Check Commits and Colab Images #204
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| name: Check Commits and Colab Images | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| paths: | |
| - ".github/workflows/test_colab.yml" | |
| - "notebooks/getting_started/part**.ipynb" | |
| pull_request: | |
| branches: [ "master" ] | |
| paths: | |
| - ".github/workflows/test_colab.yml" | |
| - "notebooks/getting_started/part**.ipynb" | |
| workflow_dispatch: | |
| schedule: | |
| - cron: 0 12 */1 * * | |
| jobs: | |
| check_colab_images: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Install dependencies | |
| run: pip install requests==2.31.0 pandas==2.1.1 google-cloud-bigquery==3.12.0 pyarrow==13.0.0 nbformat==5.9.2 | |
| - name: Authorize Google Cloud | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/auth@v1 | |
| with: | |
| credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| create_credentials_file: true | |
| export_environment_variables: true | |
| - name: Run check-colab-images.py and preprocess notebooks | |
| run: | | |
| python test/src/check-colab-images.py | |
| python test/src/preProcessNotebooks.py | |
| - name: Set result output | |
| id: set-result | |
| run: | | |
| if [[ -f "check_colab_images_result.txt" ]]; then | |
| RESULT=$(cat "check_colab_images_result.txt") | |
| echo "RESULT=$RESULT" >> $GITHUB_ENV | |
| fi | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Docker login | |
| if: github.event_name != 'pull_request' | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Pull from GCP and Push Docker image to Docker Hub | |
| if: github.event_name != 'pull_request' && env.RESULT == 'true' | |
| run: | | |
| docker pull us-docker.pkg.dev/colab-images/public/runtime:latest | |
| docker tag us-docker.pkg.dev/colab-images/public/runtime:latest imagingdatacommons/idc-testing-colab:latest | |
| docker push imagingdatacommons/idc-testing-colab:latest | |
| - name: Pull Docker image from Docker Hub | |
| if: github.event_name == 'pull_request' || env.RESULT == 'false' | |
| run: | | |
| docker pull imagingdatacommons/idc-testing-colab:latest | |
| - name: Copy Google Cloud credentials to Docker container | |
| if: github.event_name != 'pull_request' | |
| run: | | |
| CREDENTIALS_FILE_PATH="${{ env.GOOGLE_APPLICATION_CREDENTIALS }}" | |
| CREDENTIALS_FILE_NAME=$(basename "$CREDENTIALS_FILE_PATH") | |
| GOOGLE_APPLICATION_CREDENTIALS="/content/$CREDENTIALS_FILE_NAME" | |
| echo "GOOGLE_APPLICATION_CREDENTIALS=$GOOGLE_APPLICATION_CREDENTIALS" >> $GITHUB_ENV | |
| - name: Run notebook with papermill | |
| if: github.event_name != 'pull_request' | |
| run: | | |
| for nb in part1_prerequisites part2_searching_basics part3_exploring_cohorts; do | |
| # Create a new directory for each notebook | |
| sudo mkdir -p "temp/${nb}" | |
| docker run -d --name colab -v "$(pwd):/content" -e GOOGLE_APPLICATION_CREDENTIALS="${{ env.GOOGLE_APPLICATION_CREDENTIALS }}" imagingdatacommons/idc-testing-colab:latest | |
| docker exec -t colab /bin/bash -c "pip install papermill==2.4.0" | |
| # Change the working directory to the new directory | |
| docker exec -t colab /bin/bash -c "set -o xtrace && set -o errexit && set -o pipefail && set -o nounset && set +o errexit && cd /content/temp/${nb} && papermill --log-level='DEBUG' /content/notebooks/getting_started/${nb}.ipynb /content/temp/${nb}_papermill_output.ipynb && set -o errexit && ls -A" | |
| docker stop colab | |
| docker rm colab | |
| sudo rm -r "temp" | |
| done | |
| - name: Create Pull Request to update the colab image metadata database | |
| if: github.event_name != 'pull_request' | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| title: Update colab images list | |
| body: Update colab-images-list.csv so that when a colab image is updated, we do not keep pulling colab docker image from gcp and pushing to dockerhub everytime | |
| base: master | |
| branch: update-colab-images-list | |
| add-paths: | | |
| test/colab-images-list.csv | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |