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Test Coverage

Test Coverage #281

Workflow file for this run

# 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}