integration-test.yml

name: Integration Workflow

on:
  pull_request:
  push:
    branches: [main]
    tags: ["*"]
  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-latest
    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@v3.0.0
        with:
          extra_args: --all-files
  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-latest
          - ubuntu-latest
        python-version: ["3.8", "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"
    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-latest')  && (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
        continue-on-error: true
        if: (matrix.os == 'ubuntu-latest') && (matrix.python-version == env.TARGET_PYTHON_VERSION )
        uses: codecov/codecov-action@v3
        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
      - name: Run pytest
        # For every other version and/or OS, run pytest without coverage
        if: (matrix.os != 'ubuntu-latest') || (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-latest
    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