bluecellulab 2.5.6__tar.gz → 2.5.7__tar.gz

{bluecellulab-2.5.6 → bluecellulab-2.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.6
+Version: 2.5.7
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.6 → bluecellulab-2.5.7}/bluecellulab/circuit_simulation.py

@@ -599,10 +599,10 @@ class CircuitSimulation:
             forward_skip_value = self.circuit_access.config.forward_skip
         if celsius is None:
             celsius = self.circuit_access.config.celsius
-            NeuronGlobals.get_instance().temperature = celsius
+        NeuronGlobals.get_instance().temperature = celsius
         if v_init is None:
             v_init = self.circuit_access.config.v_init
-            NeuronGlobals.get_instance().v_init = v_init
+        NeuronGlobals.get_instance().v_init = v_init
 
         sim = bluecellulab.Simulation(self.pc)
         for cell_id in self.cells:

{bluecellulab-2.5.6 → bluecellulab-2.5.7}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.5.6
+Version: 2.5.7
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.5.6 → bluecellulab-2.5.7}/tests/test_ssim_sonata.py

@@ -6,6 +6,7 @@ import numpy as np
 import pytest
 
 from bluecellulab import CircuitSimulation
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
 
 parent_dir = Path(__file__).resolve().parent
 
@@ -71,27 +72,49 @@ def test_sim_quick_scx_sonata_multicircuit(input_type):
         assert rms_error < 0.25
 
 
-@pytest.mark.v6
-def test_circuit_sim_intersect_pre_gids_multipopulation():
-    """Test instantiate_gids with intersect_pre_gids on Sonata."""
-    sonata_sim_path = (
-        parent_dir
-        / "examples"
-        / "sim_quick_scx_sonata_multicircuit"
-        / "simulation_config_noinput.json"
-    )
-    cell_ids = [("NodeA", 0), ("NodeA", 1)]
-
-    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 = 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
+class TestCircuitSim:
+    def setup_method(self):
+        self.sonata_sim_path = (
+            parent_dir
+            / "examples"
+            / "sim_quick_scx_sonata_multicircuit"
+            / "simulation_config_noinput.json"
+        )
+        self.cell_ids = [("NodeA", 0), ("NodeA", 1)]
+
+    @pytest.mark.v6
+    def test_intersect_pre_gids_multipopulation(self):
+        """Test instantiate_gids with intersect_pre_gids on Sonata."""
+        sim = CircuitSimulation(self.sonata_sim_path)
+        sim.instantiate_gids(self.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 = CircuitSimulation(self.sonata_sim_path)
+        sim2.instantiate_gids(self.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
+
+    @pytest.mark.v6
+    def test_run_with_v_init(self):
+        """Test run with v_init."""
+        sim = CircuitSimulation(self.sonata_sim_path)
+        sim.instantiate_gids(self.cell_ids, add_stimuli=True)
+        t_stop = 2.0
+        assert NeuronGlobals.get_instance().v_init != -99.0
+        sim.run(t_stop, v_init=-99.0)
+        assert NeuronGlobals.get_instance().v_init == -99.0
+
+    @pytest.mark.v6
+    def test_run_with_celsius(self):
+        """Test run with celsius."""
+        sim = CircuitSimulation(self.sonata_sim_path)
+        sim.instantiate_gids(self.cell_ids, add_stimuli=True)
+        t_stop = 2.0
+        assert NeuronGlobals.get_instance().temperature != 66.0
+        sim.run(t_stop, celsius=66.0)
+        assert NeuronGlobals.get_instance().temperature == 66.0
 
 
 @pytest.mark.v6

{bluecellulab-2.5.6 → bluecellulab-2.5.7}/tox.ini

@@ -41,7 +41,7 @@ deps =
     ruff>=0.0.270
     docformatter>=1.7.2
 commands =
-    ruff . --select F541,F401 --per-file-ignores="__init__.py:F401"
+    ruff check . --select F541,F401 --per-file-ignores="__init__.py:F401"
     pycodestyle {[base]name} --ignore=E501,W504,W503
     pycodestyle tests --ignore=E501,W504,W503,E741
     mypy . --ignore-missing-imports --disable-error-code=call-overload  # remove once pandas-stubs makes a release after 1.5.3.230321