Restructure code and update README for NEURON-CoreNEURON workflow

neuronsimulator / ringtest

Ring network model test to demonstrate the use of CoreNEURON

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Restructure code and update README for NEURON-CoreNEURON workflow #2

Closed pramodk closed 7 years ago

pramodk commented 7 years ago

Michael : Some members from OIST asked about brief document/tutorial for using CoreNEURON. As we don't have concrete document yet, I thought it would be good idea to update this ringtest as an example to show the complete workflow. I have done following modifications :

split ringtest.py into smaller bits (all functionality remains same)
Update READM with instructions for
- downloading and building NEURON, CoreNEURON and MOD2c
- running ringtest with NEURON
- resuming simulation with CoreNEURON
- sample bash script to do above (on standard linux system)
Some additional details about benchmarking/common errors

There are some todo sections that you can update.

Let me know what you think.

pramodk commented 7 years ago

And then we can add link to this repository in CoreNEURON and mod2c github pages.

pramodk commented 7 years ago

forgot to mention that the scripts and old instructions are moved to scripts directory.

nrnhines commented 7 years ago

Hi Pramod, Rather than accept a merge, I selected for the changesets to be rebased onto the master so that the extra merge commit was avoided. Perhaps with the 5 related commits it would have been better to make the graph clear that they were together. My question is whether the rebase causes any extra effort on your side. If so, from now on I'll accept the merge style.

I'm working mostly on the grant application this month. In looking at the changes I did notice a few typos and things I would like to change. However they are minor and can be done later. It is nice to have a much more complete explanation about getting started.

Cheers, Michael

pramodk commented 7 years ago

My question is whether the rebase causes any extra effort on your side.

No.

Rebase is fine for merging such feature branches (except some scenarios described as Golden Rule of Rebasing).

For modifications from this type of pull request, I would prefer squashing all commits into single commit while merging (as described here).

However they are minor and can be done later. It is nice to have a much more complete explanation about getting started.

I will update the README with more information.