bluecellulab-2.6.71.dist-info}/RECORD

@@ -10,7 +10,7 @@ bluecellulab/plotwindow.py,sha256=ePU-EegZ1Sqk0SoYYiQ6k24ZO4s3Hgfpx10uePiJ5xM,27
 bluecellulab/psection.py,sha256=FSOwRNuOTyB469BM-jPEf9l1J59FamXmzrQgBI6cnP4,6174
 bluecellulab/psegment.py,sha256=PTgoGLqM4oFIdF_8QHFQCU59j-8TQmtq6PakiGUQhIo,3138
 bluecellulab/rngsettings.py,sha256=2Ykb4Ylk3XTs58x1UIxjg8XJqjSpnCgKRZ8avXCDpxk,4237
-bluecellulab/tools.py,sha256=XvfWGSbNevAEUa8TYlAJtRurKOvbARY0wLa6qHkm93g,21925
+bluecellulab/tools.py,sha256=ePal9-y6AnIgSdRzqqL8fH57M96VXUWPEGvJ7mpz4Ps,21926
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=0NhwlzyLnSi8kziSfDsQf7pokO4qDkMJVAO33kSX4O0,2227
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
@@ -21,7 +21,7 @@ bluecellulab/analysis/plotting.py,sha256=PqRoaZz33ULMw8A9YnZXXrxcUd84M_dwlYMTFhG
 bluecellulab/analysis/utils.py,sha256=eMirP557D11BuedgSqjripDxOq1haIldNbnYNetV1bg,121
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=VE7pi-NsMVRSmo-PSdbiLYmolDOu0Gc6JxFBkuQpFdk,1346
-bluecellulab/cell/core.py,sha256=PKus_O8iREcU5-SDBjM7XbRUwromPz-K9imGo2Q11-4,37875
+bluecellulab/cell/core.py,sha256=xNyY3Ly4E7wb4LGIYcA2vT0EKsQYd1tNItcmxgKKK2o,38267
 bluecellulab/cell/injector.py,sha256=GB0pmyZMOHNV-lzd_t4cLoDE87S58IMbe7-qU1zBWvE,19033
 bluecellulab/cell/plotting.py,sha256=t2qDUabFtsBb-nJMkDh5UfsgW-wvQ2wfDwAVZ8-hWPo,4032
 bluecellulab/cell/random.py,sha256=pemekc11geRBKD8Ghb82tvKOZLfFWkUz1IKLc_NWg-A,1773
@@ -50,7 +50,7 @@ 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=cotKRDHOjzZKNgNSrZ29voU-66W8jaGt5yuge1hyv18,2953
 bluecellulab/circuit/config/sections.py,sha256=QRnU44-OFvHxcF1LX4bAEP9dk3I6UKsuPNBbWkdfmRE,7151
-bluecellulab/circuit/config/sonata_simulation_config.py,sha256=J1DFqNxIJKAxD1KU_oJV9tigMdpT_Not0Q8SF5q2EeQ,7271
+bluecellulab/circuit/config/sonata_simulation_config.py,sha256=8b3OkjYG7MJnrm498Tx6x1B2MbvwDZO0aAAxy6iHuts,7983
 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
@@ -69,16 +69,16 @@ bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQ
 bluecellulab/simulation/report.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bluecellulab/simulation/simulation.py,sha256=OfrzeHvLmOV2ptYcGie_fVGrtkDfizLpE6ZyQWVxnIE,6492
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
-bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=h_SqjJ-L3yNxiEO8I6Cy7i-lhfZXjrdCc92dl8bjOog,17229
+bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=Xdd4j3oiGHNsuGEjI-KLy0EQd-Qd7C9JvOSLJwIr7pE,17113
 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=D35LE_131CtIzeeePAPz1OFzncGjAcvF02lSIvGvL2E,21331
-bluecellulab-2.6.69.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.69.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.69.dist-info/METADATA,sha256=FWJpgOEcP_8xqAXBDpNrlgkB0wqEj6YF1z8NUDd2nSM,8359
-bluecellulab-2.6.69.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.69.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.69.dist-info/RECORD,,
+bluecellulab-2.6.71.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.71.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.71.dist-info/METADATA,sha256=1dFG_vPcTlOZSX9CTbOdsa1uPxdc1OmlLrCdxTaDccA,8359
+bluecellulab-2.6.71.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.71.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.71.dist-info/RECORD,,