Brainlit Documentation Fixes

[tathey1]

I'd like to start fixing the notebooks in our documentation page since many of them do not run. If we split the work it can be done faster. I think the below assignments make the most sense, but let me know if you have other ideas.

@bvarjavand :

• utils
• uploading_brains
• downloading_brains

@shreyasingh1 : I know that you are still trying to figure out what's going on with the precomputed skeletons, but when you are able to fix things in these notebooks, please do.

• downloading_benchmarking
• uploading benchmarking

@alishakodibagkar : there are a couple more files I found that still rely on swc.py

• pipelines/seg_pipeline_demo
• viz/visualization

[tathey1]

Recall that you can build the documentation pages locally using docs/build_docs.sh then go to docs/html/index.html and open it. The notebooks are in the "tutorial" section.

Please develop according to the errors on your locally built docs. We are having issues with our environment building the docs on the web, apparently brainlit cannot be found e.g. see here. @bvarjavand not sure if you have any tips?

[bvarjavand]

The python kernel that the notebooks are running do not have brainlit pip-installed. This is an issue with specifying the kernel of the notebook, see conf.py. I guess the "python3" kernel isn't the same as the system python3. Not sure exactly how to fix, but it would be there.

Nevermind, fixed by just pip installing brainlit via netlify.tml

[tathey1]

Let's have everyone fix their respective notebooks so the docs correctly build locally. Then PR into this branch.

At that point, I will need to fix some netlify things before we can PR all of our fixes into develop.

[tathey1]

I changed my mind, go ahead and just PR into the develop branch like Bijan did, I think PR'ing into my branch will be too complicated.

[tathey1]

Updates:

• this PR makes the notebooks run now (although I am still trying to figure out how to get netlify to install brainlit). So, as I said above, please make your PR directly into develop.
• this PR adds the updates to the utils notebooks from the bvarjavand-fixdocs branch. However, there is still an issue with downloading_brains notebook (I think credential related), so I requested @bvarjavand to review/fix that.

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