update readme #45
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| name: Check Commits and Colab Images | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| workflow_dispatch: | |
| schedule: | |
| - cron: 0 12 */1 * * | |
| jobs: | |
| check_commits_and_images: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 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 | |
| uses: google-github-actions/auth@v1 | |
| with: | |
| credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| create_credentials_file: true | |
| export_environment_variables: true | |
| - name: Run check-commits.py and check-colab-images.py, preprocess notebooks scripts | |
| run: | | |
| python test/src/check-commits.py | |
| python test/src/check-colab-images.py | |
| python test/src/preProcessNotebooks.py | |
| - name: Set result output | |
| id: set-result | |
| run: | | |
| if [[ -f "check_colab_images_result.txt" ]]; then | |
| RESULT=$(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 | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Pull from GCP and Push Docker image to Docker Hub | |
| if: env.RESULT == 'true' | |
| run: | | |
| docker pull us-docker.pkg.dev/colab-images/public/runtime:latest | |
| docker tag us-docker.pkg.dev/colab-images/public/runtime:latest imagingdatacommons/idc-testing-colab:latest | |
| docker push imagingdatacommons/idc-testing-colab:latest | |
| - name: Pull Docker image from Docker Hub | |
| if: env.RESULT == 'false' | |
| run: | | |
| docker pull imagingdatacommons/idc-testing-colab:latest | |
| - name: Copy Google Cloud credentials to Docker container | |
| run: | | |
| CREDENTIALS_FILE_PATH="${{ 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" >> $GITHUB_ENV | |
| - name: Run notebook with papermill | |
| run: | | |
| for nb in part1_prerequisites part2_searching_basics part3_exploring_cohorts; do | |
| docker run -d --name colab -v "$(pwd):/content" -e GOOGLE_APPLICATION_CREDENTIALS="${{ env.GOOGLE_APPLICATION_CREDENTIALS }}" imagingdatacommons/idc-testing-colab:latest | |
| docker exec -t colab /bin/bash -c "pip install papermill==2.4.0" | |
| docker exec -t colab /bin/bash -c "set -o xtrace && set -o errexit && set -o pipefail && set -o nounset && set +o errexit && cd content/ && papermill /content/notebooks/getting_started/${nb}.ipynb /content/test/outputs/${nb}_papermill_output.ipynb && set -o errexit && ls -A" | |
| #docker exec -t colab /bin/bash -c "jupyter nbconvert --to html --ExtractOutputPreprocessor.enabled=False /content/test/outputs/output_${nb}.ipynb" | |
| docker stop colab | |
| docker rm colab | |
| done | |
| # skip commit | |
| #- name: Commit changes | |
| # if: ${{ github.event_name != 'pull_request' }} | |
| # uses: stefanzweifel/git-auto-commit-action@v4 | |
| # with: | |
| # commit_message: 'Check colab env' | |
| # file_pattern: 'test/*.csv test/outputs/*.ipynb' | |
| # branch: 'master' | |
| #- name: Check output notebooks for errors | |
| # run: | | |
| # for nb in part1_prerequisites part2_searching_basics part3_exploring_cohorts; do | |
| # if grep -q '"name": "stderr"\|"status": "failed"' test/outputs/output_${nb}.ipynb; then | |
| # echo "Error messages found in the ${nb} notebook output:" | |
| # cat test/outputs/output_${nb}.ipynb | |
| # exit 1 | |
| # else | |
| # echo "No errors found in the ${nb} notebook output." | |
| # fi | |
| # done | |
| # exit $EXIT_CODE |