ci.yml

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

name: build

on:
  push:
    branches:
      - develop

  pull_request:

  release:
    types:
      - created

jobs:

  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8, 3.9]
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo apt-get install -y bedtools
        python -m pip install --upgrade pip
        pip install flake8 pytest pytest-cov cython
        pip install .
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    # - name: Lint with flake8
    #   run: |
    #     # stop the build if there are Python syntax errors or undefined names
    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test with pytest
      run: |
        pytest tests/ --cov=genie --cov=genie_registry --cov-report=html
    - name: Upload pytest test results
      uses: actions/upload-artifact@v2
      with:
        name: pytest-results-${{ matrix.python-version }}
        path: htmlcov
      # Use always() to always run this step to publish test results when there are test failures
      if: ${{ always() }}

  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: psf/black@stable

  deploy:
    needs: [test, lint]
    runs-on: ubuntu-latest
    if: github.event_name == 'release'
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.x'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install setuptools wheel twine
    - name: Build and publish
      env:
        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
      run: |
        python setup.py sdist bdist_wheel
        twine upload dist/*