bluecellulab 2.5.4__tar.gz → 2.5.6__tar.gz

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.4
-Summary: The Pythonic Blue Brain simulator access
+Version: 2.5.6
+Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
 Project-URL: Homepage, https://github.com/BlueBrain/BlueCelluLab

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/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-2.5.4 → bluecellulab-2.5.6}/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-2.5.4 → bluecellulab-2.5.6}/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-2.5.4/bluecellulab/ssim.py → bluecellulab-2.5.6/bluecellulab/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-2.5.4 → bluecellulab-2.5.6}/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-2.5.4 → bluecellulab-2.5.6}/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-2.5.4 → bluecellulab-2.5.6}/bluecellulab.egg-info/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.4
-Summary: The Pythonic Blue Brain simulator access
+Version: 2.5.6
+Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
 Project-URL: Homepage, https://github.com/BlueBrain/BlueCelluLab

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/bluecellulab.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ tox.ini
 .github/workflows/release.yml
 .github/workflows/test.yml
 bluecellulab/__init__.py
+bluecellulab/circuit_simulation.py
 bluecellulab/connection.py
 bluecellulab/dendrogram.py
 bluecellulab/exceptions.py
@@ -26,7 +27,6 @@ bluecellulab/plotwindow.py
 bluecellulab/psection.py
 bluecellulab/psegment.py
 bluecellulab/rngsettings.py
-bluecellulab/ssim.py
 bluecellulab/tools.py
 bluecellulab/type_aliases.py
 bluecellulab/utils.py

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/docs/source/api.rst

@@ -12,6 +12,7 @@ bluecellulab
    :toctree: _autosummary
    :recursive:
 
+   analysis
    cell
    circuit
    connection
@@ -25,7 +26,7 @@ bluecellulab
    psegment
    rngsettings
    simulation
-   ssim
+   circuit_simulation
    stimulus
    synapse
    tools

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/examples/2-sonata-network/sonata-network.ipynb

@@ -64,7 +64,7 @@
     "\n",
     "from matplotlib import pyplot as plt\n",
     "\n",
-    "from bluecellulab import SSim\n",
+    "from bluecellulab import CircuitSimulation\n",
     "from bluecellulab.graph import build_graph, plot_graph"
    ]
   },
@@ -221,7 +221,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Here the simulation is loaded using the SSim object."
+    "Here the circuit simulation is loaded using the CircuitSimulation object."
    ]
   },
   {
@@ -230,7 +230,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim = SSim(simulation_config)"
+    "sim = CircuitSimulation(simulation_config)"
    ]
   },
   {

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bluecellulab"
-description = "The Pythonic Blue Brain simulator access"
+description = "Biologically detailed neural network simulations and analysis."
 readme = "README.rst"
 authors = [{ name = "Blue Brain Project, EPFL" }]
 dynamic = ["version"]
@@ -48,7 +48,7 @@ version_scheme = "python-simplified-semver"
 local_scheme = "no-local-version"
 
 [tool.setuptools.packages.find]
-include = ["bluecellulab", "bluecellulab.*"]
+include = ["bluecellulab"]
 
 [tool.pytest.ini_options]
 markers = [

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_cell/test_core.py

@@ -13,7 +13,7 @@ import bluecellulab
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.cell.template import NeuronTemplate, public_hoc_cell, shorten_and_hash_string
 from bluecellulab.exceptions import BluecellulabError
-from bluecellulab.ssim import SSim
+from bluecellulab import CircuitSimulation
 
 warnings.filterwarnings("ignore", message="numpy.dtype size changed")
 warnings.filterwarnings("ignore", message="numpy.ndarray size changed")
@@ -435,13 +435,13 @@ def test_add_synapse_replay():
         / "synapse_replay"
         / "simulation_config.json"
     )
-    ssim = bluecellulab.SSim(sonata_sim_path)
-    ssim.spike_threshold = -900.0
+    circuit_sim = bluecellulab.CircuitSimulation(sonata_sim_path)
+    circuit_sim.spike_threshold = -900.0
     cell_id = ("hippocampus_neurons", 0)
-    ssim.instantiate_gids(cell_id,
-                          add_stimuli=True, add_synapses=True,
-                          interconnect_cells=False)
-    cell = ssim.cells[cell_id]
+    circuit_sim.instantiate_gids(cell_id,
+                                 add_stimuli=True, add_synapses=True,
+                                 interconnect_cells=False)
+    cell = circuit_sim.cells[cell_id]
     assert len(cell.connections) == 3
     assert cell.connections[
         ("hippocampus_projections__hippocampus_neurons__chemical", 0)
@@ -460,10 +460,10 @@ class TestWithinCircuit:
             / "simulation_config_noinput.json"
         )
         cell_id = ("NodeA", 0)
-        ssim = SSim(sonata_sim_path)
-        ssim.instantiate_gids(cell_id, add_synapses=True, add_stimuli=False)
-        self.cell = ssim.cells[cell_id]
-        self.ssim = ssim  # for persistance
+        circuit_sim = CircuitSimulation(sonata_sim_path)
+        circuit_sim.instantiate_gids(cell_id, add_synapses=True, add_stimuli=False)
+        self.cell = circuit_sim.cells[cell_id]
+        self.circuit_sim = circuit_sim  # for persistance
 
     def test_pre_gids(self):
         """Test get_pre_gids within a circuit."""

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_circuit/test_node_id.py

@@ -1,18 +1,16 @@
 """Unit tests for node_id.py"""
-from bluecellulab.circuit.node_id import create_cell_id, CellId
+from bluecellulab.circuit.node_id import create_cell_id, create_cell_ids, CellId
 
 
 def test_create_cell_id():
-    """SSim: Testing creation of CellId."""
+    """Testing creation of CellId."""
     assert create_cell_id(1) == CellId("", 1)
     assert create_cell_id(("", 2)) == CellId("", 2)
     assert create_cell_id(("pop1", 2)) == CellId("pop1", 2)
 
 
 def test_create_cell_ids():
-    """SSim: Testing creation of CellIds."""
-    from bluecellulab.circuit.node_id import create_cell_ids, CellId
-
+    """Testing creation of CellIds."""
     assert create_cell_ids([1, 2]) == [CellId("", 1), CellId("", 2)]
     assert create_cell_ids([("", 2), ("pop1", 2)]) == [
         CellId("", 2),

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_graph.py

@@ -6,7 +6,7 @@ from pathlib import Path
 import matplotlib
 from matplotlib import pyplot as plt
 
-from bluecellulab import SSim
+from bluecellulab import CircuitSimulation
 from bluecellulab.graph import build_graph, plot_graph
 from bluecellulab.circuit import CellId
 
@@ -22,7 +22,7 @@ class TestGraph():
             script_dir
             / "examples/sim_quick_scx_sonata_multicircuit/simulation_config_hypamp.json"
         )
-        self.sim = SSim(circuit_path)
+        self.sim = CircuitSimulation(circuit_path)
         dstut_cells = [('NodeA', 0), ('NodeA', 1), ('NodeB', 0), ('NodeB', 1)]
 
         self.sim.instantiate_gids(dstut_cells, add_stimuli=True, add_synapses=True)

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_ssim.py

@@ -1,11 +1,11 @@
-"""Unit tests for SSim."""
+"""Unit tests for CircuitSimulation."""
 import numpy as np
 
-import bluecellulab
+from bluecellulab import CircuitSimulation
 
 
 def test_merge_pre_spike_trains():
-    """SSim: Testing merge_pre_spike_trains"""
+    """CircuitSimulation: Testing merge_pre_spike_trains"""
 
     train1 = {1: [5, 100], 2: [5, 8, 120]}
     train2 = {2: [7], 3: [8]}
@@ -15,18 +15,18 @@ def test_merge_pre_spike_trains():
 
     np.testing.assert_equal(
         {},
-        bluecellulab.ssim.SSim.merge_pre_spike_trains(None))
+        CircuitSimulation.merge_pre_spike_trains(None))
     np.testing.assert_equal(
         train1,
-        bluecellulab.ssim.SSim.merge_pre_spike_trains(train1))
+        CircuitSimulation.merge_pre_spike_trains(train1))
     np.testing.assert_equal(
         train1,
-        bluecellulab.ssim.SSim.merge_pre_spike_trains(
+        CircuitSimulation.merge_pre_spike_trains(
             None,
             train1))
     np.testing.assert_equal(
         trains_merged,
-        bluecellulab.ssim.SSim.merge_pre_spike_trains(
+        CircuitSimulation.merge_pre_spike_trains(
             train1,
             None,
             train2,

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_ssim_sonata.py

@@ -1,11 +1,11 @@
-"""Testing SSim with SONATA simulations."""
+"""Testing CircuitSimulation with SONATA simulations."""
 
 from pathlib import Path
 
 import numpy as np
 import pytest
 
-from bluecellulab import SSim
+from bluecellulab import CircuitSimulation
 
 parent_dir = Path(__file__).resolve().parent
 
@@ -25,8 +25,7 @@ def test_sim_quick_scx_sonata(input_type):
         / f"simulation_config_{input_type}.json"
     )
 
-    # Create SSim object
-    sim = SSim(sonata_sim_path)
+    sim = CircuitSimulation(sonata_sim_path)
     cell_id = ("NodeA", 2)  # has a spike + hyperpolarises
     sim.instantiate_gids(cell_id, add_stimuli=True)
     t_stop = 10.0
@@ -59,8 +58,7 @@ def test_sim_quick_scx_sonata_multicircuit(input_type):
     cell_ids = [("NodeA", 1), ("NodeA", 2)]
     # investivate NodeA, 0 further. It shows small discrepancies,
     # even on a single population circuit
-    # Create SSim object
-    sim = SSim(sonata_sim_path)
+    sim = CircuitSimulation(sonata_sim_path)
     sim.instantiate_gids(cell_ids, add_stimuli=True)
     t_stop = 20.0
     sim.run(t_stop)
@@ -74,7 +72,7 @@ def test_sim_quick_scx_sonata_multicircuit(input_type):
 
 
 @pytest.mark.v6
-def test_ssim_intersect_pre_gids_multipopulation():
+def test_circuit_sim_intersect_pre_gids_multipopulation():
     """Test instantiate_gids with intersect_pre_gids on Sonata."""
     sonata_sim_path = (
         parent_dir
@@ -84,13 +82,13 @@ def test_ssim_intersect_pre_gids_multipopulation():
     )
     cell_ids = [("NodeA", 0), ("NodeA", 1)]
 
-    sim = SSim(sonata_sim_path)
+    sim = CircuitSimulation(sonata_sim_path)
     sim.instantiate_gids(cell_ids, add_synapses=True)
     assert len([x.synapses for x in sim.cells.values()][0]) == 6
     assert len([x.synapses for x in sim.cells.values()][1]) == 2
 
     # pre gids are intersected, synapses are filtered
-    sim2 = SSim(sonata_sim_path)
+    sim2 = CircuitSimulation(sonata_sim_path)
     sim2.instantiate_gids(cell_ids, add_synapses=True, intersect_pre_gids=[("NodeB", 0)])
     assert len([x.synapses for x in sim2.cells.values()][0]) == 2
     assert len([x.synapses for x in sim2.cells.values()][1]) == 0
@@ -107,9 +105,9 @@ def test_merge_pre_spike_trains_edge_case():
         / "simulation_config_noinput.json"
     )
     cell_id = ("NodeA", 0)
-    ssim = SSim(sonata_sim_path)
-    ssim.instantiate_gids(cell_id, add_minis=True, add_replay=True,
-                          add_stimuli=False, add_synapses=True,
-                          intersect_pre_gids=None)
-    cell_info_dict = ssim.cells[cell_id].info_dict
+    circuit_sim = CircuitSimulation(sonata_sim_path)
+    circuit_sim.instantiate_gids(cell_id, add_minis=True, add_replay=True,
+                                 add_stimuli=False, add_synapses=True,
+                                 intersect_pre_gids=None)
+    cell_info_dict = circuit_sim.cells[cell_id].info_dict
     assert cell_info_dict["connections"] != {}

{bluecellulab-2.5.4 → bluecellulab-2.5.6}/tests/test_tools.py

@@ -5,9 +5,10 @@ from pathlib import Path
 import numpy as np
 import pytest
 
-import bluecellulab
+from bluecellulab import CircuitSimulation
 from bluecellulab.cell.ballstick import create_ball_stick
 from bluecellulab.circuit.circuit_access import EmodelProperties
+from bluecellulab.circuit.node_id import create_cell_id
 from bluecellulab.exceptions import UnsteadyCellError
 from bluecellulab.tools import calculate_SS_voltage, calculate_SS_voltage_subprocess, calculate_input_resistance, detect_hyp_current, detect_spike, detect_spike_step, detect_spike_step_subprocess, holding_current, holding_current_subprocess, search_threshold_current, template_accepts_cvode, check_empty_topology
 
@@ -212,9 +213,9 @@ class TestOnSonataCircuit:
     def test_holding_current_subprocess(self):
         """Unit test for holding_current_subprocess on a SONATA circuit."""
         v_hold = -80
-        ssim = bluecellulab.SSim(self.circuit_path)
-        cell_id = bluecellulab.circuit.node_id.create_cell_id(self.cell_id)
-        cell_kwargs = ssim.fetch_cell_kwargs(cell_id)
+        circuit_sim = CircuitSimulation(self.circuit_path)
+        cell_id = create_cell_id(self.cell_id)
+        cell_kwargs = circuit_sim.fetch_cell_kwargs(cell_id)
         i_hold, v_control = holding_current_subprocess(
             v_hold, enable_ttx=True, cell_kwargs=cell_kwargs
         )