fix logs #542
Workflow file for this run
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| # 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 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| name: test-coverage.yaml | |
| permissions: read-all | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: "https://stan-dev.r-universe.dev" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::covr | |
| any::xml2 | |
| any::jsonlite | |
| any::rstudioapi | |
| any::DT | |
| any::htmltools | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path( | |
| normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), | |
| "package" | |
| ) | |
| ) | |
| print(cov) | |
| saveRDS(cov, "cov.rds") | |
| # Write cobertura report for Codecov | |
| covr::to_cobertura(cov) | |
| # ------------------------------------------------------------ | |
| # HTML coverage report (artifact) | |
| # ------------------------------------------------------------ | |
| pct <- covr::percent_coverage(cov) | |
| cat(sprintf("Coverage: %.2f%%\n", pct)) | |
| covr::report(cov, file = "covr.html", browse = FALSE) | |
| # Optional: write to GitHub Actions summary | |
| summ <- Sys.getenv("GITHUB_STEP_SUMMARY") | |
| if (nzchar(summ)) { | |
| cat(sprintf("\n## Coverage\n\n- Total: **%.2f%%**\n", pct), file = summ, append = TRUE) | |
| cat("- HTML report uploaded as artifact: `covr-report`\n", file = summ, append = TRUE) | |
| } | |
| # ------------------------------------------------------------ | |
| # Uncovered line reporting (structured CSV + readable MD) | |
| # ------------------------------------------------------------ | |
| z_all <- covr::zero_coverage(cov) | |
| # Restrict to R source files | |
| z_r <- z_all[grepl("^R/.*\\.R$", z_all$filename), , drop = FALSE] | |
| # Write a tidy CSV: one row per uncovered line | |
| cols <- intersect(c("filename", "functions", "line", "value"), names(z_r)) | |
| if (length(cols) < 2) { | |
| utils::write.csv(z_r, "uncovered_lines.csv", row.names = FALSE) | |
| } else { | |
| utils::write.csv(z_r[, cols, drop = FALSE], "uncovered_lines.csv", row.names = FALSE) | |
| } | |
| collapse_ranges <- function(x) { | |
| x <- sort(unique(as.integer(x))) | |
| if (length(x) == 0) return(character()) | |
| runs <- split(x, cumsum(c(1, diff(x) != 1))) | |
| vapply(runs, function(r) { | |
| if (length(r) == 1) as.character(r) | |
| else paste0(min(r), "-", max(r)) | |
| }, character(1)) | |
| } | |
| md <- c("# Uncovered line ranges (covr::zero_coverage)", "") | |
| if (nrow(z_r) == 0) { | |
| md <- c(md, "_No uncovered lines found in `R/` files._") | |
| } else { | |
| files <- sort(unique(z_r$filename)) | |
| for (f in files) { | |
| sub <- z_r[z_r$filename == f, , drop = FALSE] | |
| line_ranges <- collapse_ranges(sub$line) | |
| md <- c(md, paste0("## ", f)) | |
| md <- c(md, "", paste0("**Lines:** ", paste(line_ranges, collapse = ", ")), "") | |
| md <- c(md, "```", paste(utils::capture.output(print(sub)), collapse = "\n"), "```", "") | |
| } | |
| } | |
| writeLines(md, "uncovered_lines.md") | |
| summ <- Sys.getenv("GITHUB_STEP_SUMMARY") | |
| if (nzchar(summ)) { | |
| cat("## Coverage: uncovered lines\n\n", file = summ, append = TRUE) | |
| cat("- Wrote `uncovered_lines.csv` (tidy rows) and `uncovered_lines.md` (grouped by file).\n", file = summ, append = TRUE) | |
| cat("- See artifact: `covr-uncovered-lines`.\n", file = summ, append = TRUE) | |
| } | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} | |
| files: ./cobertura.xml | |
| plugins: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Upload covr HTML report | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: covr-report | |
| path: | | |
| covr.html | |
| covr_files/ | |
| if-no-files-found: warn | |
| - name: Upload uncovered lines report | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: covr-uncovered-lines | |
| path: | | |
| uncovered_lines.md | |
| uncovered_lines.csv | |
| cov.rds | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |