main.yml

name: main

on:
  push:
    branches: [ "master", "devel" ]
  pull_request:
    branches: [ "master", "devel" ]
  schedule:
    - cron: "0 14 * * 1"

jobs:
  quicktest:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Install dependencies
        run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+

      - name: Run build
        run: pip3 install .[test]

      - name: Run tests and collect coverage
        run: pytest -v -m "not slow" --cov=./src

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  slowtest:
    runs-on: ubuntu-latest

    strategy:
      fail-fast: false
      matrix:
        testcase: ["tests/test_end_to_end.py::test_large", "tests/test_end_to_end.py::test_large_csv", "tests/test_end_to_end.py::test_large_hxb2"]

    steps:
      - uses: actions/checkout@v3

      - name: Install dependencies
        run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+

      - name: Run build
        run: pip3 install .[test]

      - name: Run tests and collect coverage
        run: pytest -v ${{ matrix.testcase }}

  installtest:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, ubuntu-20.04, ubuntu-22.04]
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Install dependencies
        run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+

      - name: Run build
        run: pip3 install .

      - name: Check installed version
        run: test "$(git describe --tags --abbrev=0)" == "v$(cfeintact version)"

      - name: Run test
        run: cfeintact check --subtype B tests/data-small.fasta && test -f "defects.csv"

  dockerinstall:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Build the Docker image
        run: docker build . --tag cfeintact

      - name: Run test
        run: |
          docker run --volume "/home:/home" --workdir "$PWD" --rm cfeintact check --subtype B "tests/data-small.fasta"
          test -f "defects.csv"

  linter:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Install dependencies
        run: sudo apt-get update && sudo apt-get install -y python3 python3-pip

      - name: Run build
        run: pip3 install .[dev]

      - name: Run linter
        run: flake8

  typechecker:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Install dependencies
        run: sudo apt-get update && sudo apt-get install -y python3 python3-pip

      - name: Run build
        run: pip3 install .[dev]

      - name: Run typechecker
        run: mypy