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NeuroML / jNeuroML

A single package (command line tool and library) in Java to validate, simulate, translate and analyse NeuroML 2 models
https://docs.neuroml.org/Userdocs/Software/jNeuroML.html
GNU Lesser General Public License v3.0
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Python 3 compatible getneuroML file #57

Closed kapilkd13 closed 6 years ago

kapilkd13 commented 6 years ago

I was trying to setup jNeuroML from source in a python3 environment and getNeuroml.py file posed an issue as it is not python 3 compatible. Although its functionality is just to setup repos for jNeuroML which is still possible via python2, but it would be great if we don't have to switch python for using it. I changed few things to make it python 2+3 compatible.

Also I noticed that setting up jNeuroML from source with java 9 throw error with jdx lib. As per my research we need to update the minimum ersion of this lib to 2.2, still there are other issues with java 9 compatibility. It would be great if you can mention that use java 8 to build from source on readme file. I can make a commit if you want.

pgleeson commented 6 years ago

Thanks. Will check through it.

pgleeson commented 6 years ago

Thanks for this @kapilkd13. Some of these changes for python3 were already made on the development branch, but I've synced the changes for py3 compatibility between master and development now. By the way, to get the very latest jneuroml functionality I'd build from the development branches (highly recommended). This should just involve a local update of jnml, followed by:

python getNeuroML.py clean
python getNeuroML.py development
kapilkd13 commented 6 years ago

Thanks @pgleeson for this information. I will move to development branch. As you might remember I would be working on "GSoC project #13.1: Import NeuroML morphologies" as you already helped me there with the valuable info. on parsing tools for NeuroML. I would be working with JneuroML, Pylems and libNeuroML and you are a core developer in all these repos. So I hope you would be able to help me in this project. Till now I did some research on above mentioned libraries and as per me libNeuuroML best suits our need as it is light, developed in python and is focused on NeuroML. what do you think?

Also should I mail you or create an issue page on libNeuroML to discuss any further issues/ideas.

Thanks.

kapilkd13 commented 6 years ago

Thanks @pgleeson for this information. I will move to development branch. As you might remember I would be working on "GSoC project #13.1: Import NeuroML morphologies" as you already helped me there with the valuable info. on parsing tools for NeuroML. I would be working with JneuroML, Pylems and libNeuroML and you are a core developer in all these repos. So I hope you would be able to help me in this project. Till now I did some research on above mentioned libraries and as per me libNeuuroML best suits our need as it is light, developed in python and is focused on NeuroML. what do you think?

Also should I mail you or create an issue page on libNeuroML to discuss any further issues/ideas.

Thanks.

pgleeson commented 6 years ago

Sure, libNeuroML seems like the best option for your project. You can mail me, but if it's a question thta others might have an issue on that repo would be best. I mentioned to @mstimberg that we could have a skype/hangout some time once you get going in the project for general questions.