Merge pull request #12 from jiajic/dev #1
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| # See https://github.com/r-lib/actions/tree/master/examples#readme for | |
| # additional example workflows available for the R community. | |
| name: Dev Workflow - Test and check | |
| on: | |
| push: | |
| branches: [ "dev" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| R-CMD-check: | |
| name: R CMD Check | |
| env: | |
| GITHUB_PAT: ${{ secrets.WORKFLOW_PAT }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Remove vignettes dir | |
| run: rm -rf 'vignettes/' | |
| shell: bash | |
| - 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 | |
| - name: Set up dependencies (GiottoData) | |
| run: | | |
| suppressWarnings({ | |
| remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE) | |
| }) | |
| shell: Rscript {0} | |
| - name: Run R CMD check | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| error-on: '"error"' # workflow errors on error only, can change to include warnings | |
| # show testthat output for ease of access | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| 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 | |
| needs: coverage | |
| - name: Set up dependencies (GiottoData) | |
| run: | | |
| suppressWarnings({ | |
| remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE) | |
| }) | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| # add code cov | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| lint: | |
| runs-on: ubuntu-latest | |
| 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::lintr, local::. | |
| needs: lint | |
| - name: Lint | |
| run: lintr::lint_package() | |
| shell: Rscript {0} | |
| env: | |
| LINTR_ERROR_ON_LINT: false | |