fix: Issue #101 #5
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: | |
| pull_request: | |
| branches: [main, master, devel, devel-staging] | |
| name: test-coverage-nocodecov | |
| permissions: read-all | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout current ref | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ./new-state | |
| - name: Checkout Biostrings devel ref | |
| id: devel-checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: Bioconductor/Biostrings | |
| path: ./original-state | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: setup dependencies for old state | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: ./original-state | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: setup dependencies for new state | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: ./new-state | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Test coverage on base branch | |
| run: | | |
| dirpath <- file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| dir.create(dirpath) | |
| ## first check unit tests | |
| cat("Checking test results...\n") | |
| res <- testthat::test_local("./new-state", stop_on_failure=FALSE, reporter="check") | |
| res <- as.data.frame(res) | |
| test_report <- c(sum(res$failed), sum(res$warning), sum(res$skipped), sum(res$passed)) | |
| shouldStop <- test_report[1] > 0 | |
| shouldPrint <- sum(test_report[1:2]) > 0 | |
| test_report <- paste(c("FAIL", "WARN", "SKIP", "PASS"), test_report, collapse=' | ') | |
| test_report <- paste('Unit Tests: [', test_report, ']') | |
| ## build the output message | |
| out_msg <- '# Testing Report\n\n' | |
| out_msg <- paste0(out_msg, "## Test Results:\n\n") | |
| out_msg <- paste0(out_msg, "Please note that test coverage is **not** an ", | |
| "end-all-be-all measure of robustness. Having tests that ", | |
| "correctly cover intended use cases and potential errors ", | |
| "is significantly more important than maximizing coverage.\n\n") | |
| out_msg <- paste0(out_msg, "```\n", test_report, '\n```\n\n') | |
| ## if any tests failed or threw warnings, report them | |
| if(shouldPrint){ | |
| p_toprint <- which(res$failed + res$warning > 0) | |
| ptp <- res[p_toprint,] | |
| failed_tests <- ptp[,c("file", "test", "warning", "failed")] | |
| failed_tests <- apply(failed_tests, 1L, paste, collapse=" | ") | |
| failed_tests <- paste("|", failed_tests, "| ") | |
| failed_tests <- paste(failed_tests, collapse='\n') | |
| md_tab <- paste0("| Test File :page_facing_up: | Test Name :id: | Warnings :warning: | Failures :x: | \n", | |
| "| :----- | :----- | :-----: | :-----: | \n", | |
| failed_tests, "\n\n") | |
| out_msg <- paste0(out_msg, "### Warning/Failing Tests:\n\n", md_tab) | |
| } | |
| if(shouldStop){ | |
| cat(out_msg, file='./test_status.md') | |
| stop("Some tests failed! Skipping coverage report.") | |
| } | |
| ## if no tests failed, check coverage of old vs. new | |
| library(covr) | |
| # exclude lines with no content | |
| options(covr.exclude_pattern=c("^[ \t{}()]+$")) | |
| # get results on old state | |
| files_to_ignore <- list("R/AMINO_ACID_CODE.R", "R/GENETIC_CODE.R", | |
| "R/zzz.R", "R/IUPAC_CODE_MAP.R", | |
| "R/getSeq.R") | |
| cov <- covr::package_coverage( | |
| path = "./original-state", | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(dirpath, "old-state"), | |
| function_exclusions = "^\\.", | |
| line_exclusions=files_to_ignore | |
| ) | |
| head_res <- covr::coverage_to_list(cov) | |
| # get results on new state | |
| cov <- covr::package_coverage( | |
| path = "./new-state", | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(dirpath, "new-state"), | |
| function_exclusions = "^\\.", # excludes functions starting with . | |
| line_exclusions=files_to_ignore | |
| ) | |
| new_res <- covr::coverage_to_list(cov) | |
| ## compare difference in coverage | |
| f_old <- head_res$filecoverage | |
| f_new <- new_res$filecoverage | |
| cat("Old Coverage:\n") | |
| print(f_old) | |
| cat("***************\n") | |
| cat("New Coverage:\n") | |
| print(f_new) | |
| cat("***************\n") | |
| all_files <- union(names(f_old), names(f_new)) | |
| file_changes <- rep(0, length(all_files)) | |
| names(file_changes) <- all_files | |
| file_changes[names(f_new)] <- file_changes[names(f_new)] + f_new | |
| final_cov <- file_changes | |
| file_changes[names(f_old)] <- file_changes[names(f_old)] - f_old | |
| total_change <- new_res$totalcoverage - head_res$totalcoverage | |
| out_msg <- paste0(out_msg, "## Negatively Impacted Files\n\n") | |
| ## build warning message | |
| n <- names(file_changes) | |
| pos_neg <- which(file_changes < 0) | |
| if(length(pos_neg) > 0){ | |
| pos_neg <- pos_neg[order(file_changes[pos_neg], decreasing=FALSE)] | |
| warn_changes <- sprintf("%+.01f%%", file_changes) | |
| header <- "| File name | Coverage | Change |\n | :----- | :-----: | :-----: |\n" | |
| warn_tab <- paste0('| ', n[pos_neg], ' | ', sprintf("%0.02f%%", final_cov[pos_neg]), ' | ', | |
| unname(warn_changes[pos_neg]), ' |', collapse='\n') | |
| warn_tab <- paste0(header, warn_tab) | |
| out_msg <- paste0(out_msg, "The following files have lost coverage:\n", warn_tab, '\n') | |
| } else { | |
| out_msg <- paste0(out_msg, "No negatively impacted files. Nice job!\n\n") | |
| } | |
| ## build extended diff table | |
| p_Rfiles <- grepl("^R/", n) | |
| n <- vapply(strsplit(n, '/'), .subset, character(1L), 2L) | |
| all_diffs <- data.frame(filename=n, | |
| coverage=sprintf("%.02f%%", final_cov), | |
| change=sprintf("%+.01f%%", file_changes)) | |
| max_nchar <- max(nchar(all_diffs$filename)) | |
| all_diffs$filename <- sprintf(paste0("%", max_nchar, "s"), all_diffs$filename) | |
| all_diffs$coverage <- sprintf("%7s", all_diffs$coverage) | |
| all_diffs$change <- sprintf("%7s", all_diffs$change) | |
| all_diffs$mark_char <- 1L | |
| all_diffs$mark_char[file_changes > 0] <- 2L | |
| all_diffs$mark_char[file_changes < 0] <- 3L | |
| all_diffs$mark_char <- c(" ", "+", "-")[all_diffs$mark_char] | |
| all_rows <- apply(all_diffs[c(4,1:3)], 1L, paste, collapse=' ') | |
| w <- nchar(all_rows[1L]) | |
| title0 <- "Total Coverage" | |
| n_padding <- (w - nchar(title0) - 4) / 2 | |
| title0 <- paste0("@@", paste(rep(' ', floor(n_padding)), collapse=''), | |
| title0, paste(rep(' ', ceiling(n_padding)), collapse=''), "@@") | |
| row0 <- paste(ifelse(total_change < 0, "-", ifelse(total_change>0, "+", " ")), | |
| sprintf(paste0("%", max_nchar, "s"), "Total Coverage"), | |
| sprintf("%6.02f%%", new_res$totalcoverage), | |
| sprintf("%+6.01f%%", total_change), collapse=' ') | |
| title1 <- "R/... Files" | |
| n_padding <- (w - nchar(title1) - 4) / 2 | |
| title1 <- paste0("@@", paste(rep(' ', floor(n_padding)), collapse=''), | |
| title1, paste(rep(' ', ceiling(n_padding)), collapse=''), "@@") | |
| title2 <- "src/... Files" | |
| n_padding <- (w - nchar(title2) - 4) / 2 | |
| title2 <- paste0("@@", paste(rep(' ', floor(n_padding)), collapse=''), | |
| title2, paste(rep(' ', ceiling(n_padding)), collapse=''), "@@") | |
| spacer <- paste(rep('=', w), collapse='') | |
| entries1 <- paste(all_rows[p_Rfiles], collapse='\n') | |
| entries2 <- paste(all_rows[!p_Rfiles], collapse='\n') | |
| diff_table <- paste(title0, spacer, '\n', row0, '\n', spacer, | |
| title1, spacer, entries1, spacer, | |
| title2, spacer, entries2, spacer, | |
| collapse='\n', sep='\n') | |
| diff_table <- paste0("<details>\n<summary>Additional Details and Impacted Files:</summary>\n\n", | |
| "```diff\n", diff_table, '\n\n```\n\n</details>') | |
| out_msg <- paste0(out_msg, diff_table, '\n') | |
| cat(out_msg, file='./test_status.md') | |
| shell: Rscript {0} | |
| ## This is a better option than step summary, but requires | |
| ## the "pull-request: write" permission, which I'd rather | |
| ## not allow on a public repository | |
| # - name: Print comment to PR | |
| # uses: thollander/actions-comment-pull-request@v2 | |
| # with: | |
| # GITHUB_TOKEN: ${{ env.GITHUB_PAT }} | |
| # filePath: ./test_status.md | |
| # comment_tag: unit-test-results | |
| - name: Print results to summary | |
| if: always() | |
| run: cat ./test_status.md >> $GITHUB_STEP_SUMMARY | |
| - name: Upload package on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package | |
| - name: Upload status on success | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-results | |
| path: ./test_status.md |