main.yml

name: CI-CD

on:
  create:
    tags:
    - '^v[0-9]+.[0-9]+.[0-9]+(?:.dev[0-9])?$'
  workflow_dispatch:
      inputs:
        py-act:
          description: 'Python 3.X for GH Actions'
          required: false
          default: '3.8'
        pip_opts:
          description: Install options (pip)
          required: false
          default: '--upgrade --upgrade-strategy eager'
env:
  ACTIONS_SETUP_PY3: ${{ github.event.inputs.py-act || '3.8' }}
  PIP_INSTALL_OPTS: ${{ github.event.inputs.pip_opts || '--upgrade --upgrade-strategy eager' }}
  PY_COLORS: 1
  GHCR: ghcr.io
  DOCKER_IMAGE: sbrg/pymodulon

jobs:
  test:
    runs-on: ${{ matrix.os }}
    name: Test code (Python ${{ matrix.py }} - ${{ matrix.os }})
    strategy:
      max-parallel: 3
      fail-fast: true
      matrix:
        os: [ubuntu-latest]
        py: [3.7, 3.8]
    steps:
      -
        name: Checkout repository
        id: checkout
        uses: actions/checkout@v2
      -
        name: Set up Python ${{ matrix.py }}
        id: setup
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.py }}
      -
        name: Set Python ${{ matrix.py }} cache
        id: cache
        uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.os }}-pydeps-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('pyproject.toml') }}
      -
        name : Install dependencies
        id: install-deps
        run: |
          python -m pip install ${{ env.PIP_INSTALL_OPTS }} pip setuptools tox tox-gh-actions coverage[toml]
          sudo apt-get install ncbi-blast+
      -
        name: Run tests via tox
        id: run-tox
        run: |
          python -m tox
      -
        name: Generate an XML report of coverage results
        id: cov-report-xml
        run: |
          python -m coverage xml
      -
        name: Upload coverage report to Codecov.io
        id: codecov-upload
        uses: codecov/codecov-action@v1
        with:
          name: "py${{ matrix.py }}-${{ matrix.os }}"
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true

  docs:
    runs-on: ubuntu-latest
    name: Check documentation
    steps:
      -
        name: Checkout
        id: checkout
        uses: actions/checkout@v2
      -
        name: Set up Python ${{ env.ACTIONS_SETUP_PY3 }}
        id: setup
        uses: actions/setup-python@v2
        with:
          python-version: ${{ env.ACTIONS_SETUP_PY3 }}
      -
        name: Set Python ${{ env.ACTIONS_SETUP_PY3 }} cache
        id: cache
        uses: actions/cache@v2
        with:
          path: |
            ${{ env.pythonLocation }}
          key: ${{ runner.os }}-pydeps-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('pyproject.toml') }}
      -
        name : Install dependencies
        id: install-deps
        run: |
          python -m pip install ${{ env.PIP_INSTALL_OPTS }} pip setuptools tox
      -
        name: Set up pandoc
        id: pandoc
        uses: r-lib/actions/setup-pandoc@v1
      -
        name: Run additional checks via tox
        id: run-tox
        run: |
          python -m tox -e "docs, pypi-description"

  publish-pypi:
    needs: [test, docs]
    runs-on: ubuntu-latest
    name: Publish package to Python Packaging Index (PyPi)
    if: startsWith(github.ref, 'refs/tags/v')
    steps:
      -
        name: Checkout
        id: checkout
        uses: actions/checkout@v2
      -
        name: Set up Python
        id: setup
        uses: actions/setup-python@v2
        with:
          python-version: ${{ env.ACTIONS_SETUP_PY3 }}
      -
        name: Set Python ${{ env.ACTIONS_SETUP_PY3 }} cache
        id: cache
        uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.os }}-pydeps-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('pyproject.toml') }}
      -
        name : Install dependencies
        id: install-deps
        run: |
          python -m pip install ${{ env.PIP_INSTALL_OPTS }} pip setuptools wheel build
      -
        name: Build package
        id: build
        run: |
          python -m build -s -w .
      -
        name: Publish package to Test PyPI
        id: test-publish
        uses: pypa/gh-action-pypi-publish@master
        with:
          user: __token__
          password: ${{ secrets.SBRG_MACHINE_PYPI_TEST_TOKEN }}
          repository_url: https://test.pypi.org/legacy/
          skip_existing: true
      -
        name: Publish package to PyPI
        id: publish
        uses: pypa/gh-action-pypi-publish@master
        with:
          user: __token__
          password: ${{ secrets.SBRG_MACHINE_PYPI_TOKEN }}

  push-to-registries:
    needs: [publish-pypi]
    name: Build and push Docker images to registries
    runs-on: ubuntu-latest
    if: startsWith(github.ref, 'refs/tags/v')
    steps:
      -
        name: Checkout
        id: checkout
        uses: actions/checkout@v2
      -
        name: Docker meta
        id: docker-meta
        uses: crazy-max/ghaction-docker-meta@v1
        with:
          images: |
            ${{ env.DOCKER_IMAGE }}
            ${{ env.GHCR }}/${{ env.DOCKER_IMAGE }}
          tag-sha: true
          tag-match: '^v[0-9]+.[0-9]+.[0-9]+(?:.dev[0-9])?$'
          # e.g., v{MAJOR}.{MINOR}.{PATCH}(.dev{})
      -
        name: Set up Docker Buildx
        id: docker-buildx-setupx
        uses: docker/setup-buildx-action@v1
      -
        name: Login to DockerHub
        id: docker-login
        uses: docker/login-action@v1
        with:
          username: ${{ secrets.SBRG_MACHINE_DOCKERHUB_USERNAME }}
          password: ${{ secrets.SBRG_MACHINE_DOCKERHUB_TOKEN }}
      -
        name: Login to GitHub Container Registry
        id: ghcr-login
        uses: docker/login-action@v1
        with:
          registry: ${{ env.GHCR }}
          username: ${{ secrets.SBRG_MACHINE_GHCR_USERNAME }}
          password: ${{ secrets.SBRG_MACHINE_GHCR_TOKEN }}
      -
        name: Build and push image to registry
        id: docker-build-push
        uses: docker/build-push-action@v2
        with:
          file: Dockerfile
          push: true
          tags: ${{ steps.docker-meta.outputs.tags }}