pulse_stimulus.ipynb is completely broken

[nicain]

While trying to fix the nightly build, lacking neuron as a dependency was identified as one of many problems with the current state of the "make notebooks" CI task:

• On master branch: notebook tests failing #661
• failing notebook builds should cause nightly build to fail #607
• nightly build failing #592

When investigating, I found that even with neuron installed (conda install -c conda-forge neuron), this notebook will not execute. This issue further splits this scope-of-work off of the resolution provided by #665, to be handled later.

In #665, the hook to drive the notebook was refactored so that "make notebooks-neuron" will drive the testing of the notebook.

[nicain]

CC @gouwens @corinneteeter

[gouwens]

I haven't had much success with the neuron from conda-forge. I've had to install NEURON from source, and there are issues with Anaconda and building NEURON. In my experience, if you have a gcc installed by Anaconda (which it'll try to use), NEURON configuration fails. So you need to have it configured to use the built-in compiler but also set the --with-nrnpython flag to use your desired (presumably Anaconda) python. Also, after make; make install, you also still need to run python setup.py install in the src/nrnpython directory (with the right python active).

However, this notebook looks broken beyond just not having NEURON available. It's expecting a modfiles directory to be in its directory, which isn't in the repository (here) and doesn't get downloaded with the API call. Also, compiling the files from within the notebook may not work because of the Anaconda C compiler issues I mentioned.

[wesley-jones]

Hey @nicain @wbwakeman ,
I got this notebook working again. The issue I fixed was due to a different way Python 3 handles file paths, but I couldn't find the original error, so I don't know if this fix resolves the original issue. Here is the error I fixed:

IndexError: tuple index out of range

Could you share the error from the logs after you installed neuron?