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AllenInstitute / ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes
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Docs build is broken #2

Open NileGraddis opened 6 years ago

NileGraddis commented 6 years ago

sphinx.apidoc was moved to sphinx.ext.apidoc and a reroute was added to cover. This reroute strips out the first element passed to it, which breaks our docs build.

NileGraddis commented 6 years ago

oh dang, matlab's python bindings are a dependency. I don't actually know much about how those work. @jsiegle how are you guys handling this deployment currently? It might make sense to deploy the matlab python bindings to our internal artifactory server, so that they can be easily installed.

jsiegle commented 6 years ago

So, the spike sorting code is dependent on 3 pieces of "external" software: NpxExtractor, a binary that converts raw data files into arrays of int16s, SpikeBandMedianSubtraction, another binary that removes common-mode noise from the continuous data, and Kilosort2, which does the actual spike sorting. Kilosort2 is what requires the matlab python bindings.

Putting the matlab engine on the artifactory server sounds like a good idea—can you show me how to do that?

What's the best way to make sure the other elements are installed and up-to-date?

NileGraddis commented 6 years ago

I don't have read access to those stash repos.

Without knowing how the matlab engine is structured it is difficult to say what would be needed to deploy it to artifactory. Maybe we could sit down and walk through how you guys deploy it on your machines?

jsiegle commented 6 years ago

I just made them public.

The matlab engine comes with the Matlab install, but you have to run setup.py install to use it. The version for R2017a is only compatible with Python 3.5 or lower, so that's something we'll have to keep in mind.