test prod workflow #3
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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: Master Workflow - Deploy to production | |
| on: | |
| pull_request: | |
| types: closed | |
| branches: [ "main" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| R-CMD-check: | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: # matrix of system runners to run workflow on | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| # - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| 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: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| 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 | |
| - name: Set up dependencies (GiottoData) | |
| run: | | |
| suppressWarnings({ | |
| remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE) | |
| }) | |
| shell: Rscript {0} | |
| - name: Test python env build | |
| run: | | |
| if (!GiottoClass::checkGiottoEnvironment()) { | |
| GiottoClass::installGiottoEnvironment() | |
| } | |
| 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, any::xml2 | |
| 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} | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| # lint: | |
| # runs-on: ubuntu-latest | |
| # needs: R-CMD-check | |
| # 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::lintr, local::. | |
| # needs: lint | |
| # | |
| # - name: Lint | |
| # run: lintr::lint_package() | |
| # shell: Rscript {0} | |
| # env: | |
| # LINTR_ERROR_ON_LINT: true | |
| # render-rmarkdown: | |
| # name: Update README.Rmd | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout repo | |
| # uses: actions/checkout@v3 | |
| # with: | |
| # fetch-depth: 0 | |
| # | |
| # - uses: r-lib/actions/setup-pandoc@v2 | |
| # | |
| # - uses: r-lib/actions/setup-r@v2 | |
| # | |
| # - uses: r-lib/actions/setup-renv@v2 | |
| # | |
| # - name: Install rmarkdown | |
| # run: Rscript -e 'install.packages("rmarkdown")' | |
| # | |
| # - name: Render README | |
| # run: Rscript -e 'rmarkdown::render("README.Rmd")' | |
| # | |
| # - name: Commit results | |
| # run: | | |
| # git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit" | |
| # git push origin || echo "No changes to commit" | |