build.yml

name: Python package

on:
  push:
    branches:
      - master
    paths-ignore:
      - 'README.md'
  pull_request:
    paths-ignore:
      - 'README.md'

# https://stackoverflow.com/a/72408109/6388696
# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-concurrency-to-cancel-any-in-progress-job-or-run
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

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<4.0.0"
      - 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: ['3.9', '3.10', '3.11']
    env:
      PLATFORM: ${{ matrix.platform }}
    steps:
    - uses: actions/checkout@v4
    - name: Install poetry (not on MacOS)
      if: runner.os != 'macOS'
      run: pip install poetry

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: ${{ matrix.platform != 'macos-latest' && 'poetry' || '' }}

    - name: Install poetry (only on MacOS)
      if: runner.os == 'macOS'
      run: pip install 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: Store coverage report as an artifact
      uses: actions/upload-artifact@v4
      with:
        name: coverage-reports-unit-${{ matrix.platform }}-${{ matrix.python-version }}
        path: ./coverage.xml

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

    strategy:
      max-parallel: 5
      matrix:
        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: 15
        env:
          SLURM_CLUSTER: localhost

      - name: Store coverage report as an artifact
        uses: actions/upload-artifact@v4
        with:
          name: coverage-reports-mock-${{ matrix.platform }}-${{ matrix.python-version }}
          path: ./coverage.xml

  real-slurm-integration-tests:

    name: integration tests with a real SLURM cluster
    needs: [mock-slurm-integration-tests]

    strategy:
      max-parallel: 1
      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: ['3.11']
        cluster: ['mila']
    uses: ./.github/workflows/testing.yml
    with:
      cluster: ${{ matrix.cluster }}
      python-version: ${{ matrix.python-version }}
      timeout-minutes: 30

  # https://about.codecov.io/blog/uploading-code-coverage-in-a-separate-job-on-github-actions/
  upload-coverage-codecov:
    needs: [real-slurm-integration-tests]
    runs-on: ubuntu-latest
    name: Upload coverage reports to Codecov
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Download artifacts
        uses: actions/download-artifact@v4
        with:
          pattern: coverage-reports-*
          merge-multiple: false
          # download all the artifacts in this directory (each .coverage.xml will be in a subdirectory)
          # Next step if this doesn't work would be to give the coverage files a unique name and use merge-multiple: true
          path: coverage_reports
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          # file: ./coverage.xml  # Search for all coverage files from each workflow.
          # flags: integrationtests
          # env_vars: PLATFORM,PYTHON
          # name: codecov-umbrella
          directory: coverage_reports
          fail_ci_if_error: true