bluecellulab 2.6.72__py3-none-any.whl → 2.6.73__py3-none-any.whl

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -19,6 +19,7 @@ import os
 from pathlib import Path
 from typing import Optional
 
+from bluecellulab.circuit.circuit_access.definition import CircuitAccess
 import neuron
 import pandas as pd
 from bluecellulab import circuit
@@ -42,7 +43,7 @@ if BLUEPY_AVAILABLE:
 logger = logging.getLogger(__name__)
 
 
-class BluepyCircuitAccess:
+class BluepyCircuitAccess(CircuitAccess):
     """Bluepy implementation of CircuitAccess protocol."""
 
     def __init__(self, simulation_config: str | Path | SimulationConfig) -> None:

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -25,7 +25,7 @@ from bluepysnap import Circuit as SnapCircuit
 import neuron
 import pandas as pd
 from bluecellulab import circuit
-from bluecellulab.circuit.circuit_access.definition import EmodelProperties
+from bluecellulab.circuit.circuit_access.definition import CircuitAccess, EmodelProperties
 from bluecellulab.circuit import CellId, SynapseProperty
 from bluecellulab.circuit.config import SimulationConfig
 from bluecellulab.circuit.synapse_properties import SynapseProperties
@@ -38,7 +38,7 @@ from bluecellulab.circuit.synapse_properties import (
 logger = logging.getLogger(__name__)
 
 
-class SonataCircuitAccess:
+class SonataCircuitAccess(CircuitAccess):
     """Sonata implementation of CircuitAccess protocol."""
 
     def __init__(self, simulation_config: str | Path | SimulationConfig) -> None:

bluecellulab/circuit/config/bluepy_simulation_config.py

@@ -188,6 +188,16 @@ class BluepySimulationConfig:
         else:
             return None
 
+    @property
+    def tstart(self) -> Optional[float]:
+        return 0.0
+
+    @property
+    def tstop(self) -> Optional[float]:
+        if 'Duration' in self.impl.Run:
+            return float(self.impl.Run['Duration'])
+        return None
+
     def add_connection_override(
         self,
         connection_override: ConnectionOverrides

bluecellulab/circuit/node_id.py

@@ -31,6 +31,6 @@ def create_cell_id(cell_id: int | tuple[str, int] | CellId) -> CellId:
         return CellId("", cell_id)
 
 
-def create_cell_ids(cell_ids: list[int] | list[tuple[str, int] | CellId]) -> list[CellId]:
+def create_cell_ids(cell_ids: list[int | tuple[str, int] | CellId]) -> list[CellId]:
     """Make a list of CellId from a list of tuple or int."""
     return [create_cell_id(cell_id) for cell_id in cell_ids]

bluecellulab/circuit_simulation.py

@@ -125,7 +125,7 @@ class CircuitSimulation:
 
     def instantiate_gids(
         self,
-        cells: int | tuple[str, int] | list[int] | list[tuple[str, int]],
+        cells: int | tuple[str, int] | list[int | tuple[str, int]],
         add_replay: bool = False,
         add_stimuli: bool = False,
         add_synapses: bool = False,
@@ -223,7 +223,7 @@ class CircuitSimulation:
                                 will automatically set this option to
                                 True.
         """
-        if not isinstance(cells, Iterable) or isinstance(cells, tuple):
+        if not isinstance(cells, list):
             cells = [cells]
 
         # convert to CellId objects

bluecellulab/plotwindow.py

@@ -42,7 +42,7 @@ class PlotWindow:
         linenumber = 0
         for var_name in self.var_list:
             recording = self.cell.get_recording(var_name)
-            if recording:
+            if recording is not None and recording.size > 0:
                 time = self.cell.get_time()
             else:
                 time = self.cell.get_time()[1:]

bluecellulab/utils.py

@@ -53,7 +53,7 @@ class NumpyEncoder(json.JSONEncoder):
             ),
         ):
             return int(obj)
-        elif isinstance(obj, (np.float_, np.float16, np.float32, np.float64)):
+        elif isinstance(obj, (np.float64, np.float16, np.float32, np.float64)):
             return float(obj)
         elif isinstance(obj, np.ndarray):
             return obj.tolist()

{bluecellulab-2.6.72.dist-info → bluecellulab-2.6.73.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.72
+Version: 2.6.73
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -19,7 +19,7 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.txt
 Requires-Dist: NEURON<9.0.0,>=8.0.2
-Requires-Dist: numpy<2.0.0,>=1.8.0
+Requires-Dist: numpy>=2.0.0
 Requires-Dist: matplotlib<4.0.0,>=3.0.0
 Requires-Dist: pandas<3.0.0,>=1.0.0
 Requires-Dist: bluepysnap<4.0.0,>=3.0.0
@@ -102,7 +102,7 @@ Main dependencies
 =================
 
 * `Python 3.9+ <https://www.python.org/downloads/release/python-390/>`_
-* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
+* `NEURON <=8.2.7 <https://pypi.org/project/NEURON/>`__
 
 Installation
 ============

{bluecellulab-2.6.72.dist-info → bluecellulab-2.6.73.dist-info}/RECORD

@@ -1,18 +1,18 @@
 bluecellulab/__init__.py,sha256=1d_CKIJLIpon7o13h3lBnV_-33obZEPwa9KDTjlFPD8,880
-bluecellulab/circuit_simulation.py,sha256=CryoBSUGc9z6nIAyNzCsyppeSlc_URJX6hZoZPgQI2Q,36807
+bluecellulab/circuit_simulation.py,sha256=GGAkJq0Jk_ClB1XTyrf8g6Sirntj0E9IBeI76acJ2yU,36769
 bluecellulab/connection.py,sha256=-xT0mU7ppeHI_qjCKj17TtxXVVcUDgBsaMKt9ODmcEU,4640
 bluecellulab/dendrogram.py,sha256=FjS6RZ6xcp5zJoY5d5qv_edqPM13tL2-UANgbZuDBjY,6427
 bluecellulab/exceptions.py,sha256=1lKD92VIyD8cUggAI1SLxeKzj_09Ik_TlHCzPLCvDHg,2379
 bluecellulab/graph.py,sha256=o-9NnRrli0AqfGcw0-nhjaICH2IeqCH76uAlbZbo2dQ,3419
 bluecellulab/importer.py,sha256=ePxoquSRGGK123mR_VWDLKf9CE-N28NXAAY1DCm3T7Y,2900
 bluecellulab/neuron_interpreter.py,sha256=Nerehh6SNIRcTH8NHvyZvL_axadeix67uer-lRGuw9U,2185
-bluecellulab/plotwindow.py,sha256=ePU-EegZ1Sqk0SoYYiQ6k24ZO4s3Hgfpx10uePiJ5xM,2721
+bluecellulab/plotwindow.py,sha256=496tNvrd7xQ9SbSLRXF1VPIvWWqA2jl03-ZPMJ-wx_0,2756
 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=OamYjgBBBiUiXlf4zCDOjI-SuA6o9Ck8UsKsAi_8gEg,19483
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
-bluecellulab/utils.py,sha256=0NhwlzyLnSi8kziSfDsQf7pokO4qDkMJVAO33kSX4O0,2227
+bluecellulab/utils.py,sha256=tATZ814TtQO3fTsm5Q0KiANCDLFDZYtkfFQlI-Kxx_U,2228
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bluecellulab/analysis/analysis.py,sha256=qZN2R7IKMOda8sVEDU61TkTDNUbaZjIWbwP3pM6Fcm8,24184
@@ -38,16 +38,16 @@ bluecellulab/cell/ballstick/morphology.asc,sha256=EO0VIRilJAwpiDP2hIevwusfvYptNY
 bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGpmZs,361
 bluecellulab/circuit/format.py,sha256=90gWOXg6HK0R9a4WFSnnRH8XezxmzOGk5dRpJHbvbbU,1674
 bluecellulab/circuit/iotools.py,sha256=Q65xYDaiensMtrulC3OLsS2_hcWr_Kje0nXFrAizMMo,1589
-bluecellulab/circuit/node_id.py,sha256=FdoFAGq0_sCyQySOuNI0chdbVr3L8R0w2Y1em5MyIDA,1265
+bluecellulab/circuit/node_id.py,sha256=g_f_PvjaX59yXBTWRIpXibbgFny6xBWVErjVErahTTc,1259
 bluecellulab/circuit/simulation_access.py,sha256=8LX5nbKw_Hu7AR3pGLdTFGwehvhaj-r8Mh1q3dVoiVg,7745
 bluecellulab/circuit/synapse_properties.py,sha256=TvUMiXZAAeYo1zKkus3z1EUvrE9QCIQ3Ze-jSnPSJWY,6374
 bluecellulab/circuit/validate.py,sha256=wntnr7oIDyasqD1nM-kqz1NpfWDxBGhx0Ep3e5hHXIw,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
-bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=m5PWSYrrkORb55HN1ZgJpQFLeSHxsNBtzyJ1n0zuVro,14295
+bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=Ivj7RqIK0OYUuraTpQU1h_oeE2somBn_Tnji6XcjFt8,14383
 bluecellulab/circuit/circuit_access/definition.py,sha256=_sUU0DkesGOFW82kS1G9vki0o0aQP76z3Ltk7Vo9KK4,4435
-bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=tADHxVZw4VgZAz2z4NKMUwc0rd_EO40EZggw5fDhnF4,10411
+bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=OfqVS3z_t7dsnRuihF15fW-KuOCd7BXqRoFblpo2VL4,10441
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
-bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=V3eqOzskX7VrMDpl-nMQVEhDg8QWgRmRduyJBii5sgI,6974
+bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=3l0TqoQhsltvQnF-rKK_zFEu0-L6dAhW-Ch6z9C4wZw,7216
 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=M3dD9B69VK01lRaR84PiAj8th-x8hrAE80IpGDLqvi8,8056
@@ -76,9 +76,9 @@ bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HA
 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-2.6.72.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.72.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.72.dist-info/METADATA,sha256=wlI-kK0juc84JZFmdgzQLXarBPJ8gWpc2riGNVHZsg8,8359
-bluecellulab-2.6.72.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.72.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.72.dist-info/RECORD,,
+bluecellulab-2.6.73.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.73.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.73.dist-info/METADATA,sha256=5caaaN9HbahBUG9GX5Q4jhWNe4NiREQHB2WqfPdj8Sc,8354
+bluecellulab-2.6.73.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.73.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.73.dist-info/RECORD,,