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ImagingDataCommons / IDC-Tutorials

Self-guided notebook tutorials to help get started with using IDC
BSD 3-Clause "New" or "Revised" License
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A github actions workflow to test if getting_started colab notebooks running properly in latest colab docker runtime env. #38

Closed vkt1414 closed 10 months ago

vkt1414 commented 11 months ago

Prior to activating this workflow, we need to set three env variables:

SERVICE_ACCOUNT_KEY: Google Cloud service account key JSON (make sure to convert it to ONE LINE JSON). Note: minimum permissions required for the service account: Bigquery User DOCKER_USERNAME: Docker Hub username. DOCKER_PASSWORD: Docker Hub password or access token.

While this workflow is setup to test only the three getting_started notebooks, we can test any notebook that does not require a GPU. To accomplish that, every new notebook will need to be assessed if it requires any additional preprocessing steps.

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vkt1414 commented 11 months ago

A service account is now dedicated for this. Whenever we are ready to merge this PR, I can provide the service account key to create the github repo secret.

vkt1414 commented 10 months ago

@fedorov I modified the preprocessingNotebooks.py script to let the users know whenever we inject something. I also modified the papermill output notebook names. So I believe we are good to go. Could you use your dockerhub credentials while creating these?

DOCKER_USERNAME: Docker Hub username. DOCKER_PASSWORD: Docker Hub password or access token. SERVICE_ACCOUNT_KEY