update bumpversion #26
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: "Install libraries" | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y git bzip2 \ | |
| cmake autoconf automake make gcc perl zlib1g-dev libbz2-dev \ | |
| liblzma-dev samtools | |
| - name: "Install aligners and SLIMM" | |
| run: | | |
| rm -rf vignettes | |
| curl -L https://github.com/lh3/minimap2/releases/download/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxf - | |
| sudo cp ./minimap2-2.13_x64-linux/minimap2 /usr/bin/ && rm -rf ./minimap2-* | |
| git clone --recursive https://github.com/seqan/slimm | |
| (cd slimm && mkdir build && cd build && cmake .. && make && sudo cp bin/slimm /usr/bin/) | |
| rm -rf slimm | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::XML | |
| needs: coverage | |
| - name: Test coverage | |
| run: covr::codecov() | |
| shell: Rscript {0} |