main.yml

name: gh-ci-checks
concurrency:
  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }}
  cancel-in-progress: true
on:
  pull_request:
    paths:
      - "**.py"
      - pyproject.toml
      - .github/workflows/main.yml
  push:
    branches: [main]
    paths:
      - "**.py"
    tags:
      - "v*.*.*"
  workflow_dispatch:

jobs:
  style:
    timeout-minutes: 10
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Setup Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
          architecture: "x64"
      - name: Install packages for Ubuntu
        run: |
          sudo apt-get update
          sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev

      - name: Install dependencies
        run: |
          pip install --upgrade pip
          pip install -r style_requirements.txt

      # check formatting of the code style
      - name: Check code formatting
        run: make pre-commit

  build:
    timeout-minutes: 15
    strategy:
      fail-fast: false
      matrix:
        # upgrade to macos-latest when 3.10 is removed
        os: ["ubuntu-latest", "macos-13", "windows-latest"]
        python-version: ["3.10", "3.11", "3.12"]
    name: build ${{ matrix.os }} - py${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Setup Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          architecture: "x64"
      - name: Install and setup package
        run: |
          python -m pip install --progress-bar off .[build]
      - name: Test package install
        run: |
          python -c "import dodiscover; print(dodiscover.__version__)"
      - name: Remove package install
        run: |
          python -m pip uninstall -yq dodiscover
      - name: Build package
        run: python -m build
      - name: Upload package distribution files
        if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.11' }}
        uses: actions/upload-artifact@v3
        with:
          name: package
          path: dist

      #
      # Test wheel-based Installation
      #
      - name: Install wheel
        run: pip install ./dist/*.whl
      - name: Test wheel install
        run: python -c "import dodiscover; print(dodiscover.__version__)"
      - name: Remove wheel install
        run: python -m pip uninstall -yq dodiscover

      #
      # Test sdist-based Installation
      #
      - name: Install sdist
        run: pip install ./dist/*.tar.gz
      - name: Test sdist install
        run: python -c "import dodiscover; print(dodiscover.__version__)"
      - name: Remove sdist install
        run: python -m pip uninstall -yq dodiscover

  test:
    timeout-minutes: 30
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
        # oldest and newest supported versions
        python-version: ["3.10", "3.11"] # TODO: update to 3.12 when statsmodels supports
        networkx: [stable, main]
        exclude:
          - { python-version: "3.10", os: "macos-latest" }
        include:
          - { python-version: "3.10", os: "macos-13" }
    name: Unit-test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Setup Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          architecture: "x64"
      - name: Install packages via pip
        run: |
          pip install --upgrade pip
          pip install numpy scipy networkx statsmodels
      
      - name: Install package
        run: |
          pip install .[test]
          pip install .

      - name: Install Networkx (main)
        if: "matrix.networkx == 'main'"
        run: |
          pip uninstall -yq networkx
          pip install --progress-bar off git+https://github.com/networkx/networkx
      - name: Run pytest
        run: |
          pytest --cov dodiscover ./tests/unit_tests/
      - name: Upload coverage stats to codecov
        if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.10' && matrix.networkx == 'stable' }}
        uses: codecov/codecov-action@v3
        with:
          files: ./coverage.xml
          fail_ci_if_error: true
          verbose: true

  integration_test:
    timeout-minutes: 30
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        python-version: ["3.11"]
        networkx: [main]
    name: Integration test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Setup Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          architecture: "x64"

      - name: Install packages for Ubuntu
        run: |
          sudo apt-get update
          sudo apt-get install -y graphviz optipng libxft2 graphviz-dev

      - name: Setup torch
        run: |
          sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc

      - name: Install packages via pip
        run: |
          pip install --upgrade pip
          pip install numpy scipy networkx statsmodels
          pip install .[test,doc]
      - name: Run pytest # headless via Xvfb on linux
        run: |
          pytest tests/integration_tests

  # release is ran when a release is made on Github
  release:
    name: Release
    runs-on: ubuntu-latest
    needs: [style, build, test]
    if: startsWith(github.ref, 'refs/tags/')
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Setup Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
          architecture: "x64"
      - name: Install dependencies
        run: |
          python -m pip install --progress-bar off --upgrade pip setuptools wheel
          python -m pip install --progress-bar off build twine
      - name: Prepare environment
        run: |
          echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV
          echo "TAG=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV
      - name: Download package distribution files
        uses: actions/download-artifact@v4
        with:
          name: package
          path: dist
      # TODO: refactor scripts to generate release notes from `whats_new.rst` file instead
      # - name: Generate release notes
      #   run: |
      #     python scripts/release_notes.py > ${{ github.workspace }}-RELEASE_NOTES.md
      - name: Publish package to PyPI
        run: |
          twine upload -u ${{ secrets.PYPI_USERNAME }} -p ${{ secrets.PYPI_PASSWORD }} dist/*
      - name: Publish GitHub release
        uses: softprops/action-gh-release@v2
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          # body_path: ${{ github.workspace }}-RELEASE_NOTES.md
          prerelease: ${{ contains(env.TAG, 'rc') }}
          files: |
            dist/*