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suny-downstate-medical-center / netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.
http://www.netpyne.org
MIT License
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Update to NeuroML export & more testing #609

Closed pgleeson closed 3 years ago

pgleeson commented 3 years ago

Also updates the python serialisation of the NetPyNE model (as used in NetPyNE-UI menu option) to allow the model to be converted to NeuroML with an -neuroml option. @joewgraham @salvadord I'd be grateful if you could have a look at this so we could use it in the CNS demos for NetPyNE-UI on OSBv2 next week. Thanks!

salvadord commented 3 years ago

@pgleeson I merged the PR, but the tests seem to be failing during the export to neuroml: https://github.com/Neurosim-lab/netpyne/blob/development/tests/examples/test_HHTut.py#L19 . Any idea why this could be?

pgleeson commented 3 years ago

@salvadord Apologies, an issue with a missing dependency in pylems. It's solved now with a new release and I tried rerunning some of your tests and they pass now, e.g. https://github.com/Neurosim-lab/netpyne/actions/runs/988034232