Test Coverage #281
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
name: Test Coverage | |
on: | |
push: | |
branches: main | |
paths-ignore: | |
- ".github/**" | |
- ".devcontainer/**" | |
workflow_run: | |
workflows: "R-CMD-check" | |
types: completed | |
workflow_dispatch: | |
concurrency: | |
group: ${{ github.workflow }} | |
cancel-in-progress: true | |
jobs: | |
test-coverage: | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
BCFTOOLS_VERSION: 1.15.1 | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: any::covr, local::. | |
needs: coverage | |
- name: Install BCFtools | |
if: runner.os == 'Linux' | |
run: | | |
sudo apt-get update && \ | |
sudo apt-get install -y --no-install-recommends \ | |
libxt6 \ | |
ca-certificates \ | |
bzip2 \ | |
wget \ | |
autoconf \ | |
automake \ | |
make \ | |
cmake \ | |
libbz2-dev \ | |
liblzma-dev \ | |
libjpeg-dev \ | |
libxml2-dev \ | |
zlib1g-dev \ | |
libgdal-dev | |
wget -q -P /tmp/ https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ | |
tar -C /tmp/ -xjf /tmp/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ | |
cd /tmp/bcftools-${BCFTOOLS_VERSION} && \ | |
sudo autoreconf -i && \ | |
sudo ./configure --prefix=/usr && \ | |
sudo make && \ | |
sudo make install | |
- name: Test coverage | |
run: covr::codecov(quiet = FALSE) | |
shell: Rscript {0} |