python-ci.yml

# This GitHub Action workflow will

# - Format code using Black
# - Build project with all dependencies
# - Check code with flake8 linter
# - Run tests with pytest


# ubuntu-latest has 7GB RAM and 14GB SSD. macos-latest has 14GB RAM and 14GB SSD. Using macos assuming more RAM -> faster tests -> less timeouts
# Nonetheless, our tests seem to need >10 GB RAM and >16,7 GB SSD Space. Test refactoring needed.
# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources

name: Build and test

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  formatting:
    outputs:
      new_sha: ${{ steps.sha.outputs.SHA }}
    runs-on: macos-latest

    steps:
      - name: Checkout code
        uses: actions/checkout@v3
        with:
          ref: ${{ github.event.pull_request.head.ref }} # ${{ github.event.pull_request.head.sha }} 

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: "3.8"
          cache: 'pip'

      - name: Setup isort and Black
        run: |
          python -m pip install --upgrade pip
          pip install isort black

      - name: Run isort
        run: |
          isort --profile black .

      - name: Run Black formatter
        run: |
          black .

      - name: Commit changes
        uses: EndBug/add-and-commit@v8
        with:
          message: 'Fix styling'
          add: '*.py'
      
      - name: Get commit hash
        id: sha
        run: |
          sha_new=$(git rev-parse HEAD)
          echo $sha_new
          echo "::set-output name=SHA::$sha_new"


  build:
    if: always()
    needs: formatting
    runs-on: macos-latest

    steps:
    - name: Checkout to latest changes
      uses: actions/checkout@v3
      with:
        ref: ${{ needs.formatting.outputs.new_sha }}
        fetch-depth: 0

    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: "3.8"
        cache: 'pip'

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest pytest-cov pytest-github-actions-annotate-failures
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        pip install -e .

    - name: Install model dependencies
      run: |
        python src/medigan/execute_model/install_model_dependencies.py

  lint:
    needs: build
    runs-on: macos-latest

    steps:
    - name: Checkout to latest changes
      uses: actions/checkout@v3
      with:
        ref: ${{ needs.formatting.outputs.new_sha }}
        fetch-depth: 0

    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: "3.8"
        cache: 'pip'

    - name: Install cached dependencies
      run: |
        python -m pip install --upgrade pip
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        pip install flake8
        pip install -e .
   
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --max-line-length=88 --extend-ignore=E203,E501
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --extend-ignore=E203,E501 --statistics
  
  test:
    needs: build
    runs-on: macos-latest #windows-latest

    steps:
    - name: Checkout to latest changes
      uses: actions/checkout@v3
      with:
        ref: ${{ needs.formatting.outputs.new_sha }}
        fetch-depth: 0

    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: "3.8"
        cache: 'pip'

    - name: Install cached dependencies
      run: |
        python -m pip install --upgrade pip
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        pip install pytest pytest-cov pytest-github-actions-annotate-failures
        pip install -e .
        python src/medigan/execute_model/install_model_dependencies.py
      # for windows: pip install -r requirements.txt
      # for mac/linux: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - name: Test with pytest
      run: |
        pytest tests -W ignore::DeprecationWarning --verbose --failed-first --log-cli-level=INFO #--cov=. --cov-report html  #--capture=tee-sys