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:
  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@v1-alpha.15
        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@v1-alpha.15
        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 }}