ci-tests.yaml

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:
  check-changelog:
    name: "Enforce CHANGELOG updates"
    runs-on: ubuntu-24.04
    if: github.event_name == 'pull_request'
    steps:
      - name: Checkout
        uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - name: Check if CHANGELOG.md changed
        run: |
          BASE_BRANCH="${{ github.event.pull_request.base.ref }}"          
          git fetch origin $BASE_BRANCH
          if ! git diff --name-only origin/$BASE_BRANCH...HEAD | grep -q "^CHANGELOG.md$"; then
            echo "Error: CHANGELOG.md has not been updated!"
            exit 1
          fi
  code-ql-check:
    name: "StreamFlow CodeQL check"
    runs-on: ubuntu-24.04
    permissions:
      security-events: write
    steps:
      - uses: actions/checkout@v6
      - uses: github/codeql-action/init@v4
        with:
          config-file: .github/codeql/config.yml
          languages: python
      - uses: github/codeql-action/analyze@v4
  cwl-conformance:
    name: "CWL conformance tests"
    strategy:
      matrix:
        on: [ "ubuntu-24.04" ]
        python: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
        version: [ "v1.0", "v1.1", "v1.2", "v1.3" ]
        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"
          - commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
            exclude: "docker_entrypoint,modify_file_content"
            version: "v1.3"
          - docker: "singularity"
            commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
            exclude: "docker_entrypoint,modify_file_content,iwd-container-entryname1"
            on: "ubuntu-24.04"
            python: "3.14"
            version: "v1.3"
          - docker: "kubernetes"
            commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
            exclude: "docker_entrypoint,modify_file_content"
            on: "ubuntu-24.04"
            python: "3.14"
            version: "v1.3"
          - on: "macos-15-intel"
            python: "3.14"
            commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
            exclude: "docker_entrypoint,modify_file_content"
            version: "v1.3"
    runs-on: ${{ matrix.on }}
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/setup-uv@v7
        with:
          version: "0.9.16"
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python }}
      - uses: actions/setup-node@v6
        with:
          node-version: "24"
      - name: "Install Docker (MacOS X)"
        uses: docker/setup-docker-action@v5
        env:
          LIMA_START_ARGS: '--vm-type=vz --mount-type=virtiofs --mount /private/var/folders:w'
        if: ${{ startsWith(matrix.on, 'macos-') }}
      - uses: docker/setup-qemu-action@v4
        if: ${{ startsWith(matrix.on, 'ubuntu-') }}
      - name: "Install Apptainer"
        uses: eWaterCycle/setup-apptainer@v2
        with:
          apptainer-version: 1.4.2
        if: ${{ matrix.docker == 'singularity' }}
      - name: "Install KinD"
        uses: helm/kind-action@v1.14.0
        with:
          config: .github/kind/config.yaml
          kubectl_version: v1.35.0
          version: v0.31.0
        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: "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 test results"
        if: ${{ !cancelled() }}
        uses: codecov/codecov-action@v6
        with:
          flags: ${{ startsWith(matrix.on, 'macos-') && 'macos' || 'ubuntu' }}
          report_type: test_results
          token: ${{ secrets.CODECOV_TOKEN }}
      - name: "Upload coverage report for conformance tests"
        uses: actions/upload-artifact@v7
        with:
          name: ${{ format('{0}-py{1}-cwl{2}-{3}-conformance-tests', matrix.on, matrix.python, matrix.version, matrix.docker) }}
          path: |
            ./coverage.xml
          retention-days: 1
          if-no-files-found: error
  docker-image:
    name: "StreamFlow Docker image tests"
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v6
      - uses: docker/setup-qemu-action@v4
      - uses: docker/setup-buildx-action@v4
      - name: "Build Docker image"
        uses: docker/build-push-action@v7
        with:
          build-args: |
            HELM_VERSION=v4.1.1
          load: true
          tags: alphaunito/streamflow:latest
      - name: "Run test with Docker"
        run: |
          mkdir -p "${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 and Test Sphinx documentation"
    strategy:
      matrix:
        on: [ "ubuntu-24.04" ]
        python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
    runs-on: ${{ matrix.on }}
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/setup-uv@v7
        with:
          version: "0.9.16"
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python }}
      - uses: actions/setup-node@v6
        with:
          node-version: "24"
      - uses: docker/setup-qemu-action@v4
      - name: "Install KinD"
        uses: helm/kind-action@v1.14.0
        with:
          config: .github/kind/config.yaml
          kubectl_version: v1.35.0
          version: v0.31.0
      - name: "Configure Calico on KinD"
        run: |
          kubectl apply -f https://docs.projectcalico.org/v3.25/manifests/calico.yaml
          kubectl -n kube-system set env daemonset/calico-node FELIX_IGNORELOOSERPF=true
      - name: "Install Helm"
        uses: azure/setup-helm@v5
        with:
          version: v4.1.1
      - name: "Install Python Dependencies"
        run: uv sync --locked --no-dev --group docs --group test
      - name: "Build documentation and check for consistency"
        env:
          CHECKSUM: "1c672c7b3fd0250d381384631d0a547ac3c50a32e6d6536d479b87a39506b2b2"
        run: |
          cd docs
          HASH="$(uv run --no-sync make checksum | tail -n1)"
          echo "Docs checksum is ${HASH}"
          test "${HASH}" == "${CHECKSUM}"
      - name: "Run documentation example tests"
        run: |
          cd docs
          uv run --no-sync make coverage.xml
      - name: "Upload test results"
        if: ${{ !cancelled() }}
        uses: codecov/codecov-action@v6
        with:
          files: docs/junit.xml
          report_type: test_results
          token: ${{ secrets.CODECOV_TOKEN }}
      - name: "Upload coverage report for documentation tests"
        uses: actions/upload-artifact@v7
        with:
          name: ${{ format('{0}-py{1}-documentation-tests', matrix.on, matrix.python) }}
          path: |
            ./docs/coverage.xml
          retention-days: 1
          if-no-files-found: error
  test-flux:
    runs-on: ubuntu-24.04
    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@v6
      - 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-24.04
    strategy:
      matrix:
        step: [ "bandit", "lint" ]
    env:
      TOXENV: ${{ matrix.step }}
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/setup-uv@v7
        with:
          version: "0.9.16"
      - uses: actions/setup-python@v6
        with:
          python-version: "3.14"
      - name: "Install Tox"
        run: uv tool install tox --with tox-uv
      - name: "Run StreamFlow static analysis via Tox"
        run: tox
  unit-tests:
    name: "StreamFlow unit tests"
    strategy:
      matrix:
        on: [ "ubuntu-24.04" ]
        python: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
        include:
          - on: "macos-15-intel"
            python: "3.14"
    runs-on: ${{ matrix.on }}
    env:
      TOXENV: ${{ format('py{0}-unit', matrix.python) }}
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/setup-uv@v7
        with:
          version: "0.9.16"
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python }}
      - uses: actions/setup-node@v6
        with:
          node-version: "24"
      - name: "Install Docker (MacOs X)"
        uses: docker/setup-docker-action@v5
        env:
          LIMA_START_ARGS: '--vm-type=vz --mount-type=virtiofs --mount /private/var/folders:w'
        if: ${{ startsWith(matrix.on, 'macos-') }}
      - name: "Install Docker Compose (MacOS X)"
        uses: docker/setup-compose-action@v2
        if: ${{ startsWith(matrix.on, 'macos-') }}
      - uses: docker/setup-qemu-action@v4
        if: ${{ startsWith(matrix.on, 'ubuntu-') }}
      - name: "Install Apptainer"
        uses: eWaterCycle/setup-apptainer@v2
        with:
          apptainer-version: 1.4.2
        if: ${{ startsWith(matrix.on, 'ubuntu-') }}
      - name: "Install KinD"
        uses: helm/kind-action@v1.14.0
        with:
          config: .github/kind/config.yaml
          kubectl_version: v1.35.0
          version: v0.31.0
        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 Tox"
        run: uv tool install tox --with tox-uv
      - name: "Run StreamFlow tests via Tox"
        run: tox
      - name: "Upload test results"
        if: ${{ !cancelled() }}
        uses: codecov/codecov-action@v6
        with:
          flags: ${{ startsWith(matrix.on, 'macos-') && 'macos' || 'ubuntu' }}
          report_type: test_results
          token: ${{ secrets.CODECOV_TOKEN }}
      - name: "Upload coverage report for unit tests"
        uses: actions/upload-artifact@v7
        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", "documentation", "unit-tests"]
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v6
      - name: "Download conformance tests artifacts"
        uses: actions/download-artifact@v8
        with:
          pattern: "*-conformance-tests"
      - name: "Download documentation tests artifacts"
        uses: actions/download-artifact@v8
        with:
          pattern: "*-documentation-tests"
      - name: "Download unit tests artifacts"
        uses: actions/download-artifact@v8
        with:
          pattern: "*-unit-tests"
      - name: "Upload coverage to Codecov"
        uses: codecov/codecov-action@v6
        with:
          fail_ci_if_error: true
          token: ${{ secrets.CODECOV_TOKEN }}