Proposal: Improved ProvenanceProfile definition
#2434
Workflow file for this run
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| name: CI Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| concurrency: | |
| group: build-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| TOX_SKIP_MISSING_INTERPRETERS: False | |
| # Rich (pip) | |
| FORCE_COLOR: 1 | |
| # Tox | |
| PY_COLORS: 1 | |
| # Mypy (see https://github.com/python/mypy/issues/7771) | |
| TERM: xterm-color | |
| MYPY_FORCE_COLOR: 1 | |
| MYPY_FORCE_TERMINAL_WIDTH: 200 | |
| # Pytest | |
| PYTEST_ADDOPTS: --color=yes | |
| jobs: | |
| tox: | |
| name: Tox | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| py-ver-major: [3] | |
| py-ver-minor: [9, 10, 11, 12, 13] | |
| step: [lint, unit, bandit, mypy] | |
| env: | |
| py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }} | |
| TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Singularity and environment-modules | |
| if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }} | |
| run: | | |
| wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb | |
| sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules | |
| - name: Give the test runner user a name to make provenance happy. | |
| if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }} | |
| run: sudo usermod -c 'CI Runner' "$(whoami)" | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.py-semver }} | |
| allow-prereleases: true | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| tox.ini | |
| - name: Upgrade setuptools and install tox | |
| run: | | |
| pip install -U pip setuptools wheel | |
| pip install "tox<4" "tox-gh-actions<3" | |
| - name: MyPy cache | |
| if: ${{ matrix.step == 'mypy' }} | |
| uses: actions/cache@v4 | |
| with: | |
| path: .mypy_cache/${{ env.py-semver }} | |
| key: mypy-${{ env.py-semver }} | |
| - name: Test with tox | |
| run: APPTAINER_TMPDIR=${RUNNER_TEMP} tox | |
| - name: Upload coverage to Codecov | |
| if: ${{ matrix.step == 'unit' }} | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| tox-style: | |
| name: Linters | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| step: [lintreadme, shellcheck, pydocstyle] | |
| env: | |
| py-semver: "3.12" | |
| TOXENV: ${{ format('py312-{0}', matrix.step) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.py-semver }} | |
| cache: pip | |
| - name: Upgrade setuptools and install tox | |
| run: | | |
| pip install -U pip setuptools wheel | |
| pip install "tox<4" "tox-gh-actions<3" | |
| - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}} | |
| name: Create local branch for diff-quality for PRs | |
| run: git branch ${{github.base_ref}} origin/${{github.base_ref}} | |
| - name: Test with tox | |
| run: tox | |
| clean_working_dir: | |
| name: No leftovers | |
| runs-on: ubuntu-22.04 | |
| env: | |
| py-semver: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Singularity and environment-modules | |
| run: | | |
| wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb | |
| sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules | |
| - name: Give the test runner user a name to make provenance happy. | |
| run: sudo usermod -c 'CI Runner' "$(whoami)" | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.py-semver }} | |
| cache: pip | |
| - name: install with test dependencies | |
| run: | | |
| pip install -U pip setuptools wheel | |
| pip install --no-build-isolation -rtest-requirements.txt .[deps] | |
| - name: make working directory read-only | |
| run: | | |
| mkdir .pytest_cache | |
| chmod a-w . | |
| - name: run tests | |
| run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test | |
| conformance_tests: | |
| name: CWL conformance | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| cwl-version: [v1.0, v1.1, v1.2] | |
| container: [docker, singularity, podman] | |
| extras: [""] | |
| include: | |
| - cwl-version: v1.2 | |
| container: docker | |
| extras: "--fast-parser" | |
| - cwl-version: v1.3.0-dev1 | |
| extras: "--relax-path-checks" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Singularity and environment-modules | |
| if: ${{ matrix.container == 'singularity' }} | |
| run: | | |
| wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb | |
| sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules | |
| - name: Singularity cache | |
| if: ${{ matrix.container == 'singularity' }} | |
| uses: actions/cache@v4 | |
| with: | |
| path: sifcache | |
| key: singularity | |
| - name: Set up Podman | |
| if: ${{ matrix.container == 'podman' }} | |
| run: sudo rm -f /usr/bin/docker ; sudo apt-get install -y podman | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| cache: pip | |
| - name: "Test CWL ${{ matrix.cwl-version }} conformance" | |
| env: | |
| VERSION: ${{ matrix.cwl-version }} | |
| CONTAINER: ${{ matrix.container }} | |
| GIT_TARGET: main | |
| CWLTOOL_OPTIONS: ${{ matrix.cwl-version == 'v1.2' && '--relax-path-checks' || '' }} ${{ matrix.extras }} | |
| run: ./conformance-test.sh | |
| - name: Archive test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: cwl-${{ matrix.cwl-version }}-${{ matrix.container }}${{ matrix.extras }}-conformance-results | |
| path: | | |
| **/cwltool_conf*.xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| release_test: | |
| name: cwltool release test | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Singularity and environment-modules | |
| run: | | |
| wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb | |
| sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| test-requirements.txt | |
| - name: Give the test runner user a name to make provenance happy. | |
| run: sudo usermod -c 'CI Runner' "$(whoami)" | |
| - name: Install packages | |
| run: | | |
| pip install -U pip setuptools wheel | |
| pip install virtualenv | |
| - name: Release test | |
| env: | |
| RELEASE_SKIP: head | |
| run: ./release-test.sh | |
| build_test_container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: record cwltool version | |
| run: pip install -U setuptools wheel && pip install setuptools_scm[toml] && python setup.py --version | |
| - name: build & test cwltool_module container | |
| run: ./build-cwltool-docker.sh | |
| macos: | |
| name: Test on macos-latest | |
| runs-on: macos-13 # not latest, that is now an Apple Silicon M1, for which seqtk is not yet built on bioconda | |
| env: | |
| TOXENV: py312-unit | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| tox.ini | |
| - name: Upgrade setuptools and install tox | |
| run: | | |
| pip install -U pip setuptools wheel | |
| pip install "tox<4" "tox-gh-actions<3" | |
| # # docker for mac install is not currently stable | |
| # - name: 'SETUP MacOS: load Homebrew cache' | |
| # uses: actions/cache@v4 | |
| # if: runner.os == 'macOS' | |
| # with: | |
| # path: | | |
| # ~/Library/Caches/Homebrew/downloads/*--Docker.dmg | |
| # key: brew-actions-setup-docker-1.0.11 | |
| # restore-keys: brew-actions-setup-docker- | |
| # - name: setup docker on macos (default stable version) | |
| # uses: docker-practice/actions-setup-docker@master | |
| - name: Test with tox | |
| run: tox | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |