integration-test.yml

name: Integration Workflow

on:
  pull_request:
  push:
    branches: [main]
    tags: ["*"]
  schedule:
    # runs every Wednesday at 7 AM UTC
    - cron: "0 7 * * 3"
  workflow_dispatch:
    inputs:
      pytest_addopts:
        description: Extra options for pytest; use -vv for full details; see
          https://docs.pytest.org/en/latest/example/simple.html#how-to-change-command-line-options-defaults
        required: false
        default: ""

env:
  LANG: "en_US.utf-8"
  LC_ALL: "en_US.utf-8"
  PIP_CACHE_DIR: ${{ github.workspace }}/.cache/pip
  POETRY_CACHE_DIR: ${{ github.workspace }}/.cache/pypoetry
  POETRY_VIRTUALENVS_IN_PROJECT: "true"
  PRE_COMMIT_HOME: ${{ github.workspace }}/.cache/pre-commit
  PYTEST_ADDOPTS: ${{ github.event.inputs.pytest_addopts }}
  PYTHONIOENCODING: "UTF-8"
  TARGET_PYTHON_VERSION: "3.9"

jobs:
  quality-test:
    # This job is used to run pre-commit checks to ensure that all files are
    # are formatted correctly.
    name: Pre-commit checks
    # Runs pre-commit checks on all files
    # This job doesn't fail fast to ensure that feedback on function is still provided
    strategy:
      fail-fast: false
    runs-on: ubuntu-22.04
    if: github.event_name != 'schedule'
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          # Full history required for branch-based pre-commit checks
          fetch-depth: 0
      - name: Setup python, and check pre-commit cache
        uses: ./.github/actions/setup-env
        with:
          python-version: ${{ env.TARGET_PYTHON_VERSION }}
          cache-pre-commit: true
          cache-venv: false
          setup-poetry: false
          install-deps: false
      - name: Run pre-commit checks on all files
        uses: pre-commit/action@v3.0.1
        with:
          extra_args: --all-files
  python-type-checks:
    # This job is used to check Python types
    name: Python type checks
    # Avoid fail-fast to retain output
    strategy:
      fail-fast: false
    runs-on: ubuntu-22.04
    if: github.event_name != 'schedule'
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4
      - name: Setup python, and check pre-commit cache
        uses: ./.github/actions/setup-env
        with:
          python-version: ${{ env.TARGET_PYTHON_VERSION }}
          cache-pre-commit: false
          cache-venv: true
          setup-poetry: true
          install-deps: true
      - name: Run mypy
        run: |
          poetry run mypy .
  integration-test:
    name: Pytest (Python ${{ matrix.python-version }} on ${{ matrix.os }})
    # Runs pytest on all tested versions of python and OSes
    strategy:
      fail-fast: false
      matrix:
        os:
          - macos-13
          - ubuntu-22.04
        python-version: ["3.9", "3.10", "3.11"]
    runs-on: ${{ matrix.os }}
    env:
      OS: ${{ matrix.os }}
      # This is needed to avoid a warning from SQLAlchemy
      # https://sqlalche.me/e/b8d9
      # We can remove this once we upgrade to SQLAlchemy >= 2.0
      SQLALCHEMY_SILENCE_UBER_WARNING: "1"
    if: github.event_name != 'schedule'
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4
      - name: Setup python, and load cache
        uses: ./.github/actions/setup-env
        with:
          python-version: ${{ matrix.python-version }}
          cache-pre-commit: false
          cache-venv: true
          setup-poetry: true
          install-deps: true
      - name: Run pytest and generate coverage report
        # For the target version and ubuntu, run pytest and generate coverage report
        if: (matrix.os == 'ubuntu-22.04')  && (matrix.python-version == env.TARGET_PYTHON_VERSION)
        run: poetry run pytest --cov=./ --cov-report=xml ${{ github.event.inputs.pytest_addopts }}
      - name: Upload coverage to Codecov
        # For the target version and ubuntu, upload coverage to Codecov
        if: (matrix.os == 'ubuntu-22.04') && (matrix.python-version == env.TARGET_PYTHON_VERSION )
        uses: codecov/codecov-action@v4
        env:
          OS: ${{ matrix.os }}
          PYTHON: ${{ matrix.python-version }}
        with:
          file: ./coverage.xml
          files: ./coverage1.xml,./coverage2.xml
          directory: ./coverage/reports/
          env_vars: OS,PYTHON
          fail_ci_if_error: true
          flags: unittests
          name: pycytominer
          # Adds codecov token. See the link below for more information:
          # https://docs.codecov.com/docs/adding-the-codecov-token
          token: ${{ secrets.CODECOV_TOKEN }}
      - name: Run pytest
        # For every other version and/or OS, run pytest without coverage
        if: (matrix.os != 'ubuntu-22.04') || (matrix.python-version != env.TARGET_PYTHON_VERSION )
        run: poetry run pytest ${{ github.event.inputs.pytest_addopts }}
  build:
    name: Build versioned package
    # This job is used to build the package and upload the artifacts to GitHub Actions workflow results.
    # See https://github.com/actions/upload-artifact?tab=readme-ov-file#where-does-the-upload-go
    runs-on: ubuntu-22.04
    outputs:
      version: ${{ steps.get_version.outputs.version }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup python, and load cache
        uses: ./.github/actions/setup-env
        with:
          python-version: ${{ env.TARGET_PYTHON_VERSION }}
          cache-pre-commit: false
          cache-venv: true
          setup-poetry: true
          install-deps: true
      - name: Build
        run: poetry build
      - name: Get pycytominer version
        id: get_version
        run: |
          echo "version=$(poetry version | cut -d' ' -f2 )" >> "$GITHUB_OUTPUT"
      - name: Upload artifacts
        uses: actions/upload-artifact@v4
        with:
          name: wheel
          path: dist/*.whl
          if-no-files-found: error
          retention-days: 90
      - name: Upload artifacts
        uses: actions/upload-artifact@v4
        with:
          name: sdist
          path: dist/*.tar.gz
          if-no-files-found: error
          retention-days: 90
  docker-image-test-and-push:
    runs-on: ubuntu-22.04
    # set a dependency sequence to occur after build job completion
    needs: build
    env:
      version: ${{ needs.build.outputs.version }}
      sdist_filename: pycytominer-${{ needs.build.outputs.version}}.tar.gz
      sdist_extracted_name: pycytominer-${{ needs.build.outputs.version}}
    steps:
      # checks out selected files for docker image build testing
      - name: Checkout selected files
        uses: actions/checkout@v4
        with:
          sparse-checkout: |
            build/docker/Dockerfile
            tests
          sparse-checkout-cone-mode: false
      - name: Download sdist artifact
        uses: actions/download-artifact@v4
        with:
          name: sdist
      # gather the sdist tar.gz name (which varies)
      # unzips the sdist
      - name: Extract sdist
        run: |
          tar -xzvf "${{ env.sdist_filename}}"
      # note: roughly follows Docker documentation on GitHub Actions usage
      # found on the following https://github.com/docker/build-push-action
      - name: Set up QEMU
        uses: docker/setup-qemu-action@v3
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3
      # attempts to build a test image for observing test behavior
      # and modeling a production image build. Version label
      # assumes pwd of, for example: pycytominer-1.0.1.post37.dev0+55690e4,
      # where we attempt to use 1.0.1.post37.dev0+55690e4 as a version label.
      - name: Build docker image for testing
        run: |
          cd "${{ env.sdist_extracted_name }}" && \
          cp -r ../tests . && \
          docker build -f ../build/docker/Dockerfile \
            -t pycytominer:testing \
            --label version="${{ env.version }}" \
            --target testing \
            .
      # runs pytest for pycytominer within a docker container based on the image above
      - name: Run tests through docker image
        run: |
          docker run pycytominer:testing pytest
      # Gather and prepare the dynamic version and other vars for use with work below.
      # For example, 1.1.0.post6.dev0+bc093ef becomes 1.1.0.post6.dev0_bc093ef
      - name: Gather dynamic version and set env var
        if: (github.event_name == 'push'||  github.event_name == 'schedule') && github.ref == 'refs/heads/main'
        id: env-vars
        run: >-
          echo "CLEAN_VERSION=$(echo ${{ env.sdist_extracted_name }} | tr '+' '_' )" >> "$GITHUB_OUTPUT" &&
          echo "DATE_TAG=$(date +'%y%m%d')" >> "$GITHUB_OUTPUT"
      - name: Login to Docker Hub
        # only run this task if we have a pull request merged or the schedule triggers from main
        if: (github.event_name == 'push'||  github.event_name == 'schedule') && github.ref == 'refs/heads/main'
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USER }}
          password: ${{ secrets.DOCKER_TOKEN }}
      # Docker image push based on weekly schedule
      - name: Schedule-based docker image push
        # only run this task if we have a schedule trigger from main on cytomining/pycytominer
        if: github.event_name == 'schedule' &&  github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
        uses: docker/build-push-action@v6
        with:
          context: "${{ env.sdist_extracted_name }}"
          push: true
          file: ./build/docker/Dockerfile
          target: production
          tags: cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }}_${{ steps.env-vars.outputs.DATE_TAG }}
      # Docker image push based on GitHub pushes to main
      - name: Push-based docker image push
        # only run this task if we have a pull request which is merged
        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
        uses: docker/build-push-action@v6
        with:
          context: "${{ env.sdist_extracted_name }}"
          push: true
          file: ./build/docker/Dockerfile
          target: production
          tags: cytomining/pycytominer:latest,cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }}
      # update docker hub description using readme on merge
      - name: Update Docker Hub repository description from readme
        # only run this task if we have a pull request which is merged
        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer'
        uses: peter-evans/dockerhub-description@v4
        with:
          username: ${{ secrets.DOCKER_USER }}
          password: ${{ secrets.DOCKER_TOKEN }}
          repository: cytomining/pycytominer
          readme-filepath: "${{ env.sdist_extracted_name }}/README.md"