Migrate CWL parsing from cwltool to cwl-utils #2525
Workflow file for this run
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| name: "CI Tests" | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| concurrency: | |
| group: build-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| code-ql-check: | |
| name: "StreamFlow CodeQL check" | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| security-events: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: github/codeql-action/init@v3 | |
| with: | |
| config-file: .github/codeql/config.yml | |
| languages: python | |
| - uses: github/codeql-action/analyze@v3 | |
| cwl-conformance: | |
| name: "CWL conformance tests" | |
| strategy: | |
| matrix: | |
| on: [ "ubuntu-22.04" ] | |
| python: [ "3.9", "3.10", "3.11", "3.12", "3.13" ] | |
| version: [ "v1.0", "v1.1", "v1.2" ] | |
| docker: [ "docker" ] | |
| include: | |
| - commit: "1c1f122f780075d910fdfdea7e15e46eef3c078d" | |
| exclude: "docker_entrypoint" | |
| version: "v1.0" | |
| - commit: "6397014050177074c9ccd0d771577f7fa9f728a3" | |
| exclude: "docker_entrypoint,stdin_shorcut,inplace_update_on_file_content" | |
| version: "v1.1" | |
| - commit: "76bdf9b55e2378432e0e6380ccedebb4a94ce483" | |
| exclude: "docker_entrypoint,modify_file_content" | |
| version: "v1.2" | |
| - docker: "singularity" | |
| commit: "76bdf9b55e2378432e0e6380ccedebb4a94ce483" | |
| exclude: "docker_entrypoint,modify_file_content,iwd-container-entryname1" | |
| on: "ubuntu-22.04" | |
| python: "3.13" | |
| version: "v1.2" | |
| - docker: "kubernetes" | |
| commit: "76bdf9b55e2378432e0e6380ccedebb4a94ce483" | |
| exclude: "docker_entrypoint,modify_file_content" | |
| on: "ubuntu-22.04" | |
| python: "3.13" | |
| version: "v1.2" | |
| - on: "macos-13" | |
| python: "3.13" | |
| commit: "76bdf9b55e2378432e0e6380ccedebb4a94ce483" | |
| exclude: "docker_entrypoint,modify_file_content" | |
| version: "v1.2" | |
| runs-on: ${{ matrix.on }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| test-requirements.txt | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: "Install Docker (MacOS X)" | |
| uses: douglascamata/setup-docker-macos-action@main | |
| with: | |
| colima-additional-options: '--mount /private/var/folders:w --mount-type virtiofs' | |
| if: ${{ startsWith(matrix.on, 'macos-') }} | |
| - uses: docker/setup-qemu-action@v3 | |
| if: ${{ startsWith(matrix.on, 'ubuntu-') }} | |
| - name: "Install Apptainer" | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.2 | |
| if: ${{ matrix.docker == 'singularity' }} | |
| - name: "Install KinD" | |
| uses: helm/kind-action@v1.10.0 | |
| with: | |
| config: .github/kind/config.yaml | |
| kubectl_version: v1.30.3 | |
| version: v0.21.0 | |
| if: ${{ matrix.docker == 'kubernetes' }} | |
| - name: "Configure Calico on KinD" | |
| run: | | |
| kubectl apply -f https://docs.projectcalico.org/v3.25/manifests/calico.yaml | |
| kubectl -n kube-system set env daemonset/calico-node FELIX_IGNORELOOSERPF=true | |
| if: ${{ matrix.docker == 'kubernetes' }} | |
| - name: "Install StreamFlow" | |
| run: | | |
| python -m pip install . --user | |
| - name: "Test CWL ${{ matrix.version }} conformance" | |
| env: | |
| VERSION: ${{ matrix.version }} | |
| COMMIT: ${{ matrix.commit }} | |
| EXCLUDE: ${{ matrix.exclude }} | |
| DOCKER: ${{ matrix.docker }} | |
| run: ./cwl-conformance-test.sh | |
| - name: "Upload coverage report for conformance tests" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ format('{0}-py{1}-cwl{2}-{3}-conformance-tests', matrix.on, matrix.python, matrix.version, matrix.docker) }} | |
| path: ./coverage.xml | |
| retention-days: 1 | |
| if-no-files-found: error | |
| docker-image: | |
| name: "StreamFlow Docker image tests" | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-qemu-action@v3 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: "Build Docker image" | |
| uses: docker/build-push-action@v6 | |
| with: | |
| build-args: | | |
| HELM_VERSION=v3.7.2 | |
| load: true | |
| tags: alphaunito/streamflow:latest | |
| - name: "Run test with Docker" | |
| run: | | |
| mkdir -p "${TMPDIR:-/tmp}"/project "${TMPDIR:-/tmp}"/results "${TMPDIR:-/tmp}"/streamflow | |
| docker run --rm \ | |
| --mount type=bind,source="$(pwd)/tests/data/cwl/example",target="/streamflow/project" \ | |
| --mount type=bind,source="${TMPDIR:-/tmp}"/results,target="/streamflow/results" \ | |
| --mount type=bind,source="${TMPDIR:-/tmp}"/streamflow,target="/tmp/streamflow" \ | |
| alphaunito/streamflow:latest \ | |
| streamflow run /streamflow/project/streamflow.yml | |
| documentation: | |
| name: "Build Sphinx documentation" | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.13 | |
| cache: pip | |
| cache-dependency-path: | | |
| docs/requirements.txt | |
| - name: "Install Python Dependencies" | |
| run: | | |
| python -m pip install -r docs/requirements.txt | |
| - name: "Build documentation and check for consistency" | |
| env: | |
| CHECKSUM: "6642d8d7533c7cf3ec9de7bdbf1871e3a313dd73fa6551fe3bb10e4e94e7ff08" | |
| run: | | |
| cd docs | |
| HASH="$(make checksum | tail -n1)" | |
| echo "Docs checksum is ${HASH}" | |
| test "${HASH}" == "${CHECKSUM}" | |
| test-flux: | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| packages: read | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| container: ["fluxrm/flux-sched:noble-v0.39.0-amd64"] | |
| container: | |
| image: ${{ matrix.container }} | |
| options: "--platform=linux/amd64 --user root -it" | |
| name: ${{ matrix.container }} | |
| steps: | |
| - name: Make Space | |
| run: | | |
| rm -rf /usr/share/dotnet | |
| rm -rf /opt/ghc | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install Python modules | |
| run: | | |
| apt update | |
| apt install -yq python3-pip python3-venv | |
| su fluxuser | |
| - name: Install StreamFlow | |
| run: | | |
| python3 -m venv /tmp/venv | |
| . /tmp/venv/bin/activate | |
| pip install . | |
| pip install --upgrade --force-reinstall attrs lockfile | |
| which streamflow | |
| - name: Start Flux and Test Workflow | |
| run: | | |
| . /tmp/venv/bin/activate | |
| which streamflow | |
| cd examples/flux | |
| flux start streamflow run streamflow.yml | |
| static-checks: | |
| name: "StreamFlow static checks" | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| step: [ "bandit", "lint" ] | |
| env: | |
| TOXENV: ${{ matrix.step }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| test-requirements.txt | |
| tox.ini | |
| - name: "Install Python Dependencies and StreamFlow" | |
| run: | | |
| python -m pip install tox --user | |
| python -m pip install . --user | |
| - name: "Run StreamFlow static analysis via Tox" | |
| run: tox | |
| unit-tests: | |
| name: "StreamFlow unit tests" | |
| strategy: | |
| matrix: | |
| on: [ "ubuntu-22.04"] | |
| python: [ "3.9", "3.10", "3.11", "3.12", "3.13" ] | |
| include: | |
| - on: "macos-13" | |
| python: "3.13" | |
| runs-on: ${{ matrix.on }} | |
| env: | |
| TOXENV: ${{ format('py{0}-unit', matrix.python) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements.txt | |
| tox.ini | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: "Install Docker (MacOs X)" | |
| uses: douglascamata/setup-docker-macos-action@main | |
| with: | |
| colima-additional-options: '--mount /private/var/folders:w --mount-type virtiofs' | |
| if: ${{ startsWith(matrix.on, 'macos-') }} | |
| - uses: docker/setup-qemu-action@v3 | |
| if: ${{ startsWith(matrix.on, 'ubuntu-') }} | |
| - name: "Install Apptainer" | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.2 | |
| if: ${{ startsWith(matrix.on, 'ubuntu-') }} | |
| - name: "Install KinD" | |
| uses: helm/kind-action@v1.10.0 | |
| with: | |
| config: .github/kind/config.yaml | |
| kubectl_version: v1.30.3 | |
| version: v0.21.0 | |
| if: ${{ startsWith(matrix.on, 'ubuntu-') }} | |
| - name: "Configure Calico on KinD" | |
| run: | | |
| kubectl apply -f https://docs.projectcalico.org/v3.25/manifests/calico.yaml | |
| kubectl -n kube-system set env daemonset/calico-node FELIX_IGNORELOOSERPF=true | |
| if: ${{ startsWith(matrix.on, 'ubuntu-') }} | |
| - name: "Install Python Dependencies and StreamFlow" | |
| run: | | |
| python -m pip install tox --user | |
| python -m pip install . --user | |
| - name: "Run StreamFlow tests via Tox" | |
| run: python -m tox | |
| - name: "Upload coverage report for unit tests" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ format('{0}-py{1}-unit-tests', matrix.on, matrix.python) }} | |
| path: ./coverage.xml | |
| retention-days: 1 | |
| if-no-files-found: error | |
| upload-to-codecov: | |
| name: "Codecov report upload" | |
| needs: ["cwl-conformance", "unit-tests"] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Download conformance tests artifacts" | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: "*-conformance-tests" | |
| - name: "Download unit tests artifacts" | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: "*-unit-tests" | |
| - name: "Upload coverage to Codecov" | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |