Workflow tests #9
Workflow file for this run
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| name: Workflow tests | |
| # These permissions are needed to interact with GitHub's OIDC Token endpoint. | |
| permissions: | |
| id-token: write | |
| contents: read | |
| packages: write | |
| actions: write | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| container-tag: | |
| description: 'Container tag' | |
| required: true | |
| default: 'dev' | |
| keep-workdirs: | |
| description: 'Keep working directories for debugging' | |
| required: false | |
| default: 'false' | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - 'v*' | |
| schedule: | |
| # 01:00 every day | |
| - cron: "0 1 * * *" | |
| jobs: | |
| pre_job: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| # Map a step output to a job output | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| paths_result: ${{ steps.skip_check.outputs.paths_result }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@v5 | |
| with: | |
| concurrent_skipping: "same_content_newer" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["workflow_dispatch"]' | |
| paths_filter: | | |
| pixelator: | |
| paths: | |
| - 'src/pixelator/**' | |
| - 'tests/**' | |
| - 'pyproject.toml' | |
| - 'poetry.lock' | |
| paths_ignore: | |
| - 'tests/**/*.md' | |
| setup: | |
| runs-on: ubuntu-latest | |
| needs: pre_job | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).pixelator.should_skip | |
| outputs: | |
| docker_username: ${{ steps.login-ecr.outputs.docker_username_890888997283_dkr_ecr_eu_north_1_amazonaws_com }} | |
| docker_password: ${{ steps.login-ecr.outputs.docker_password_890888997283_dkr_ecr_eu_north_1_amazonaws_com }} | |
| steps: | |
| - name: Configure AWS credentials | |
| id: configure-aws-credentials | |
| uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-region: eu-north-1 | |
| role-to-assume: arn:aws:iam::890888997283:role/GithubActionsRole | |
| role-session-name: GitHubActions | |
| - name: Login to Amazon ECR | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v1 | |
| with: | |
| mask-password: 'false' | |
| test: | |
| # runs-on: [ "self-hosted", "linux", "x64", "ubuntu-latest" ] | |
| runs-on: ubuntu-latest | |
| needs: [setup] | |
| container: | |
| image: 890888997283.dkr.ecr.eu-north-1.amazonaws.com/pixelator:${{ github.event.inputs.container-tag || 'dev' }} | |
| credentials: | |
| username: ${{ needs.setup.outputs.docker_username }} | |
| password: ${{ needs.setup.outputs.docker_password }} | |
| volumes: | |
| - /mnt/github-actions-data:/data | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test: [ "small" ] | |
| # test: [ "small", "single-cell", "tissue" ] | |
| steps: | |
| - name: Install dev dependencies | |
| working-directory: /pixelator | |
| run: | | |
| poetry export -f requirements.txt --output requirements_only_dev.txt --only dev | |
| pip install -r requirements_only_dev.txt | |
| - name: Prepare test case string | |
| uses: actions/github-script@v6 | |
| id: test_case_file | |
| with: | |
| script: | | |
| const test_name = "${{ matrix.test }}" | |
| const test_file_name = `test_${test_name.replace(/-/g, '_')}.py` | |
| core.setOutput('filename', test_file_name) | |
| - name: Test pixelator | |
| run: | | |
| CMD="pytest /pixelator/tests/integration/${{ steps.test_case_file.outputs.filename }} --log-cli-level=DEBUG" | |
| if [[ "${{ github.event.inputs.keep-workdirs }}" == "true" ]]; then | |
| CMD="$CMD --keep-workdirs" | |
| fi | |
| $CMD -m "workflow_test" |