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test.sh
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set -ex
## Test readers
python -m c302.SpreadsheetDataReader
python -m c302.UpdatedSpreadsheetDataReader
python -m c302.UpdatedSpreadsheetDataReader2
python -m c302.OpenWormReader
## (Re)generate NeuroML 2 & LEMS files from the python scripts
python -m c302.c302_IClamp A
python -m c302.c302_Syns A
python -m c302.c302_Social A
python -m c302.c302_Pharyngeal A
python -m c302.c302_Full A
python -m c302.c302_Muscles A
python -m c302.c302_Oscillator A
python -m c302.c302_IClamp B
python -m c302.c302_Syns B
python -m c302.c302_Social B
python -m c302.c302_Pharyngeal B
python -m c302.c302_Full B
python -m c302.c302_Muscles B
python -m c302.c302_Oscillator B
python -m c302.c302_IClamp C
python -m c302.c302_Syns C
python -m c302.c302_Social C
python -m c302.c302_Pharyngeal C
python -m c302.c302_Full C
python -m c302.c302_Muscles C
python -m c302.c302_Oscillator C
python -m c302.c302_IClamp C0
python -m c302.c302_Syns C0
python -m c302.c302_Social C0
python -m c302.c302_Pharyngeal C0
python -m c302.c302_Full C0
python -m c302.c302_Muscles C0
python -m c302.c302_Oscillator C0
python -m c302.c302_IClamp C1
python -m c302.c302_Syns C1
python -m c302.c302_Social C1
python -m c302.c302_Pharyngeal C1
python -m c302.c302_Full C1
python -m c302.c302_Muscles C1
python -m c302.c302_Oscillator C1
python -m c302.c302_IClamp C2
python -m c302.c302_Syns C2
python -m c302.c302_Social C2
python -m c302.c302_Pharyngeal C2
python -m c302.c302_Full C2
python -m c302.c302_Muscles C2
python -m c302.c302_Oscillator C2
python -m c302.c302_FW C2
python -m c302.c302_IClamp D
python -m c302.c302_Syns D
python -m c302.c302_Social D
python -m c302.c302_Pharyngeal D
python -m c302.c302_Full D
python -m c302.c302_Muscles D
python -m c302.c302_Oscillator D
python -m c302.c302_IClamp D1
python -m c302.c302_Syns D1
python -m c302.c302_Social D1
python -m c302.c302_Pharyngeal D1
python -m c302.c302_Full D1
python -m c302.c302_Muscles D1
python -m c302.c302_Oscillator D1
cd examples
## Validate generated NeuroML 2
pynml -validate c302_A_Full.net.nml
pynml -validate c302_A_Pharyngeal.net.nml
pynml -validate c302_A_Syns.net.nml
pynml -validate c302_A_Social.net.nml
pynml -validate c302_A_Muscles.net.nml
# Not validating B files as they use non NeuroML 2 compliant IaFCell model with activity...
pynml -validate c302_C_Full.net.nml
pynml -validate c302_C_Pharyngeal.net.nml
pynml -validate c302_C1_Full.net.nml
pynml -validate c302_C1_Pharyngeal.net.nml
pynml -validate c302_D_Full.net.nml
pynml -validate c302_D_Pharyngeal.net.nml
#pynml -validate c302_D1_Full.net.nml
#pynml -validate c302_D1_Pharyngeal.net.nml
## Try running these in jNeuroML with no GUI
#pynml LEMS_c302_A_Full.xml -nogui # Takes 2 mins to run!
pynml LEMS_c302_A_Pharyngeal.xml -nogui
pynml LEMS_c302_A_Syns.xml -nogui
pynml LEMS_c302_A_Social.xml -nogui
#pynml LEMS_c302_B_Full.xml -nogui # Takes 2 mins to run!
pynml LEMS_c302_B_Pharyngeal.xml -nogui
pynml LEMS_c302_B_Syns.xml -nogui
pynml LEMS_c302_B_Social.xml -nogui
## Try regenerating using command line options
cd ..
c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300
c302 c302_A_Syns2 parameters_A -cells ["ADAL","AIBL","RIVR","RMEV"] -cellstostimulate ["ADAL","RIVR"] -duration 500 -dt 0.1 -vmin -72 -vmax -48
c302 c302_A_Weights parameters_A -cells ["ADAL","AIBL","I1L","I3","DB5","PVCR"] -cellstostimulate ["ADAL","I1L","PVCR"] -connnumberoverride=["I1L-I3":2.5] -connnumberscaling=["PVCR-DB5":5] -duration 500 -dt 0.1 -vmin -72 -vmax -48
c302 c302_C1_Test parameters_C1 -cellstostimulate AFDL -connnumberscaling {"I1L-I3":2}
mkdir -p cells
c302 c302_D1_Weights parameters_D1 -cells ["ADAL","AIBL","I1L","I3","DB5","PVCR"] -cellstostimulate ["ADAL","I1L","PVCR"] -connnumberoverride=["I1L-I3":2.5] -connnumberscaling=["PVCR-DB5":5] -duration 500 -dt 0.1
cd examples
## Try converting some to NEURON
pynml LEMS_c302_A_Full.xml -neuron
pynml LEMS_c302_B_Pharyngeal.xml -neuron
pynml LEMS_c302_C_Syns.xml -neuron
nrnivmodl
cd -
## Try helper scripts
python -m c302.runAndPlot -test
python -m c302.c302_utils -nogui
echo
echo " Successfully completed all c302 tests!"
echo