Add functions for integrating CITE-seq data #49
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| 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/[email protected] | |
| 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/[email protected] | |
| with: | |
| auth: ${{ secrets.GIST_SECRET }} | |
| gistID: ${{ secrets.GIST_ID }} | |
| filename: version.json | |
| label: version | |
| message: ${{ env.VERSION }} | |
| color: blue |