build.yml

name: Python package

on: [push, pull_request]

jobs:
  linting:
    name: Run linting/pre-commit checks
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v4
        with:
          python-version: '3.10'
      - run: pip install pre-commit
      - run: pre-commit --version
      - run: pre-commit install
      - run: pre-commit run --all-files

  unit-tests:
    needs: [linting]
    runs-on: ${{ matrix.platform }}
    strategy:
      max-parallel: 4
      matrix:
        platform: [ubuntu-latest, windows-latest, macos-latest]
        python-version: ['3.8', '3.9', '3.10', '3.11']
    env:
      PLATFORM: ${{ matrix.platform }}
    steps:
    - uses: actions/checkout@v4
    - name: Install poetry
      run: |
        python -m pip install --upgrade pip
        pip install poetry
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: poetry

    - name: Install dependencies
      run: poetry install --with=dev

    - name: Setup passwordless SSH access to localhost for tests
      # Adapted from https://stackoverflow.com/a/60367309/6388696
      if: runner.os == 'Linux'
      run: |
        ssh-keygen -t ed25519 -f ~/.ssh/testkey -N ''
        cat > ~/.ssh/config <<EOF
          Host localhost
            User $USER
            HostName 127.0.0.1
            IdentityFile ~/.ssh/testkey
        EOF
        echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys
        chmod og-rw ~
        ssh -o 'StrictHostKeyChecking no' localhost id

    - name: Test with pytest
      run: poetry run pytest --cov=milatools --cov-report=xml --cov-append

    - name: Upload coverage reports to Codecov
      uses: codecov/codecov-action@v3
      with:
        file: ./coverage.xml
        flags: unittests
        env_vars: PLATFORM,PYTHON
        name: codecov-umbrella
        fail_ci_if_error: false

  mock-slurm-integration-tests:
    name: integration tests with a mock slurm cluster
    needs: [unit-tests]
    runs-on: ${{ matrix.platform }}

    strategy:
      max-parallel: 5
      matrix:
        # TODO: We should ideally also run this with Windows/Mac clients and a Linux
        # server. Unsure how to set that up with GitHub Actions though.
        platform: [ubuntu-latest]
        python-version: ['3.8', '3.9', '3.10', '3.11']

    # For the action to work, you have to supply a mysql
    # service as defined below.
    services:
      mysql:
        image: mysql:8.0
        env:
          MYSQL_ROOT_PASSWORD: root
        ports:
          - "8888:3306"
        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3

    steps:
      - uses: actions/checkout@v4

      # NOTE: Replacing this with our customized version of
      # - uses: koesterlab/setup-slurm-action@v1
      - uses: ./.github/custom_setup_slurm_action
        timeout-minutes: 5

      - name: Test if the slurm cluster is setup correctly
        run: srun --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=1G --time=00:01:00 hostname

      - name: Setup passwordless SSH access to localhost for tests
        # Adapted from https://stackoverflow.com/a/60367309/6388696
        run: |
          ssh-keygen -t ed25519 -f ~/.ssh/testkey -N ''
          cat > ~/.ssh/config <<EOF
            Host localhost
              User $USER
              HostName 127.0.0.1
              IdentityFile ~/.ssh/testkey
          EOF
          echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys
          chmod og-rw ~
          ssh -o 'StrictHostKeyChecking no' localhost id

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install poetry
          poetry install --with=dev

      - name: Launch integration tests
        run: poetry run pytest --slow --cov=milatools --cov-report=xml --cov-append -vvv --log-level=DEBUG
        timeout-minutes: 5
        env:
          SLURM_CLUSTER: localhost

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v3
        with:
          file: ./coverage.xml
          flags: integrationtests
          env_vars: PLATFORM,PYTHON
          name: codecov-umbrella
          fail_ci_if_error: false

  real-slurm-integration-tests:
    name: integration tests with a real SLURM cluster
    needs: [mock-slurm-integration-tests]
    runs-on: self-hosted

    strategy:
      max-parallel: 5
      matrix:
        # TODO: We should ideally also run this with Windows/Mac clients and a Linux
        # server. Unsure how to set that up with GitHub Actions though.
        python-version: ['3.8', '3.9', '3.10', '3.11']

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install poetry
          poetry install --with=dev

      - name: Launch integration tests
        id: self_hosted_integration_tests
        run: poetry run pytest --slow -n 5 --cov=milatools --cov-report=xml --cov-append -vvv --log-level=DEBUG
        timeout-minutes: 60
        env:
          SLURM_CLUSTER: mila

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v3
        with:
          file: ./coverage.xml
          flags: integrationtests
          env_vars: PLATFORM,PYTHON
          name: codecov-umbrella
          fail_ci_if_error: false