First version of sim test suite

examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_build/build_network.py

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+#!/bin/env python
+
+# Sonata Simulator Test Suite
+# 1-cell circuit, single soma, only cm, 1 step current
+
+# Authors: Werner Van Geit @ BBP
+
+import bmtk.builder
+
+cell_models = [
+    {'model_name': 'soma_cm', 'x': [0.0],
+     'y': [0.0],
+     'z': [0.0],
+     'morphology': 'soma1',
+     'model_template': 'nml:soma_cm2.nml'}]
+
+bio_cells = bmtk.builder.NetworkBuilder("biophysical")
+for model_props in cell_models:
+    bio_cells.add_nodes(
+        model_type='biophysical',
+        **model_props)
+
+bio_cells.build()
+bio_cells.save_nodes(output_dir='../input/network')

examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/.gitignore

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+/output

examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/run.sh

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+#!/bin/bash
+
+set -e
+
+rm -rf output
+rm -rf __pycache__
+# python -m trace --trace ../shared_components/scripts/run_bionet.py ../input/config.json
+python ../shared_components/scripts/run_bionet.py ../input/config.json
+
+pytest -vvs

examples/sim_tests/biophysical/one_cell/soma_cm2/bmtk_test/test_output.py

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+import os
+
+import numpy
+import h5py
+import pytest
+
+output_path = os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        'output'))
+
+dt = 0.025
+tstop = 60.0
+stim_start = 20.0
+stim_end = 50.0
+
+start_voltage = -80.0
+end_voltage = -20.0
+
+# Using as 'raw' code as possible here, so as not to depend on other code
+# that could contain errors
+
+
+def test_soma_voltage():
+    """Check soma voltages"""
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+
+    voltage = h5py.File(soma_voltage_path)['data'].value
+
+    assert len(voltage) == tstop / dt
+
+    time = numpy.arange(0, len(voltage)) * dt
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+    assert voltage[0] == pytest.approx(start_voltage)
+    assert numpy.mean(
+        voltage[
+            numpy.where(time < stim_start)]) == pytest.approx(start_voltage)
+    assert start_voltage < numpy.mean(voltage[numpy.where(
+        (time >= stim_start) & (time <= stim_end))]) < end_voltage
+    assert voltage[-1] == pytest.approx(end_voltage)
+
+
+def test_spikes():
+    """Check spike times"""
+
+    spikes_path = os.path.join(output_path, 'spikes.h5')
+
+    assert os.path.exists(spikes_path)
+
+    spikes = h5py.File(spikes_path)['spikes']['timestamps'].value
+
+    assert len(spikes) == 0

examples/sim_tests/biophysical/one_cell/soma_cm2/input/circuit_config.json

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+{
+  "manifest": {
+    "$NETWORK_DIR": "../input/network",
+    "$COMPONENT_DIR": "../shared_components"
+  },
+
+  "components": {
+    "morphologies_dir": "$COMPONENT_DIR/morphologies",
+    "biophysical_neuron_models_dir": "$COMPONENT_DIR/templates/nml"
+  },
+
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_DIR/biophysical_nodes.h5",
+        "node_types_file": "$NETWORK_DIR/biophysical_node_types.csv"
+      }
+    ]
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2/input/config.json

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+../shared_components/configs/config.json

examples/sim_tests/biophysical/one_cell/soma_cm2/input/network/biophysical_node_types.csv

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+node_type_id model_type model_template morphology model_name
+100 biophysical nml:soma_cm2.nml soma1 soma_cm

examples/sim_tests/biophysical/one_cell/soma_cm2/input/node_sets.json

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+{
+  "soma_cm2": {
+    "model_type": "biophysical"
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2/input/simulation_config.json

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+{
+  "manifest": {
+    "$OUTPUT_DIR": "./output",
+    "$INPUT_DIR": "../input"
+  },
+
+  "run": {
+    "tstop": 60.0,
+    "dt": 0.025,
+    "dL": 20.0,
+    "spike_threshold": -15,
+    "nsteps_block": 5000
+  },
+
+  "target_simulator":"NEURON",
+
+  "network": "$INPUT_DIR/circuit_config.json",
+
+  "conditions": {
+    "celsius": 34.0,
+    "v_init": -80
+  },
+
+  "node_sets_file": "$INPUT_DIR/node_sets.json", 
+
+  "mechanisms_dir": "../shared_components_mechanisms",
+
+
+  "inputs": {
+   "current_clamp_1": {
+     "input_type": "current_clamp",
+     "module": "IClamp",
+     "node_set": "soma_cm2",
+     "amp": 0.0001256637,
+     "delay": 20.0,
+     "duration": 30.0
+   }
+  },
+
+  "output": {
+    "log_file": "log.txt",
+    "output_dir": "$OUTPUT_DIR",
+    "spikes_file": "spikes.h5",
+    "spikes_sort_order": "time"
+  },
+
+  "reports": {
+    "membrane_potential": {
+      "cells": "soma_cm2",
+      "variable_name": "v",
+      "module": "membrane_report",
+      "sections": "soma"
+    }
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2/pytest.ini

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+[pytest]
+filterwarnings =
+    ignore::FutureWarning

examples/sim_tests/biophysical/one_cell/soma_cm2/shared_components

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+../../../shared_components

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_build/build_network.py

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+#!/bin/env python
+
+# Sonata Simulator Test Suite
+# 1-cell circuit, single soma, only cm, 1 step current
+
+# Authors: Werner Van Geit @ BBP
+
+import bmtk.builder
+
+cell_models = [
+    {'model_name': 'soma_cm', 'x': [0.0],
+     'y': [0.0],
+     'z': [0.0],
+     'morphology': 'soma1',
+     'model_template': 'nml:soma_cm2_hh.nml'}]
+
+bio_cells = bmtk.builder.NetworkBuilder("biophysical")
+for model_props in cell_models:
+    bio_cells.add_nodes(
+        model_type='biophysical',
+        **model_props)
+
+bio_cells.build()
+bio_cells.save_nodes(output_dir='../input/network')

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/.gitignore

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+/output

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/run.sh

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+#!/bin/bash
+
+rm -rf output
+rm -rf __pycache__
+# python -m trace --trace ../shared_components/scripts/run_bionet.py ../input/config.json
+python ../shared_components/scripts/run_bionet.py ../input/config.json
+
+pytest -vvs

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/bmtk_test/test_output.py

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+import os
+
+import numpy
+import h5py
+import pytest
+
+output_path = os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        'output'))
+
+# TBD
+
+'''
+dt = 0.025
+tstop = 60.0
+stim_start = 20.0
+stim_end = 50.0
+
+start_voltage = -80.0
+end_voltage = -20.0
+
+# Using as 'raw' code as possible here, so as not to depend on other code
+# that could contain errors
+
+
+def test_soma_voltage():
+    """Check soma voltages"""
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    assert os.path.exists(soma_voltage_path)
+
+    voltage = h5py.File(soma_voltage_path)['data'].value
+
+    assert len(voltage) == tstop / dt
+
+    time = numpy.arange(0, len(voltage)) * dt
+
+    soma_voltage_path = os.path.join(output_path, 'membrane_potential.h5')
+
+    import matplotlib.pyplot as plt
+    plt.plot(voltage)
+    plt.show()
+
+    assert os.path.exists(soma_voltage_path)
+    assert voltage[0] == pytest.approx(start_voltage)
+    assert numpy.mean(
+        voltage[
+            numpy.where(time < stim_start)]) == pytest.approx(start_voltage)
+    assert start_voltage < numpy.mean(voltage[numpy.where(
+        (time >= stim_start) & (time <= stim_end))]) < end_voltage
+    assert voltage[-1] == pytest.approx(end_voltage)
+
+
+def test_spikes():
+    """Check spike times"""
+
+    spikes_path = os.path.join(output_path, 'spikes.h5')
+
+    assert os.path.exists(spikes_path)
+
+    spikes = h5py.File(spikes_path)['spikes']['timestamps'].value
+
+    assert len(spikes) == 0
+'''

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/circuit_config.json

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+{
+  "manifest": {
+    "$NETWORK_DIR": "../input/network",
+    "$COMPONENT_DIR": "../shared_components"
+  },
+
+  "components": {
+    "morphologies_dir": "$COMPONENT_DIR/morphologies",
+    "biophysical_neuron_models_dir": "$COMPONENT_DIR/templates/nml"
+  },
+
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_DIR/biophysical_nodes.h5",
+        "node_types_file": "$NETWORK_DIR/biophysical_node_types.csv"
+      }
+    ]
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/config.json

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+../shared_components/configs/config.json

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/network/biophysical_node_types.csv

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+node_type_id model_type model_template morphology model_name
+100 biophysical nml:soma_cm2_hh.nml soma1 soma_cm

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/node_sets.json

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+{
+  "soma_cm2": {
+    "model_type": "biophysical"
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/input/simulation_config.json

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+{
+  "manifest": {
+    "$OUTPUT_DIR": "./output",
+    "$INPUT_DIR": "../input"
+  },
+
+  "run": {
+    "tstop": 60.0,
+    "dt": 0.025,
+    "dL": 20.0,
+    "spike_threshold": -15,
+    "nsteps_block": 5000
+  },
+
+  "target_simulator":"NEURON",
+
+  "network": "$INPUT_DIR/circuit_config.json",
+
+  "conditions": {
+    "celsius": 34.0,
+    "v_init": -80
+  },
+
+  "node_sets_file": "$INPUT_DIR/node_sets.json", 
+
+  "mechanisms_dir": "../shared_components_mechanisms",
+
+
+  "inputs": {
+   "current_clamp_1": {
+     "input_type": "current_clamp",
+     "module": "IClamp",
+     "node_set": "soma_cm2",
+     "amp": 0.002,
+     "delay": 20.0,
+     "duration": 30.0
+   }
+  },
+
+  "output": {
+    "log_file": "log.txt",
+    "output_dir": "$OUTPUT_DIR",
+    "spikes_file": "spikes.h5",
+    "spikes_sort_order": "time"
+  },
+
+  "reports": {
+    "membrane_potential": {
+      "cells": "soma_cm2",
+      "variable_name": "v",
+      "module": "membrane_report",
+      "sections": "soma"
+    }
+  }
+}

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/pytest.ini

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+[pytest]
+filterwarnings =
+    ignore::FutureWarning

examples/sim_tests/biophysical/one_cell/soma_cm2_hh/shared_components

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+../../../shared_components

examples/sim_tests/shared_components/configs/config.json

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+{
+  "network": "./circuit_config.json",
+  "simulation": "./simulation_config.json"
+}