Merge pull request #160 from drieslab/jiajic-patch #157
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| name: code coverage | |
| on: | |
| push: | |
| branches: [ "dev" ] | |
| pull_request: | |
| types: closed | |
| branches: [ "main" ] | |
| schedule: | |
| - cron: '16 20 * * 2' | |
| jobs: | |
| test-coverage: | |
| name: Code coverage | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout repo for workflow access | |
| uses: actions/checkout@v3 | |
| - name: Set up R environment | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Set up dependencies (general) | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| env: | |
| _R_CHECK_FORCE_SUGGESTS: false | |
| _R_CHECK_RD_XREFS: false | |
| with: | |
| dependencies: '"hard"' # do not use suggested dependencies | |
| extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr, any::sp, any::stars, any::raster, any::sf | |
| needs: coverage | |
| - name: Set up dependencies (GiottoData) | |
| run: | | |
| suppressWarnings({ | |
| remotes::install_github('drieslab/GiottoData', build = FALSE) | |
| }) | |
| shell: Rscript {0} | |
| - name: Generate coverage report | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: 4c596b03-f583-4114-8c3a-f89ed373c53b | |
| fail_ci_if_error: false | |
| flags: unittests | |
| verbose: true |