bluecellulab 2.6.72__tar.gz → 2.6.73__tar.gz

{bluecellulab-2.6.72 → bluecellulab-2.6.73}/.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

{bluecellulab-2.6.72 → bluecellulab-2.6.73}/PKG-INFO

@@ -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 → bluecellulab-2.6.73}/README.rst

@@ -67,7 +67,7 @@ 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 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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-2.6.72 → bluecellulab-2.6.73}/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 → bluecellulab-2.6.73}/bluecellulab.egg-info/PKG-INFO

@@ -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 → bluecellulab-2.6.73}/bluecellulab.egg-info/requires.txt

@@ -1,5 +1,5 @@
 NEURON<9.0.0,>=8.0.2
-numpy<2.0.0,>=1.8.0
+numpy>=2.0.0
 matplotlib<4.0.0,>=3.0.0
 pandas<3.0.0,>=1.0.0
 bluepysnap<4.0.0,>=3.0.0

{bluecellulab-2.6.72 → bluecellulab-2.6.73}/pyproject.toml

@@ -29,7 +29,7 @@ keywords = [
 ]
 dependencies = [
     "NEURON>=8.0.2,<9.0.0",
-    "numpy>=1.8.0,<2.0.0",
+    "numpy>=2.0.0",
     "matplotlib>=3.0.0,<4.0.0",
     "pandas>=1.0.0,<3.0.0",
     "bluepysnap>=3.0.0,<4.0.0",

{bluecellulab-2.6.72 → bluecellulab-2.6.73}/tox.ini

@@ -37,7 +37,7 @@ commands =
 envdir={toxworkdir}/{envname}
 deps =
     pycodestyle>=2.10.0
-    mypy>=1.3.0,<1.7.0
+    mypy>=1.10,<2.0
     pandas-stubs>=2.0.0
     types-setuptools>=67.8.0.0
     ruff>=0.0.270