build.yml

name: build

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.8]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo apt update
        sudo apt install -y libxml2-utils pandoc
        sudo wget -O /usr/bin/bedtools https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
        sudo chmod +x /usr/bin/bedtools
        pip install --upgrade pip flit flake8
        flit install -s
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 scglue --count --select=E9,F63,F7,F82 --show-source --statistics
    - name: Test with pytest
      run: |
        pytest --cov="scglue" --cov-report="xml:cov.xml" tests --cpu-only
        COVERAGE=$(xmllint --xpath "/coverage/@line-rate" cov.xml | awk -F\" '{cov = sprintf("%.0f%%", $2 * 100); print(cov);}')
        echo "COVERAGE=${COVERAGE}" >> $GITHUB_ENV
    - name: Create coverage badge
      uses: schneegans/dynamic-badges-action@v1.1.0
      with:
        auth: ${{ secrets.GIST_SECRET }}
        gistID: ${{ secrets.GIST_ID }}
        filename: coverage.json
        label: coverage
        message: ${{ env.COVERAGE }}
        color: green
    - name: Build documentation
      run: |
        sphinx-build -b html docs docs/_build
    - name: Get version
      run: |
        VERSION=$(python -c "from scglue import __version__; print(__version__)")
        echo "VERSION=${VERSION}" >> $GITHUB_ENV
    - name: Create version badge
      uses: schneegans/dynamic-badges-action@v1.1.0
      with:
        auth: ${{ secrets.GIST_SECRET }}
        gistID: ${{ secrets.GIST_ID }}
        filename: version.json
        label: version
        message: ${{ env.VERSION }}
        color: blue