minor fix for avoid non-matching variants going through allele_qc to throw error in mr #514
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name: Continuous Integration | |
on: | |
pull_request: | |
paths-ignore: | |
- .github | |
- .gitignore | |
- README.md | |
jobs: | |
ci_linux-64: | |
runs-on: ubuntu-latest | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
steps: | |
- name: Checkout pull request branch | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Create YAML from recipe | |
run: | | |
cp .github/environment/environment.yaml /tmp/environment.yaml | |
grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
- name: Setup micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: /tmp/environment.yaml | |
generate-run-shell: true | |
- name: Run unit tests | |
shell: micromamba-shell {0} | |
run: R -e "devtools::test()" | |
- name: Check unit test code coverage | |
shell: micromamba-shell {0} | |
run: R -e "covr::codecov(quiet = FALSE)" | |
#- name: Run R CMD CHECK | |
#shell: micromamba-shell {0} | |
#run: R -e "rcmdcheck::rcmdcheck()" | |
#- name: Run BiocCheckGitClone | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheckGitClone()" | |
#- name: Run BiocCheck | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheck()" | |
ci_osx-64: | |
runs-on: macos-13 | |
steps: | |
- name: Checkout pull request branch | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Create YAML from recipe | |
run: | | |
cp .github/environment/environment.yaml /tmp/environment.yaml | |
grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
- name: Setup micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: /tmp/environment.yaml | |
generate-run-shell: true | |
- name: Run unit tests | |
shell: micromamba-shell {0} | |
run: R -e "devtools::test()" | |
#- name: Run R CMD CHECK | |
#shell: micromamba-shell {0} | |
#run: R -e "rcmdcheck::rcmdcheck()" | |
#- name: Run BiocCheckGitClone | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheckGitClone()" | |
#- name: Run BiocCheck | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheck()" | |
# | |
ci_osx-arm64: | |
runs-on: macos-14 | |
steps: | |
- name: Checkout pull request branch | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Create YAML from recipe | |
run: | | |
cp .github/environment/environment.yaml /tmp/environment.yaml | |
grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
- name: Setup micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: /tmp/environment.yaml | |
generate-run-shell: true | |
- name: Run unit tests | |
shell: micromamba-shell {0} | |
run: R -e "devtools::test()" | |
#- name: Run R CMD CHECK | |
#shell: micromamba-shell {0} | |
#run: R -e "rcmdcheck::rcmdcheck()" | |
#- name: Run BiocCheckGitClone | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheckGitClone()" | |
#- name: Run BiocCheck | |
#shell: micromamba-shell {0} | |
#run: R -e "BiocCheck::BiocCheck()" |