Skip to content

v0.7.2-alpha

v0.7.2-alpha #64

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
on:
release:
types: [published]
name: test-coverage
jobs:
test-coverage:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v3
- 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
needs: coverage
- name: Install vsearch
run: sudo apt-get install vsearch
- name: Install blastn
run: sudo apt-get install ncbi-blast+
- name: Install mumu
run: |
git clone https://github.com/frederic-mahe/mumu.git \
&& cd ./mumu/ \
&& make \
&& make check \
&& sudo make install
- name: Install swarm
run: |
git clone https://github.com/torognes/swarm.git \
&& cd swarm/ \
&& make
sudo cp bin/swarm /usr/bin/swarm
- name: Install cutadapt
run: |
sudo python3 -m pip install cutadapt
- name: Test coverage
run: |
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
)
shell: Rscript {0}
- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package