problems running main.py

openworm / muscle_model

Model of C elegans body wall muscle based on Boyle & Cohen 2008

http://www.opensourcebrain.org/projects/muscle_model

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problems running main.py #17

Closed VahidGh closed 9 years ago

VahidGh commented 9 years ago

Trying to run this command:

python run.py eval_file0 40.041444758152295 0.0 4514.250191560498 35.2 0.4089 0.6 --compile --plotoverlay

generates some errors in main.py. Most of errors are due to naming parameters, such as:

line 87: init() got an unexpected keyword argument 'ion_channels'
- replacing ion_channels with ion_channel solved the problem
line 112: self.cell.leak_current = self.leak
- we do not have cell attribute
NameError: global name 'kinetics' is not defined
- adding "from neuron import h" and replacing kinetics with h solved the problem
AttributeError: muscle_simulation instance has no attribute 'morphology'
- I guess there is some problem in neuroml.Segment usage

And so on...

travs commented 9 years ago

I also have this issue. Could it be related to #1?

Were you finally able to run the command after renaming?

pgleeson commented 9 years ago

Sorry, meant to point to issue https://github.com/openworm/muscle_model/issues/18 from this. As explained there these files are quite old and require an update as described...

slarson commented 9 years ago

@VahidGh @travs is this still an issue?

VahidGh commented 9 years ago

Followed your instructions, and checked out libNeuroML from development. Got an error during compilation, commenting out this line solved the compilation issue. But still the same problems when running this command: python run.py eval_file0 40.041444758152295 0.0 4514.250191560498 35.2 0.4089 0.6 --compile --plotoverlay

NameError: global name 'kinetics' is not defined

travs commented 9 years ago

Yeah I am still getting the same errors with most recent libNeuroML as well, but I am assuming this is because the code hasn't been updated yet, or has it?

pgleeson commented 9 years ago

@VahidGh @travs, unfortunately the main.py won't work unless the updates outlines in #18 are implemented. I hope to get round to this next week.

pgleeson commented 9 years ago

Think this can be closed as much of the code for neurotune etc. has moved on past its old usage in main.py etc. and pyramidal is no longer supported...

travs commented 9 years ago

Ok, great. If this problem somehow arises again we can reopen.