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NeuroML / pyNeuroML

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html
GNU Lesser General Public License v3.0
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Feat/nsgr integration #243

Closed sanjayankur31 closed 10 months ago

sanjayankur31 commented 11 months ago

For the moment, I used the HH example from docs to test it out. It was submitted and ran fine but threw up this error that I now need to debug:

  File "LEMS_HH_single_compartment_example_sim_nrn.py", line 202
    py_v_pop0_0_/v_output0 = [ float(x  / 1000.0) for x in h.v_pop0_0_/v_output0.to_python() ]  # Convert to Python list for speed, variable has dim: voltage
    ^
SyntaxError: cannot assign to operator

Can reproduce on my local machine too, will debug and see what's causing it.

TODO for this PR: add a test

sanjayankur31 commented 11 months ago

A simple test in the pyneuroml/examples directory:

python -c 'from pyneuroml.nsgr import run_on_nsg ; run_on_nsg("jneuroml_neuron", "LEMS_NML2_Ex5_DetCell.xml")'

fails because the output is expected in a results directory, but the simulation does run.

sanjayankur31 commented 11 months ago

TODO: tweak netpyne run

sanjayankur31 commented 11 months ago

This is now ready for review. It doesn't rely on newly generated files. It creates a new directory and does all its work there, so it should not be affected by any old files at all.

To test netpyne, in the examples folder, run (replace engine with jneuroml_neuron for neuron:

python -c 'from pyneuroml.nsgr import run_on_nsg ; run_on_nsg("jneuroml_netpyne", "LEMS_NML2_Ex5_DetCell.xml")'

Note that netpyne on nsgr is too old from the looks of it: https://github.com/NeuroML/NeuroML2/issues/213