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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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Bugfix for rxd reactions involving rxd parameters. #703

Closed adamjhn closed 1 year ago

adamjhn commented 2 years ago

Parameters need to be added before reactions. Parameter names should probably default to the key (in the same way as species and states). Additionally storing the hObj for rxd region geometry in netParams causes problems saving netParams, because the geometry objects are not JSON serializable.

Fix depends on NEURON pull request; https://github.com/neuronsimulator/nrn/pull/1933

urdapile commented 1 year ago

Changes included. Except that we still keep storing hObj, as in other RxD entries.

vvbragin commented 1 year ago

the rest of changes included in https://github.com/suny-downstate-medical-center/netpyne/commit/90ab1d34d51b3b82e394542d8b2c46d1d011abf5