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test-coverage.yaml
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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