diff --git a/.github/workflows/integration_checks.yaml b/.github/workflows/integration_checks.yaml new file mode 100644 index 00000000..d28c9d9f --- /dev/null +++ b/.github/workflows/integration_checks.yaml @@ -0,0 +1,74 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +name: Integration Checks + +# because `main` is a protected branch this workflow is triggered when a PR +# is opened/updated and again when it is merged +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + check-package: + # system dependencies for cannot be automatically resolved by + # `r-lib/actions/setup-r@v2` for macos or windows - to avoid having to + # maintain separate logic to infer and install system of those operating + # systems we'll only run integration checks with the ubuntu + runs-on: ubuntu-latest + + # run integration checks with R-release, R-devel, and R-oldrelease + strategy: + matrix: + r-version: ['release', 'devel', 'oldrel'] + + steps: + # pull the latest changes from the repository down to the runner + - name: Checkout + uses: actions/checkout@v4 + + # install R and any system dependencies + - name: Setup R + uses: r-lib/actions/setup-r@v2 + with: + # install the R version specified by the current strategy + r-version: ${{ matrix.r-version }} + # specify additional repositories to pull dependencies not + # available on CRAN (i.e. `BPCells`) + extra-repositories: ${{ 'https://bnprks.r-universe.dev' }} + + # install R dependencies + - name: Install Dependencies + uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: + any::rcmdcheck + any::pkgdown + # installed packages are cached by default - force an upgrade to the + # latest version of all dependencies + upgrade: 'TRUE' + + # run CRAN checks - fails if any ERRORs or WARNINGs are raised in which + # case the `rcmdcheck` output will be uploaded as an artifact + - name: Run Checks + uses: r-lib/actions/check-r-package@v2 + env: + # suppress NOTEs that are accepted by CRAN + # see: https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck + _R_CHECK_PKG_SIZES_: false + _R_CHECK_RD_XREFS_: false + _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: false + _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true + continue-on-error: true + + # build pkgdown site + - name: Build Website + run: | + pkgdown::build_site_github_pages( + new_process = FALSE, + install = FALSE + ) + shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 3868ce70..bd905595 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SeuratObject Type: Package Title: Data Structures for Single Cell Data -Version: 5.0.2 +Version: 5.0.99.9000 Authors@R: c( person(given = 'Paul', family = 'Hoffman', email = 'hoff0792@alumni.umn.edu', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')), person(given = 'Rahul', family = 'Satija', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),