Problem with NeuroML loaders and individual cell .nml

openworm / CElegansNeuroML

NeuroML based C elegans model, contained in a neuroConstruct project, as well as c302

http://opensourcebrain.org/projects/celegans

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Problem with NeuroML loaders and individual cell .nml #17

Closed wilzh40 closed 10 years ago

wilzh40 commented 10 years ago

When I try running the c302_A.py, I had an error: Not a valid NeuroML 2 doc: (<type 'exceptions.AttributeError'>, AttributeError('nsmap',), <traceback object at 0x10cf053f8>)

After doing some debugging it seems that the individual morphology files of the cells cannot be read for me.

cell_file = '../../generatedNeuroML2/%s.nml'%cell Any thoughts?

pgleeson commented 10 years ago

Are you using the latest version from the development branch of libNeuroML?

wilzh40 commented 10 years ago

@pgleeson I believe so? /Library/Python/2.7/site-packages/libNeuroML-0.2.1-py2.7.egg-info

wilzh40 commented 10 years ago

I fixed the problem, it was a faulty lxml install. pip install lxml doesn't work right off the bat for OSX Mavericks and returns an error: 'libxml/xmlversion.h' file not found, so I had to brew libxml2 and then export C_INCLUDE_PATH=/usr/local/Cellar/libxml2/2.9.1/include/libxml2:$C_INCLUDE_PATH

There were a lot of dependencies I had to install before getting the script to compile in the first place and the documentation doesn't cover all of them.