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dandi / dandi-hub

Infrastructure and code for the dandihub
https://hub.dandiarchive.org
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Include environment configuration for LINC Hub #203

Closed aaronkanzer closed 4 weeks ago

aaronkanzer commented 1 month ago

Handling some tech debt here -- consolidates some of the forked repositories in lincbrain GitHub org, also allows environment configurations to live under centralized place in dandi-hub thanks to the work of @asmacdo

@asmacdo perhaps want to give your blessing here? 😄

Cc @kabilar @satra

asmacdo commented 1 month ago

Blessing bestowed 🙏

aaronkanzer commented 1 month ago

Thank you @aaronkanzer, @asmacdo. Its great that we can now manage all three JupyterHubs (DANDI, LINC, BICAN) from this single repo.

I have a couple suggestions above to add the LINC Client and remove items that are for the DANDI users.

Thanks @kabilar -- I committed your suggestions -- thanks for the review -- @asmacdo let me know once you are 👍 and I'll merge

asmacdo commented 1 month ago

@aaronkanzer I think you want to leave the custom ipython kernel https://github.com/dandi/dandi-hub/blob/main/envs/dandi/jupyterhub-overrides.yaml#L96

kabilar commented 1 month ago

@aaronkanzer I think you want to leave the custom ipython kernel https://github.com/dandi/dandi-hub/blob/main/envs/dandi/jupyterhub-overrides.yaml#L96

Hi @asmacdo, we are not running the Allen Institute SDK. And in the future will be building images for the LINC project that don't include the Allen dependencies. Should we install the ipython kernel for the base conda environment - /opt/conda/bin/pip install --upgrade ipykernel?

kabilar commented 1 month ago

Thanks @kabilar -- I committed your suggestions -- thanks for the review

Thanks @aaronkanzer. Will we need to do anything so that these changes are reflected in the JupyterHub deployment?

asmacdo commented 1 month ago

@kabilar @aaronkanzer I think we should consider leaving the allen ipython kernel update in until we produce new images since the kernel is baked into the original image. I haven't played with those however, so it may not be necessary.

kabilar commented 1 month ago

Sounds good

asmacdo commented 1 month ago

@aaronkanzer once the kernel is back in, lgtm

aaronkanzer commented 1 month ago

@asmacdo @kabilar mind doing one last mini-review -- kernel is back in (didnt include the datalad call for dandi) -- if you are happy, I'll re-deploy the LINC Hub

kabilar commented 1 month ago

Thank you, @aaronkanzer. A few minor suggestions above.

aaronkanzer commented 4 weeks ago

@kabilar -- @asmacdo and I successfully deployed these changes this AM -- I'll default to one of the dandi-hub repo owners for merging this code.

kabilar commented 4 weeks ago

That's great, thank you.