Fix ensemble bug, add clear count #309
Workflow file for this run
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| name: Image build and test | |
| env: | |
| IMAGE_NAME: geoscienceaustralia/dea-intertidal | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - tests | |
| paths: | |
| - 'intertidal/**' | |
| - 'data/**' | |
| - 'tests/**' | |
| - '.github/workflows/dea-intertidal-image.yml' | |
| - 'Dockerfile' | |
| - 'requirements.in' | |
| - 'setup.py' | |
| - 'codecov.yaml' | |
| pull_request: | |
| branches: | |
| - develop | |
| paths: | |
| - 'intertidal/**' | |
| - 'data/**' | |
| - 'tests/**' | |
| - '.github/workflows/dea-intertidal-image.yml' | |
| - 'Dockerfile' | |
| - 'requirements.in' | |
| - 'setup.py' | |
| - 'codecov.yaml' | |
| release: | |
| types: [edited, published] | |
| permissions: | |
| id-token: write # Required for requesting Json web token | |
| contents: write # Required for actions/checkout | |
| pull-requests: write # Required for validation results comment bot | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::060378307146:role/github-actions-dea-notebooks--sandbox | |
| aws-region: ap-southeast-2 | |
| role-duration-seconds: 7200 # 2 hours | |
| - name: Get database credentials | |
| run: | | |
| username_password=$(aws ssm get-parameter --name /dea-sandbox-eks/sandbox_reader/db.creds --with-decryption --query Parameter.Value --output text) | |
| echo DATACUBE_DB_URL=postgresql://${username_password}@localhost:5432/odc >> $GITHUB_ENV | |
| - name: Open port forward to RDS | |
| run: | | |
| npx basti connect \ | |
| --custom-target-vpc vpc-086904199e505c1f6 \ | |
| --custom-target-host db-aurora-dea-sandbox-eks-1.cos5zfpkso9m.ap-southeast-2.rds.amazonaws.com \ | |
| --custom-target-port 5432 \ | |
| --local-port 5432 & | |
| # Wait until the connection comes up, but, if it doesn't, don't hang forever. | |
| npx wait-on --timeout 120000 --interval 1000 tcp:127.0.0.1:5432 | |
| echo "PGPORT=5432" >> $GITHUB_ENV | |
| echo "PGHOST=localhost" >> $GITHUB_ENV | |
| - name: Build DEA Intertidal docker image | |
| timeout-minutes: 30 | |
| shell: bash | |
| run: | | |
| docker build -t dea_intertidal . | |
| - name: Run integration tests | |
| run: | | |
| # Download tide modelling files and unzip | |
| # TODO: Replace with S3 sync from dea-non-public-data | |
| wget --no-verbose https://www.dropbox.com/s/uemd8ib2vfw5nad/tide_models.zip?dl=1 -O tide_models.zip | |
| unzip -q tide_models.zip | |
| # Run integration tests using Docker, setting up datacube access, AWS configuration and | |
| # adding volumes that provide access to tide model data and allow us to export artifacts | |
| # from the run | |
| docker run \ | |
| --net=host \ | |
| --env DATACUBE_DB_URL \ | |
| --env AWS_SESSION_TOKEN \ | |
| --env AWS_REGION \ | |
| --env AWS_ACCESS_KEY_ID \ | |
| --env AWS_SECRET_ACCESS_KEY \ | |
| --env AWS_SESSION_TOKEN \ | |
| --volume ${GITHUB_WORKSPACE}:/code \ | |
| --volume ${GITHUB_WORKSPACE}/tide_models:/var/share/tide_models \ | |
| --volume ${GITHUB_WORKSPACE}/artifacts:/mnt/artifacts \ | |
| dea_intertidal pytest -v --cov=intertidal --cov-report=xml tests | |
| # Copy out validation outputs produced by the integration tests and place them | |
| # in correct output locations so they can be committed back into the repository | |
| cp ./artifacts/validation.jpg ./tests/validation.jpg | |
| cp ./artifacts/validation.csv ./tests/validation.csv | |
| cp ./artifacts/README.md ./tests/README.md | |
| # Commit validation results produced by integration tests back into repo | |
| - name: Commit validation results into repository | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| if: github.event_name == 'pull_request' | |
| continue-on-error: true | |
| with: | |
| commit_message: Automatically update integration test validation results | |
| file_pattern: 'tests/validation.jpg tests/validation.csv tests/README.md' | |
| # Post validation tesults as comment on PR | |
| - name: Post validation results as comment | |
| uses: mshick/add-pr-comment@v2 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| message: | | |
| ![](https://github.com/GeoscienceAustralia/dea-intertidal/blob/${{ github.head_ref }}/tests/validation.jpg?raw=true") | |
| For full integration test results, refer to the [Tests directory README](https://github.com/GeoscienceAustralia/dea-intertidal/tree/${{ github.head_ref }}/tests). | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| push_ecr: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| # Only run on a push to the develop branch OR a release | |
| if: (github.event_name == 'push' && github.ref == 'refs/heads/develop') || (github.event_name == 'release') | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| role-to-assume: arn:aws:iam::538673716275:role/github-actions-role | |
| aws-region: ap-southeast-2 | |
| - name: Get tag for this build if it exists | |
| if: github.event_name == 'release' | |
| run: | | |
| echo "RELEASE=${GITHUB_REF/refs\/tags\/}" >> $GITHUB_ENV | |
| - name: Push release image to ECR | |
| uses: whoan/docker-build-with-cache-action@master | |
| if: github.event_name == 'release' | |
| with: | |
| registry: 538673716275.dkr.ecr.ap-southeast-2.amazonaws.com | |
| image_name: ${{ env.IMAGE_NAME }} | |
| image_tag: ${{ env.RELEASE }} | |
| - name: Get git commit hash for unstable image name | |
| if: github.event_name != 'release' | |
| run: | | |
| echo "TAG=dev$(git rev-parse --short HEAD)" \ | |
| >> $GITHUB_ENV | |
| - name: Push unstable image to ECR | |
| uses: whoan/docker-build-with-cache-action@master | |
| if: github.event_name != 'release' | |
| with: | |
| registry: 538673716275.dkr.ecr.ap-southeast-2.amazonaws.com | |
| image_name: ${{ env.IMAGE_NAME }} | |
| image_tag: latest,${{ env.TAG }} |