test.yml

name: test
on:
  push:
  pull_request:

jobs:
  # First, check if the types/formatting is correct.
  types-and-linting:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.11
        architecture: x64
    - name: Install Python dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install flake8 black mypy
        python -m pip install -r requirements.txt
    - name: Lint with Black
      uses: rickstaa/action-black@v1
      with:
        black_args: ". --check --diff"
    - name: Check types
      run: |
        mypy biobalm
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 biobalm --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 biobalm --ignore=E203,W503,C901 --select=C,E,F,W,B,B950 --max-line-length=127 --statistics --count --max-complexity=10
  doctests:
    runs-on: ubuntu-latest
    timeout-minutes: 5
    needs: [types-and-linting]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install clingo
        run: sudo apt-get -y install gringo
      - name: Install Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
          architecture: x64
      - name: Fetch and install native Pint
        run: | 
          wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
          sudo apt install ./pint_2019-05-24_amd64.deb
      - name: Fetch and install Mole
        run: | 
          wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz
          tar -xvf mole-140428.tar.gz
          (cd ./mole-140428 && make)
          (cd ./mole-140428 && pwd >> $GITHUB_PATH)
      - name: Install repo dependencies
        run: pip install -r requirements.txt
      - name: Run doctests
        run: python -m doctest biobalm/*.py
  # Then do a "small" test run with code coverage.
  coverage:
    runs-on: ubuntu-latest
    timeout-minutes: 20
    needs: [types-and-linting, doctests]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install clingo
        run: sudo apt-get -y install gringo
      - name: Install Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
          architecture: x64
      - name: Fetch and install native Pint
        run: | 
          wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
          sudo apt install ./pint_2019-05-24_amd64.deb
      - name: Fetch and install Mole
        run: | 
          wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz
          tar -xvf mole-140428.tar.gz
          (cd ./mole-140428 && make)
          (cd ./mole-140428 && pwd >> $GITHUB_PATH)
      - name: Install repo dependencies
        run: pip install -r requirements.txt
      - name: Install pytest
        run: pip install pytest pytest-cov      
      - name: Run pytest with coverage
        run: python3 -m pytest --networksize 20 --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=biobalm tests/ | tee pytest-coverage.txt
      - name: Pytest coverage comment
        uses: MishaKav/pytest-coverage-comment@main
        with:
          pytest-coverage-path: ./pytest-coverage.txt
          junitxml-path: ./pytest.xml
  # Then do a full test for correctness using larger networks.
  tests:
    runs-on: ubuntu-latest
    timeout-minutes: 20
    needs: [types-and-linting, doctests, coverage]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install clingo
        run: sudo apt-get -y install gringo
      - name: Install Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
          architecture: x64
      - name: Fetch and install native Pint
        run: | 
          wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
          sudo apt install ./pint_2019-05-24_amd64.deb
      - name: Fetch and install Mole
        run: | 
          wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz
          tar -xvf mole-140428.tar.gz
          (cd ./mole-140428 && make)
          (cd ./mole-140428 && pwd >> $GITHUB_PATH)
      - name: Install repo dependencies
        run: pip install -r requirements.txt
      - name: Install pytest
        run: pip install pytest
      - name: Run pytest (without coverage)
        run: python3 -m pytest --networksize 30 tests/