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ci.yml
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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()"