ci-tests.yml

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 }}