bluecellulab 2.5.3__py3-none-any.whl → 2.5.5__py3-none-any.whl

bluecellulab/__init__.py

@@ -18,7 +18,7 @@ from .psection import PSection  # NOQA
 from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
-from .ssim import SSim  # NOQA
+from .circuit_simulation import CircuitSimulation, CircuitSimulation  # NOQA
 
 
 from .simulation.neuron_globals import NeuronGlobals

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -57,7 +57,6 @@ class BluepyCircuitAccess:
             raise FileNotFoundError(
                 f"Circuit config file {simulation_config} not found.")
 
-        # to allow the usage of SimulationConfig outside of Ssim
         if isinstance(simulation_config, BluepySimulationConfig):
             simulation_config = simulation_config.impl
 

bluecellulab/circuit/iotools.py

@@ -32,7 +32,7 @@ def parse_outdat(path: str | Path) -> dict[CellId, np.ndarray]:
     # convert Series to DataFrame with 2 columns for `groupby` operation
     spike_df = spikes.to_frame().reset_index()
     if (spike_df["t"] < 0).any():
-        logger.warning('SSim: Found negative spike times in out.dat ! '
+        logger.warning('Found negative spike times in out.dat ! '
                        'Clipping them to 0')
         spike_df["t"].clip(lower=0., inplace=True)
 

bluecellulab/{ssim.py → circuit_simulation.py}

@@ -25,6 +25,8 @@ import neuron
 import numpy as np
 import pandas as pd
 from pydantic.types import NonNegativeInt
+from typing_extensions import deprecated
+
 import bluecellulab
 from bluecellulab.cell import CellDict
 from bluecellulab.cell.sonata_proxy import SonataProxy
@@ -53,9 +55,14 @@ from bluecellulab.synapse.synapse_types import SynapseID
 logger = logging.getLogger(__name__)
 
 
+@deprecated("SSim will be removed, use CircuitSimulation instead.")
 class SSim:
     """Class that loads a circuit simulation to do cell simulations."""
 
+
+class CircuitSimulation:
+    """Class that loads a circuit simulation to do cell simulations."""
+
     @load_mod_files
     def __init__(
         self,
@@ -219,16 +226,17 @@ class SSim:
                 }
 
         if self.gids_instantiated:
-            raise Exception("SSim: instantiate_gids() called twice on the \
-                    same SSim, this is not supported yet")
+            raise BluecellulabError(
+                "instantiate_gids() is called twice on the "
+                "same CircuitSimumation, this is not supported")
         else:
             self.gids_instantiated = True
 
         if pre_spike_trains or add_replay:
             if add_synapses is False:
-                raise Exception("SSim: you need to set add_synapses to True "
-                                "if you want to specify use add_replay or "
-                                "pre_spike_trains")
+                raise BluecellulabError("You need to set add_synapses to True "
+                                        "if you want to specify use add_replay or "
+                                        "pre_spike_trains")
 
         if add_projections is True:
             projections = self.circuit_access.config.get_all_projection_names()
@@ -245,8 +253,8 @@ class SSim:
                 projections=projections)
         if add_replay or interconnect_cells or pre_spike_trains:
             if add_replay and not add_synapses:
-                raise Exception("SSim: add_replay option can not be used if "
-                                "add_synapses is False")
+                raise BluecellulabError("add_replay option can not be used if "
+                                        "add_synapses is False")
             self._add_connections(add_replay=add_replay,
                                   interconnect_cells=interconnect_cells,
                                   user_pre_spike_trains=pre_spike_trains)  # type: ignore
@@ -549,7 +557,7 @@ class SSim:
         cvode: bool = False,
         show_progress: bool = False,
     ):
-        """Simulate the SSim.
+        """Simulate the Circuit.
 
         Parameters
         ----------
@@ -705,7 +713,7 @@ class SSim:
         return voltage
 
     def delete(self):
-        """Delete ssim and all of its attributes.
+        """Delete CircuitSimulation and all of its attributes.
 
         NEURON objects are explicitly needed to be deleted.
         """

bluecellulab/rngsettings.py

@@ -105,7 +105,7 @@ class RNGSettings:
         options = {"Compatibility": 0, "Random123": 1, "UpdatedMCell": 2}
         if new_val not in options:
             raise UndefinedRNGException(
-                "SSim: RNG mode %s not in accepted list: %s"
+                "RNG mode's value %s is not in the accepted list: %s"
                 % (self.mode, list(options.keys()))
             )
         else:

bluecellulab/tools.py

@@ -151,9 +151,9 @@ def holding_current(
 ) -> Tuple[float, float]:
     """Calculate the holding current necessary for a given holding voltage."""
     cell_id = bluecellulab.circuit.node_id.create_cell_id(cell_id)
-    ssim = bluecellulab.SSim(circuit_path)
+    circuit_sim = bluecellulab.CircuitSimulation(circuit_path)
 
-    cell_kwargs = ssim.fetch_cell_kwargs(cell_id)
+    cell_kwargs = circuit_sim.fetch_cell_kwargs(cell_id)
     with IsolatedProcess() as runner:
         i_hold, v_control = runner.apply(
             holding_current_subprocess, [v_hold, enable_ttx, cell_kwargs]

{bluecellulab-2.5.3.dist-info → bluecellulab-2.5.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.3
+Version: 2.5.5
 Summary: The Pythonic Blue Brain simulator access
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.3.dist-info → bluecellulab-2.5.5.dist-info}/RECORD

@@ -1,4 +1,5 @@
-bluecellulab/__init__.py,sha256=yC97iFnCVDtwqspxdpt4C-qq9vQF7AMJOWe1h_cB0Wc,827
+bluecellulab/__init__.py,sha256=-DopR1_1ji4NQlsRi4fLSUETM358o6UCdJtnhQ8wrQA,873
+bluecellulab/circuit_simulation.py,sha256=Tbw8y-4lT06nxyK9v_i7KMDu0BK-OI14na3Ao_9u7Po,33680
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
@@ -8,9 +9,8 @@ bluecellulab/neuron_interpreter.py,sha256=hXig_u3T6JmEHbkV8ZblEZtX0kY80ate4VpRtA
 bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,2721
 bluecellulab/psection.py,sha256=EgAS8IS9DcYv2xOkNISgfg_CfRc0nDfRFjvgQhyi9eY,6328
 bluecellulab/psegment.py,sha256=rBryDYHC_uDK9itfXXrFZ0DL9F6WgRICL0j5EHN56QM,3125
-bluecellulab/rngsettings.py,sha256=KACk4ujPXhlHL9iAoTdAjjLuFEcUoG6aes92ZClSoQQ,4228
-bluecellulab/ssim.py,sha256=radFcT2lWRfb1C0zKlqw0JQ6JY4b9LJiDP9JDPeQIqs,33399
-bluecellulab/tools.py,sha256=8QMNdmh9lRDOWT4kz9cI_MYNVh4ulxgY8CtHZbaMbkA,11056
+bluecellulab/rngsettings.py,sha256=Dlt34dc4AoWyxCCzUK3Jlui90VCK20xHg6gD_OJzPIw,4237
+bluecellulab/tools.py,sha256=tS0lth0La-HE13EXsfXlPro1O2lAaEBSL4ZdvMsy6jw,11083
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=fgqjgy3xzyL0zu-qjCPJdHp6PEAHADCzlr2FqyBmzHI,2012
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
@@ -33,13 +33,13 @@ bluecellulab/cell/ballstick/emodel.hoc,sha256=7WcuepK-wB9bASRvNdCwO9Woc9-SpBCFqB
 bluecellulab/cell/ballstick/morphology.asc,sha256=EO0VIRilJAwpiDP2hIevwusfvYptNYhvsu1f5GgbSQo,190
 bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGpmZs,361
 bluecellulab/circuit/format.py,sha256=eYhiBIQnPnnVBmaSDymFjQprXN9QjEYKmFhb2mIS86o,1674
-bluecellulab/circuit/iotools.py,sha256=ERtrsl9KePZ0QFKiTi5lbBgudXbcHrqxr-BY2ysFfqg,1591
+bluecellulab/circuit/iotools.py,sha256=KVE7x5LNQ4RgjNh05Q-h3Swpbs3nRFtrcWNHj62aiRI,1585
 bluecellulab/circuit/node_id.py,sha256=gaRAW3UhbPOPsoXMHLjo3qH9iNod7YB8ZOcguWprrU4,1265
 bluecellulab/circuit/simulation_access.py,sha256=QHVEN-sEZbCCvblhBHEShGX0-NEXCD1AYpavpVGCgAE,7073
 bluecellulab/circuit/synapse_properties.py,sha256=6PpMWeothomR2c-mx63yVIISJc4eSL9xMnaIM2nryNM,5494
 bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
-bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=j-DYHMBTbq1TvlYyc-w1CSyqElSm6B6SyUdkxIGNA20,14746
+bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=msAbAKH7XEPn77lTPA7-ntRiY-fCIxvLuA250gjo__Q,14681
 bluecellulab/circuit/circuit_access/definition.py,sha256=SnKBFEgdXFG-QexYRrGSzVAd7bSj7NwN0IuTsjDOrDY,4435
 bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=P1ElK_VA10_JyyKbAnqzuAlduEYE2c_NSec2TZuix1U,10345
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
@@ -61,9 +61,9 @@ bluecellulab/stimulus/factory.py,sha256=AOby3Sp2g8BJsRccz3afazfCyysyWIgLtcliWlye
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=YkvxbdGF-u-vxYdbRNTlX-9AtSC_3t_FQRFhybwzgrk,6805
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.5.3.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.5.3.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.5.3.dist-info/METADATA,sha256=rYhJTsxGMFuS6MWaiwkByBjBpVxemuA3GoybjU0PgSM,7003
-bluecellulab-2.5.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.5.3.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.5.3.dist-info/RECORD,,
+bluecellulab-2.5.5.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.5.5.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.5.5.dist-info/METADATA,sha256=lF8ZtLbDD11XzdZ2JftoUhHD7OXew_TTknWwb1Mf9x4,7003
+bluecellulab-2.5.5.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.5.5.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.5.5.dist-info/RECORD,,