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#' Provide percent coverage of package
#'
#' Calculate the total percent coverage from a coverage result object.
#' @param x the coverage object returned from [package_coverage()]
#' @param ... additional arguments passed to [tally_coverage()]
#' @return The total percentage as a `numeric(1)`.
#' @export
percent_coverage <- function(x, ...) {
res <- tally_coverage(x, ...)
(sum(res$value > 0) / length(res$value)) * 100
}
#' Tally coverage by line or expression
#'
#' @inheritParams percent_coverage
#' @param by whether to tally coverage by line or expression
#' @return a `data.frame` of coverage tallied by line or expression.
#' @export
tally_coverage <- function(x, by = c("line", "expression")) {
# Rarely something goes wrong with the source references and we get all NAs
# for them, so we omit them here
df <- na.omit(as.data.frame(x))
if (NROW(df) == 0) {
return(df)
}
by <- match.arg(by)
switch(by,
"line" = {
# if it already has a line column it has already been tallied.
if (!is.null(df$line)) {
return(df)
}
# aggregate() can't cope with zero-length data frames anyway.
if (nrow(df) == 0L) {
return(NULL)
}
# results with NA functions (such as from compiled code) are dropped
# unless NA is a level.
df$functions <- addNA(df$functions)
res <- expand_lines(df)
res <- aggregate(value ~ filename + functions + line,
data = res, FUN = min, na.action = na.pass)
res$functions <- as.character(res$functions)
# exclude blank lines from results
if (inherits(x, "coverage")) {
srcfiles <- unique(lapply(x, function(x) attr(x$srcref, "srcfile")))
srcfile_names <- vcapply(srcfiles, `[[`, "filename")
if (isTRUE(attr(x, "relative"))) {
srcfile_names <- to_relative_path(srcfile_names, attr(x, "package")$path)
}
blank_lines <- compact(
setNames(lapply(srcfiles, function(srcfile) attr(srcfile_lines(srcfile), "blanks")),
srcfile_names))
if (length(blank_lines)) {
blank_lines <- utils::stack(blank_lines)
non_blanks <- setdiff.data.frame(
res,
blank_lines,
by.x = c("filename", "line"),
by.y = c("ind", "values"))
res <- res[non_blanks, ]
}
res
}
res[order(res$filename, res$line), ]
},
"expression" = df
)
}
#' Provide locations of zero coverage
#'
#' When examining the test coverage of a package, it is useful to know if there are
#' any locations where there is **0** test coverage.
#'
#' @param x a coverage object returned [package_coverage()]
#' @param ... additional arguments passed to
#' [tally_coverage()]
#' @return A `data.frame` with coverage data where the coverage is 0.
#' @details if used within RStudio this function outputs the results using the
#' Marker API.
#' @export
zero_coverage <- function(x, ...) {
coverage_data <- tally_coverage(x, ...)
coverage_data <- coverage_data[coverage_data$value == 0, , drop = FALSE]
res <- coverage_data[
# need to use %in% rather than explicit indexing because
# tally_coverage returns a df without the columns if
# by is equal to "line"
colnames(coverage_data) %in%
c("filename",
"functions",
"line",
"first_line",
"last_line",
"first_column",
"last_column",
"value")]
if (getOption("covr.rstudio_source_markers", TRUE) &&
rstudioapi::hasFun("sourceMarkers")) {
markers <- markers(coverage_data)
rstudioapi::callFun("sourceMarkers",
name = "covr",
markers = markers,
basePath = attr(x, "package")$path,
autoSelect = "first")
invisible(res)
} else {
res
}
}
#' Print a coverage object
#'
#' @param x the coverage object to be printed
#' @param group whether to group coverage by filename or function
#' @param by whether to count coverage by line or expression
#' @param ... additional arguments ignored
#' @return The coverage object (invisibly).
#' @export
print.coverage <- function(x, group = c("filename", "functions"), by = "line", ...) {
if (length(x) == 0) {
return()
}
group <- match.arg(group)
type <- attr(x, "type")
if (is.null(type) || type == "none") {
type <- NULL
}
df <- tally_coverage(x, by = by)
if (!NROW(df)) {
return(invisible())
}
percents <- tapply(df$value, df[[group]], FUN = function(x) (sum(x > 0) / length(x)) * 100)
overall_percentage <- percent_coverage(df, by = by)
message(crayon::bold(
paste(collapse = " ",
c(attr(x, "package")$package, to_title(type), "Coverage: "))),
format_percentage(overall_percentage))
by_coverage <- percents[order(percents,
names(percents))]
for (i in seq_along(by_coverage)) {
message(crayon::bold(paste0(names(by_coverage)[i], ": ")),
format_percentage(by_coverage[i]))
}
invisible(x)
}
#' @export
print.coverages <- function(x, ...) {
for (i in seq_along(x)) {
# Add a blank line between consecutive coverage items
if (i != 1) {
message()
}
print(x[[i]], ...)
}
invisible(x)
}
format_percentage <- function(x) {
color <- if (x >= 90) crayon::green
else if (x >= 75) crayon::yellow
else crayon::red
color(sprintf("%02.2f%%", x))
}
markers <- function(x, ...) UseMethod("markers")
markers.coverages <- function(x, ...) {
mrks <- unlist(lapply(unname(x), markers), recursive = FALSE)
mrks <- mrks[order(
vcapply(mrks, `[[`, "file"),
viapply(mrks, `[[`, "line"),
vcapply(mrks, `[[`, "message")
)]
# request source markers
rstudioapi::callFun("sourceMarkers",
name = "covr",
markers = mrks,
basePath = NULL,
autoSelect = "first")
invisible()
}
markers.coverage <- function(x, ...) {
# generate the markers
markers <- lapply(unname(x), function(xx) {
filename <- get_source_filename(xx$srcref, full.names = TRUE)
list(
type = "warning",
file = filename,
line = xx$srcref[1],
column = xx$srcref[2],
message = sprintf("No %s Coverage!", to_title(attr(x, "type")))
)
})
}
markers.data.frame <- function(x, type = "test") { # nolint
# generate the markers
markers <- Map(function(filename, line, column) {
list(
type = "warning",
file = filename,
line = line,
column = column %||% 1,
message = sprintf("No %s Coverage!", to_title(type))
)},
x$filename,
x$first_line %||% x$line,
x$first_column %||% rep(list(NULL), NROW(x)),
USE.NAMES = FALSE)
}
# Expand lines given as start and end ranges to enumerate each line
expand_lines <- function(x) {
repeats <- (x$last_line - x$first_line) + 1L
lines <- unlist(Map(seq, x$first_line, x$last_line)) %||% integer()
res <- x[rep(seq_len(NROW(x)), repeats), c("filename", "functions", "value")]
res$line <- lines
rownames(res) <- NULL
res
}