pull-request.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

# Pipeline that checks branches that have been pushed to "Main" OR are the source branch in a newly created pull request into "Main"
# Fails the test if there are Python syntax errors or undefined names OR pytest fails

name: Pydicer Pytest and Pylint Validaiton

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

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.8", "3.9"]
        poetry-version: [1.7.1]
        # os: [ubuntu-20.04, macos-latest, windows-latest]
    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 Poetry
        uses: abatilo/actions-poetry@v2.0.0
        with:
          poetry-version: ${{ matrix.poetry-version }}
      - name: Install Python modules with poetry
        run: |
          poetry run pip install --upgrade pip
          poetry install
          poetry run pip install TotalSegmentator
      - name: Lint with Pylint
        run: |
          poetry run pylint pydicer
      - name: MyPy type checking
        run: |
          # TODO poetry run mypy
          echo "Skipping MyPy type checking..."
      - name: Conditional Pytest coverage
        run: |
          if [[ "${{ matrix.python-version }}" == "3.9" ]]; then
            echo "Running Pytest with coverage..."
            poetry run pip install pytest-cov coverage
            # Omit CLI from coverage report since it's not fully developed
            poetry run pytest --cov=pydicer --cov-report=xml --cov-config=.coveragerc
            poetry run coverage report --fail-under=70 # Fail if coverage is less than 70%
          else
            echo "Running Pytest without coverage..."
            poetry run pytest
          fi
      # Commit the coverage badge back to repo (only on main branch & for a specific Python version)
      - name: Generate and commit coverage badge
        if: github.ref == 'refs/heads/main' && matrix.python-version == '3.9'
        run: |
          poetry run pip install coverage-badge # These only work with python >=3.9
          # Generate an SVG coverage badge
          # poetry run coverage-badge -o coverage.svg

          # # Configure git
          # git config user.name "github-actions"
          # git config user.email "github-actions@github.com"

          # # Pull latest changes to avoid conflicts
          # git pull --rebase

          # # Stage and commit coverage.svg
          # git add coverage.svg
          # git commit -m "Update coverage badge" || echo "No changes to commit"

          # # Push commit
          # git push
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}