Add slow test for neuroml/LEMS

Author: Jaquier Aurélien Tristan

AUTHORS.txt

@@ -6,3 +6,4 @@ Giuseppe Chindemi @ BBP
 Tanguy Damart @ BBP
 Elisabetta Iavarone @ BBP
 Anil Tuncel @ BBP
+Aurelien Jaquier @ BBP

Makefile

@@ -67,8 +67,20 @@ clean:
 	rm -rf examples/l5pc/L5PC.py
 	rm -rf examples/l5pc/x86_64
 	rm -rf examples/stochkv/x86_64
+	rm -rf x86_64
 	rm -rf .coverage
 	rm -rf coverage.xml
+	rm -rf channels
+	rm -rf LEMS_l5pc.xml
+	rm -rf LEMS_l5pc_nrn.py
+	rm -rf l5pc.Pop_l5pc_0_0.v.dat
+	rm -rf time.dat
+	rm -rf l5pc.hoc
+	rm -rf l5pc.net.nml
+	rm -rf l5pc_0_0.cell.nml
+	rm -rf l5pc_0_0.hoc
+	rm -rf loadcell.hoc
+	rm -rf *.mod
 	find . -name "*.pyc" -exec rm -rf {} \;
 l5pc_start: install
 	cd examples/l5pc && \

bluepyopt/neuroml/biophys.py

@@ -36,24 +36,18 @@
     "NaTa_t": "na",
     "NaTs2_t": "na",
     "Nap_Et2": "na",
-    # "NaTg": "na",
-    # "NaTg2": "na",
     "K_Tst": "k",
     "K_Pst": "k",
     "SKv3_1": "k",
     "SK_E2": "k",
     "StochKv": "k",
-    # "StochKv2": "k",
-    # "StochKv3": "k",
     "KdShu2007": "k",
     "Im": "k",
     "Ca": "ca",
     "Ca_HVA": "ca",
-    # "Ca_HVA2": "ca",
     "Ca_LVAst": "ca",
     "pas": "pas",
     "CaDynamics_E2": "ca",
-    # "CaDynamics_DC0": "ca",
 }
 
 ion_erevs = {

bluepyopt/tests/test_neuroml_fcts.py

@@ -3,20 +3,28 @@
 import os
 import sys
 
+import efel
 import neuroml
+import numpy
 import pytest
+from pyneuroml import pynml
+from bluepyopt import ephys
 from bluepyopt.neuroml import biophys
+from bluepyopt.neuroml import cell
 from bluepyopt.neuroml import morphology
+from bluepyopt.neuroml import simulation
 
 L5PC_PATH = os.path.abspath(
     os.path.join(os.path.dirname(__file__), "../../examples/l5pc")
 )
 
 sys.path.insert(0, L5PC_PATH)
 
+import l5pc_evaluator
 import l5pc_model  # NOQA
 
 l5pc_cell = l5pc_model.create()
+protocols = l5pc_evaluator.define_protocols()
 
 release_params = {
     "gNaTs2_tbar_NaTs2_t.apical": 0.026145,
@@ -392,3 +400,91 @@ def test_add_segment_groups():
     assert "soma_group" in segment_group_names
     assert "axon_group" in segment_group_names
     assert "dendrite_group" in segment_group_names
+
+
+@pytest.mark.slow
+@pytest.mark.neuroml
+def test_neuroml_run():
+    """Test neuroml conversion and simulation"""
+    # replace axon is not supported yet
+    l5pc_cell.morphology.do_replace_axon = False
+    dt = 0.025
+    protocol_name = "Step3"
+    bpo_test_protocol = protocols[protocol_name]
+
+    # create neuroml cell
+    cell.create_neuroml_cell(
+        l5pc_cell, release_params, skip_channels_copy=False
+    )
+
+    # create LEMS simulation
+    network_filename = f"{l5pc_cell.name}.net.nml"
+    lems_filename = f"LEMS_{l5pc_cell.name}.xml"
+    simulation.create_neuroml_simulation(
+        network_filename, bpo_test_protocol, dt, l5pc_cell.name, lems_filename
+    )
+
+    # remove compiled mechanisms if any before running LEMS simulation
+    os.system("rm -rf x86_64/")
+
+    # run the simulation with the NEURON simulator,
+    # since the default jNeuroML simulator can only simulate single
+    # compartment cells
+    pynml.run_lems_with_jneuroml_neuron(
+        lems_filename, nogui=True, plot=False)
+
+    # re-compile the mechanisms before running with bluepyopt
+    os.system("rm -rf x86_64/")
+    os.system("nrnivmodl examples/l5pc/mechanisms/")
+
+    lems_output = numpy.loadtxt("l5pc.Pop_l5pc_0_0.v.dat")
+    lems_voltage = lems_output[:, 1] * 1000  # *1000 -> mV
+    lems_time = lems_output[:, 0] * 1000  # *1000 -> ms
+
+    # remove non uniform parameter to be coherent with LEMS simulation
+    to_remove = []
+    for key, param in l5pc_cell.params.items():
+        if hasattr(param, "value_scaler"):
+            if isinstance(
+                param.value_scaler,
+                ephys.parameterscalers.NrnSegmentSomaDistanceScaler,
+            ):
+                to_remove.append(key)
+
+    for param_name in to_remove:
+        l5pc_cell.params.pop(param_name)
+
+    # run with regular bluepyopt
+    sim = ephys.simulators.NrnSimulator(dt=dt, cvode_active=False)
+    bpo_output = bpo_test_protocol.run(
+        cell_model=l5pc_cell, param_values=release_params, sim=sim
+    )
+
+    response_name = f"{protocol_name}.soma.v"
+    bpo_voltage = bpo_output[response_name]["voltage"]
+    bpo_time = bpo_output[response_name]["time"]
+
+    # we don't expect the two traces to be exactly the same,
+    # but to be pretty similar
+    # we consider it satisfactory if they fire within 3 ms respectively
+    trace_lems = {
+        "T": lems_time,
+        "V": lems_voltage,
+        "stim_start": [700],
+        "stim_end": [2700]
+    }
+    trace_bpo = {
+        "T": bpo_time,
+        "V": bpo_voltage,
+        "stim_start": [700],
+        "stim_end": [2700]
+    }
+    traces = [trace_lems, trace_bpo]
+    features = ["peak_time"]
+    feature_values = efel.getFeatureValues(
+        traces, features, raise_warnings=False
+    )
+    lems_peak_time = feature_values[0]["peak_time"]
+    bpo_peak_time = feature_values[1]["peak_time"]
+
+    numpy.testing.assert_allclose(lems_peak_time, bpo_peak_time, atol=3)

pytest.ini

@@ -2,6 +2,7 @@
 markers =
     unit
     slow
+    neuroml
 filterwarnings =
     ignore::RuntimeWarning:deap.*
     ignore::DeprecationWarning

setup.py

@@ -27,6 +27,10 @@
 EXTRA_SCOOP = [
     'scoop>=0.7',
 ]
+EXTRA_NEUROML = [
+    'pyneuroml>=0.5.20',
+    'libNeuroML>=0.3.1',
+]
 
 setuptools.setup(
     name="bluepyopt",
@@ -42,12 +46,11 @@
         'Jinja2>=2.8',
         'future',
         'Pebble>=4.3.10',
-        'pyneuroml>=0.5.20',
-        'libNeuroML>=0.3.1'
         ],
     extras_require={
-        'all': EXTRA_SCOOP,
+        'all': EXTRA_SCOOP + EXTRA_NEUROML,
         'scoop': EXTRA_SCOOP,
+        'neuroml': EXTRA_NEUROML,
         },
     packages=setuptools.find_packages(
         exclude=(

tox.ini

@@ -15,6 +15,7 @@ envdir =
     py27{-unit,-functional,-style,-syntax}: {toxworkdir}/py27
     py3{5,6,7,8,9,10,}{-unit,-functional,-style,-syntax}: {toxworkdir}/py3
     docs: {toxworkdir}/docs
+extras = neuroml
 deps =
     coverage
     flake8
@@ -30,6 +31,9 @@ whitelist_externals =
     pwd
 passenv = https_proxy
 coverage_options = --cov-append --cov-report=xml --cov-config=.coveragerc
+setenv = 
+    ; for neuroml tests
+    NEURON_HOME={envdir}
 commands =
     make clean
 
@@ -38,7 +42,10 @@ commands =
 
     unit: pytest --cov=bluepyopt {[testenv]coverage_options} bluepyopt/tests -k unit
     functional: make stochkv_prepare l5pc_prepare sc_prepare meta_prepare
-    functional: pytest --cov=bluepyopt {[testenv]coverage_options} bluepyopt/tests -k 'not unit'
+    functional: pytest --cov=bluepyopt {[testenv]coverage_options} bluepyopt/tests -k 'not unit and not neuroml'
+    ; separate neuroml test from the other ones
+    ; because it redefines l5pc template which makes neuron crash and tests fail
+    functional: pytest --cov=bluepyopt {[testenv]coverage_options} bluepyopt/tests -m neuroml
 
 [testenv:docs]
 basepython = python3.6