add CWL PROV support #4505
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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') && ! contains(github.ref, 'refs/heads/master') }} | |
| steps: | |
| - uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| concurrent_skipping: "same_content_newer" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["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 }} | |
| # disable due to confusing and unhelpful messages created by codecov | |
| # (see )https://github.com/codecov/feedback/issues/304#issuecomment-2492675117) | |
| # - name: Upload test results to Codecov | |
| # if: ${{ !cancelled() && success() && matrix.test-case == 'test-coverage-only' }} | |
| # uses: codecov/test-results-action@v1 | |
| # with: | |
| # files: reports/coverage-junit.xml,!./cache | |
| # flags: ${{ matrix.python-version }} | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| - 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 |