CWL schema definition updates and fixes for Workflow steps and requir… #3585
Workflow file for this run
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| # run test suites | |
| name: Tests | |
| on: | |
| - pull_request | |
| - push | |
| - release | |
| - workflow_dispatch | |
| # cancel the current workflow if another commit was pushed on the same PR or reference | |
| # uses the GitHub workflow name to avoid collision with other workflows running on the same PR/reference | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # see: https://github.com/fkirc/skip-duplicate-actions | |
| skip_duplicate: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_duplicate.outputs.should_skip && ! contains(github.ref, 'refs/tags') }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| concurrent_skipping: "same_content" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["pull_request", "workflow_dispatch", "schedule", "release"]' | |
| # see: https://github.com/actions/setup-python | |
| tests: | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }} | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ matrix.allow-failure }} | |
| env: | |
| # override make command to install directly in active python | |
| CONDA_CMD: "" | |
| DOCKER_TEST_EXEC_ARGS: "-T" | |
| services: | |
| # Label used to access the service container | |
| mongodb: | |
| image: mongo:5.0 # DockerHub | |
| ports: | |
| - "27017:27017" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| allow-failure: [false] | |
| test-case: [test-unit-only, test-func-only] | |
| include: | |
| # experimental python | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| allow-failure: true | |
| test-case: test-unit-only | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| allow-failure: true | |
| test-case: test-func-only | |
| # linter tests | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| allow-failure: false | |
| test-case: check-all | |
| # documentation build | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| allow-failure: false | |
| test-case: docs | |
| # coverage test | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| allow-failure: false | |
| test-case: test-coverage-only | |
| # smoke test of Docker image | |
| - os: ubuntu-latest | |
| python-version: "3.10" # doesn't matter which one (in docker), but match default of repo | |
| allow-failure: false | |
| test-case: test-docker | |
| # EMS end-2-end Workflow tests | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| allow-failure: true | |
| test-case: test-workflow-only | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: "0" | |
| - name: Setup Python | |
| # skip python setup if running with docker | |
| if: ${{ matrix.test-case != 'test-docker' }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "${{ matrix.python-version }}" | |
| cache: 'pip' | |
| - name: Parse Python Version | |
| id: python-semver | |
| run: | | |
| echo "::set-output name=major:$(echo ${{ matrix.python-version }} | cut -d '.' -f 1)" | |
| echo "::set-output name=minor:$(echo ${{ matrix.python-version }} | cut -d '.' -f 2)" | |
| - uses: actions/cache@v3 | |
| name: Check Proj Lib Pre-Built in Cache | |
| id: cache-proj | |
| with: | |
| # note: '22' is v8, '21' is v7 | |
| path: /tmp/proj-8.2.1/install | |
| key: ${{ runner.os }}-python${{ matrix.python-version }}-proj | |
| - name: Install Dependencies | |
| # skip python setup if running with docker | |
| if: ${{ matrix.test-case != 'test-docker' }} | |
| # install package and dependencies directly, | |
| # skip sys/conda setup to use active python | |
| run: make install-sys install-pkg install-pip install-raw install-dev install-dev-npm | |
| - name: Display Packages | |
| # skip python setup if running with docker | |
| if: ${{ matrix.test-case != 'test-docker' }} | |
| run: | | |
| pip freeze | |
| npm list | |
| make version | |
| #- name: Setup Environment Variables | |
| # uses: c-py/action-dotenv-to-setenv@v2 | |
| # with: | |
| # env-file: ./ci/weaver.env | |
| - name: Display Environment Variables | |
| run: | | |
| hash -r | |
| env | sort | |
| - name: Run Tests | |
| run: make stop ${{ matrix.test-case }} | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v2 | |
| if: ${{ success() && matrix.test-case == 'test-coverage-only' }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./reports/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| deploy-docker: | |
| needs: tests | |
| if: ${{ success() && (contains(github.ref, 'refs/tags') || github.ref == 'refs/heads/master') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: "0" | |
| - name: Get Tag Version | |
| id: version | |
| shell: bash | |
| run: | | |
| if [[ "${GITHUB_REF}" == "refs/heads/master" ]]; then | |
| echo "::set-output name=TAG_VERSION::latest" | |
| else | |
| echo "::set-output name=TAG_VERSION::${GITHUB_REF##*/}" | |
| fi | |
| - name: Build Docker | |
| run: | | |
| make DOCKER_REPO=pavics/weaver APP_VERSION=${{ steps.version.outputs.TAG_VERSION }} docker-info docker-build | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Push to DockerHub | |
| run: | | |
| make DOCKER_REPO=pavics/weaver APP_VERSION=${{ steps.version.outputs.TAG_VERSION }} docker-push |