tests_and_lint.yml

name: Tests and lint

on:
  push:
    branches:
      - main
    tags:
      - "v*"
  pull_request:
    branches:
      - "*"
jobs:
  lint:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.9]
        lint-flags:
          - "--run-only-fast-linters"
          - "--run-only-pylint"
          - "--run-only-mypy"
          - "--run-only-bandit"
          - "--run-only-cargo-clippy"
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Run lint checks
        run: |
          ./scripts/lint.sh ${{ matrix.lint-flags }}
  unit_tests:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Install codecov dependencies
        run: |
          curl -Os https://uploader.codecov.io/latest/linux/codecov
          chmod +x codecov
      - name: Run unit tests with pytest
        run: |
          pytest --cov=src/sequence_align tests/unit
          ./codecov -t ${CODECOV_TOKEN}
  perf_tests:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Run performance tests with pytest
        run: |
          pytest tests/perf