chore: add type checks for addCellMetadata()
#24
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| name: Dev Branch Checks | |
| on: | |
| push: | |
| branches: [ "dev" ] | |
| permissions: | |
| contents: write | |
| packages: read | |
| jobs: | |
| codecov: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: giotto-deps | |
| run: remotes::install_github('drieslab/GiottoUtils', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| shell: Rscript {0} | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Build and install # needed for GiottoData install | |
| run: | | |
| R CMD build . --no-build-vignettes | |
| R CMD INSTALL *.tar.gz | |
| - name: Generate coverage report and upload | |
| run: | | |
| remotes::install_github('drieslab/GiottoData', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| # Create and save HTML report | |
| coverage_report <- covr::package_coverage( | |
| type = c("tests", "examples", "vignettes"), | |
| combine_types = TRUE, | |
| quiet = TRUE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| covr::report(coverage_report, file = "coverage-report.html", browse = FALSE) | |
| # Upload to Codecov | |
| covr::codecov( | |
| coverage = coverage_report, | |
| branch = "dev", | |
| quiet = FALSE | |
| ) | |
| shell: Rscript {0} | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Upload coverage HTML report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: coverage-report.html | |
| retention-days: 30 | |
| rcmdcheck: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: giotto-deps | |
| run: remotes::install_github('drieslab/GiottoUtils', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| shell: Rscript {0} | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Check package | |
| run: | | |
| remotes::install_github('drieslab/GiottoData', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error") | |
| shell: Rscript {0} | |
| bioccheck: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: giotto-deps | |
| run: remotes::install_github('drieslab/GiottoUtils', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| shell: Rscript {0} | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Build and install | |
| run: | | |
| R CMD build . --no-build-vignettes | |
| R CMD INSTALL *.tar.gz | |
| - name: Run BiocCheck # this is mainly formatting. No need for GiottoData | |
| run: | | |
| BiocCheck::BiocCheck() | |
| shell: Rscript {0} | |
| lintr: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| permissions: | |
| contents: write | |
| packages: read | |
| actions: read | |
| security-events: write | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Run lintr | |
| run: | | |
| results <- lintr::lint_package( | |
| ".", | |
| exclusions = list("tests", "vignettes", "pkgdown"), | |
| linters = lintr::linters_with_defaults( | |
| indentation_linter = lintr::indentation_linter(indent = 4L), | |
| object_name_linter = lintr::object_name_linter(styles = c("camelCase", "symbols", "snake_case", "UPPERCASE")) | |
| ) | |
| ) | |
| # Fix any invalid column numbers | |
| for (i in seq_along(results)) { | |
| if (!is.null(results[[i]]$column_number) && results[[i]]$column_number < 1) { | |
| results[[i]]$column_number <- 1 | |
| } | |
| } | |
| lintr::sarif_output(results, "lintr-results.sarif") | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - name: Upload analysis results to GitHub | |
| uses: github/codeql-action/upload-sarif@v3 | |
| with: | |
| sarif_file: lintr-results.sarif | |
| wait-for-processing: true |