Lm bioc 318 #516
Workflow file for this run
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| name: Test terra-jupyter-aou | |
| # Perform smoke tests on the terra-jupyter-aou Docker image to have some amount of confidence that | |
| # Python package versions are compatible. | |
| # | |
| # To configure the minimal auth needed for these tests to be able to read public data from Google Cloud Platform: | |
| # Step 1: Create a service account per these instructions: | |
| # https://github.com/google-github-actions/setup-gcloud/blob/master/setup-gcloud/README.md | |
| # Step 2: Give the service account the following permissions within the project: BigQuery User | |
| # Step 3: Store its key and project id as GitHub repository secrets TD_GCP_SA_KEY and GCP_PROJECT_ID. | |
| # https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository | |
| on: | |
| pull_request: | |
| branches: [ master ] | |
| paths: | |
| - 'terra-jupyter-aou/**' | |
| - '.github/workflows/test-terra-jupyter-aou.yml' | |
| push: | |
| # Note: GitHub secrets are not passed to pull requests from forks. For community contributions from | |
| # regular contributors, its a good idea for the contributor to configure the GitHub actions to run correctly | |
| # in their fork as described above. | |
| # | |
| # For occasional contributors, the dev team will merge the PR fork branch to a branch in upstream named | |
| # test-community-contribution-<PR#> to run all the GitHub Action smoke tests. | |
| branches: [ 'test-community-contribution*' ] | |
| paths: | |
| - 'terra-jupyter-aou/**' | |
| - '.github/workflows/test-terra-jupyter-aou.yml' | |
| workflow_dispatch: | |
| # Allows manually triggering of workflow on a selected branch via the GitHub Actions tab. | |
| # GitHub blog demo: https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/. | |
| env: | |
| GOOGLE_PROJECT: ${{ secrets.GCP_PROJECT_ID }} | |
| jobs: | |
| test_docker_image: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Free up some disk space | |
| run: sudo rm -rf /usr/share/dotnet | |
| - id: auth | |
| uses: google-github-actions/auth@v1 | |
| with: | |
| credentials_json: ${{ secrets.TD_GCP_SA_KEY }} | |
| create_credentials_file: true | |
| - name: Set up Cloud SDK | |
| uses: google-github-actions/setup-gcloud@v0.3.0 | |
| with: | |
| project_id: ${{ secrets.GCP_PROJECT_ID }} | |
| - name: Build Docker image and base images too, if needed | |
| run: | | |
| gcloud auth configure-docker | |
| ./build_smoke_test_image.sh terra-jupyter-aou | |
| - name: Run Python code specific to notebooks with nbconvert | |
| # Run all notebooks from start to finish, regardles of error, so that we can capture the | |
| # result as a workflow artifact. | |
| # See also https://github.com/marketplace/actions/run-notebook if a more complicated | |
| # workflow for notebooks is needed in the future. | |
| run: | | |
| chmod a+w -R $GITHUB_WORKSPACE | |
| chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" | |
| docker run \ | |
| --env GOOGLE_PROJECT \ | |
| --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ | |
| --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \ | |
| --volume $GITHUB_WORKSPACE:/tests \ | |
| --workdir=/tests \ | |
| --entrypoint="" \ | |
| terra-jupyter-aou:smoke-test \ | |
| /bin/bash -c 'for nb in {terra-jupyter-python/tests,terra-jupyter-aou/tests}/*ipynb ; do jupyter nbconvert --to html --ExecutePreprocessor.allow_errors=True --execute "${nb}" ; done' | |
| - name: Upload workflow artifacts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: notebook-execution-results | |
| path: | | |
| terra-jupyter-python/tests/*.html | |
| terra-jupyter-aou/tests/*.html | |
| retention-days: 30 | |
| - name: Test Python code with pytest | |
| run: | | |
| chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" | |
| docker run \ | |
| --env GOOGLE_PROJECT \ | |
| --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ | |
| --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \ | |
| --volume $GITHUB_WORKSPACE:/tests \ | |
| --workdir=/tests \ | |
| --entrypoint="" \ | |
| terra-jupyter-aou:smoke-test \ | |
| /bin/bash -c 'pip3 install pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-aou/tests/' | |
| - name: Test Python code specific to notebooks with nbconvert | |
| # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite. | |
| # If the tests throw any exceptions, execution of the notebooks will halt at that point. Look at the workflow | |
| # artifacts to understand if there are more failures than just the one that caused this task to halt. | |
| run: | | |
| chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" | |
| docker run \ | |
| --env GOOGLE_PROJECT \ | |
| --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ | |
| --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \ | |
| --volume $GITHUB_WORKSPACE:/tests \ | |
| --workdir=/tests \ | |
| --entrypoint="" \ | |
| terra-jupyter-aou:smoke-test \ | |
| /bin/bash -c 'for nb in {terra-jupyter-python/tests,terra-jupyter-aou/tests}/*ipynb ; do jupyter nbconvert --to html --execute "${nb}" ; done' |