test-ghactions.sh

set -e

pip install .

echo
echo "################################################"
echo "##   Running unit tests"


# skip a few tests that segfault etc. on GH
pytest --cov=pyneuroml -m "not localonly" .


run_neuron_examples=false

if [[ ($# -eq 1) && ($1 == '-neuron') ]]; then
    run_neuron_examples=true
fi

# export NEURON_HOME
if command -v nrniv
then
    # double dirname because we also do not want the final `bin`
    NEURON_HOME=$(dirname $(dirname $(command -v nrniv)))
    export NEURON_HOME
fi

### Test script for pyNeuroML

cd examples


echo
echo "################################################"
echo "##   Executing examples with jNeuroML"

pynml LEMS_NML2_Ex5_DetCell.xml -nogui



echo
echo "################################################"
echo "##   Validate with jNeuroML"

pynml -validate NML2_SingleCompHHCell.nml


echo "##   Multi-validate with jNeuroML"
pynml -validate *.channel.nml


echo
echo "################################################"
echo "##   Test some conversions"

pynml NML2_SingleCompHHCell.nml -svg
pynml NML2_SingleCompHHCell.nml -png
pynml LEMS_NML2_Ex5_DetCell.xml -sedml
pynml LEMS_NML2_Ex9_FN.xml -dlems
pynml LEMS_NML2_Ex9_FN.xml -brian
pynml LEMS_NML2_Ex5_DetCell.xml -neuron
pynml LEMS_NML2_Ex5_DetCell.xml -moose
pynml LEMS_NML2_Ex9_FN.xml -vertex
pynml LEMS_NML2_Ex9_FN.xml -xpp
pynml LEMS_NML2_Ex9_FN.xml -dnsim
pynml LEMS_NML2_Ex9_FN.xml -cvode
pynml LEMS_NML2_Ex9_FN.xml -matlab
pynml LEMS_NML2_Ex9_FN.xml -nineml
pynml LEMS_NML2_Ex9_FN.xml -spineml
pynml LEMS_NML2_Ex9_FN.xml -sbml


echo
echo "################################################"
echo "##   Simple SBML validation example"

pynml -validate-sbml test_data/valid_doc.sbml
pynml -validate-sbml-units test_data/valid_doc.sbml


echo
echo "################################################"
echo "##   Running some of the examples"

#  Run an example with jNeuroML
python run_jneuroml_plot_matplotlib.py -nogui -noneuron


#  Run tests on units
python units.py

#  Run test for generating LEMS file
python create_new_lems_file.py -test

#  Run test for generating LEMS file
python Vm_plot.py -nogui



echo
echo "################################################"
echo "##   Test analysis of NeuroML2 channel"

pynml-channelanalysis NaConductance.channel.nml -nogui
pynml-channelanalysis NaConductance.channel.nml -ivCurve -erev 55 -nogui

# Not on GitHub Actions:
# https://docs.github.com/en/actions/reference/environment-variables#default-environment-variables
# Requires matplotlib + display
if [[ "$CI" != "true" ]]; then
    pynml-channelanalysis NaConductance.channel.nml KConductance.channel.nml -html
fi

echo
echo "################################################"
echo "##   Test export to PovRay"

pynml-povray NML2_SingleCompHHCell.nml


# Requires pyelectro, not in .travis.yml yet...
if [[ "$CI" != "true" ]]; then
echo
echo "################################################"
echo "##   Generate a frequency vs current plot"

    python generate_if_curve.py -nogui


echo
echo "################################################"
echo "##   Generate a dt dependence plot"

    python dt_dependence.py -nogui

fi



# Only run these if NEURON is installed & -neuron flag is used
if [ "$run_neuron_examples" == true ]; then

    echo
    echo "################################################"
    echo "##   Try exporting morphologies to NeuroML from NEURON"

        nrnivmodl
        # Export NeuroML v1 from NEURON example
        python export_neuroml1.py

        # Export NeuroML v2 from NEURON example
        python export_neuroml2.py


    echo
    echo "################################################"
    echo "##   Test analysis of channel in mod file"

        # do not run nrnivmodl, modchananalysis should run it if required
        pynml-modchananalysis -stepV 20  NaConductance  -dt 0.01 -nogui


    # Requires NEURON
    echo
    echo "################################################"
    echo "##   Test some tuning examples"

        pushd tune
            python tunePyr.py -tune -nogui
        popd

    echo
    echo "################################################"
    echo "##   Finished all tests! "
    echo "################################################"

fi