test-coverage.yaml

# 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