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#' Exclusions
#'
#' covr supports a couple of different ways of excluding some or all of a file.
#'
#' @section Line Exclusions:
#'
#' The `line_exclusions` argument to `package_coverage()` can be used
#' to exclude some or all of a file. This argument takes a list of filenames
#' or named ranges to exclude.
#'
#' @section Function Exclusions:
#'
#' Alternatively `function_exclusions` can be used to exclude R functions
#' based on regular expression(s). For example `print\\\.*` can be used to
#' exclude all the print methods defined in a package from coverage.
#'
#' @section Exclusion Comments:
#'
#' In addition you can exclude lines from the coverage by putting special comments
#' in your source code. This can be done per line or by specifying a range.
#' The patterns used can be specified by the `exclude_pattern`, `exclude_start`,
#' `exclude_end` arguments to `package_coverage()` or by setting the global
#' options `covr.exclude_pattern`, `covr.exclude_start`, `covr.exclude_end`.
#' @examples
#' \dontrun{
#' # exclude whole file of R/test.R
#' package_coverage(exclusions = "R/test.R")
#'
#' # exclude lines 1 to 10 and 15 from R/test.R
#' package_coverage(line_exclusions = list("R/test.R" = c(1:10, 15)))
#'
#' # exclude lines 1 to 10 from R/test.R, all of R/test2.R
#' package_coverage(line_exclusions = list("R/test.R" = 1:10, "R/test2.R"))
#'
#' # exclude all print and format methods from the package.
#' package_coverage(function_exclusions = c("print\\.", "format\\."))
#'
#' # single line exclusions
#' f1 <- function(x) {
#' x + 1 # nocov
#' }
#'
#' # ranged exclusions
#' f2 <- function(x) { # nocov start
#' x + 2
#' } # nocov end
#' }
#' @name exclusions
NULL
exclude <- function(coverage,
line_exclusions = NULL,
function_exclusions = NULL,
exclude_pattern = getOption("covr.exclude_pattern"),
exclude_start = getOption("covr.exclude_start"),
exclude_end = getOption("covr.exclude_end"),
path = NULL) {
sources <- traced_files(coverage)
source_exclusions <- lapply(sources,
function(x) {
parse_exclusions(x$file_lines, exclude_pattern, exclude_start, exclude_end)
})
excl <- normalize_exclusions(c(source_exclusions, line_exclusions), path)
df <- as.data.frame(coverage, sort = FALSE)
to_exclude <- rep(FALSE, length(coverage))
if (!is.null(function_exclusions)) {
to_exclude <- Reduce(`|`, init = to_exclude,
Map(rex::re_matches, function_exclusions, MoreArgs = list(data = df$functions)))
to_exclude[is.na(to_exclude)] <- FALSE
}
df$full_name <- vcapply(coverage,
function(x) {
normalize_path(get_source_filename(x$srcref, full.names = TRUE))
})
to_exclude <- to_exclude | vlapply(seq_len(NROW(df)),
function(i) {
file <- df[i, "full_name"]
which_exclusion <- match(file, names(excl))
!is.na(which_exclusion) &&
(
excl[[which_exclusion]] == Inf ||
all(seq(df[i, "first_line"], df[i, "last_line"]) %in% excl[[file]])
)
})
if (any(to_exclude)) {
coverage <- coverage[!to_exclude]
}
coverage
}
parse_exclusions <- function(lines,
exclude_pattern = getOption("covr.exclude"),
exclude_start = getOption("covr.exclude_start"),
exclude_end = getOption("covr.exclude_end")) {
exclusions <- numeric(0)
starts <- which(rex::re_matches(lines, exclude_start))
ends <- which(rex::re_matches(lines, exclude_end))
if (length(starts) > 0) {
if (length(starts) != length(ends)) {
stop(length(starts), " starts but only ", length(ends), " ends!")
}
for (i in seq_along(starts)) {
exclusions <- c(exclusions, seq(starts[i], ends[i]))
}
}
exclusions <- c(exclusions, which(rex::re_matches(lines, exclude_pattern)))
sort(unique(exclusions))
}
file_exclusions <- function(x, path = NULL) {
excl <- normalize_exclusions(x, path)
full_files <- vlapply(excl, function(x1) length(x1) == 1 && x1 == Inf)
if (any(full_files)) {
names(excl)[full_files]
} else {
NULL
}
}
normalize_exclusions <- function(x, path = NULL) {
if (is.null(x) || length(x) <= 0) {
return(list())
}
# no named parameters at all
if (is.null(names(x))) {
x <- structure(relist(rep(Inf, length(x)), x), names = x)
} else {
unnamed <- names(x) == ""
if (any(unnamed)) {
# must be character vectors of length 1
bad <- vlapply(seq_along(x),
function(i) {
unnamed[i] & (!is.character(x[[i]]) | length(x[[i]]) != 1)
})
if (any(bad)) {
stop("Full file exclusions must be character vectors of length 1. items: ",
paste(collapse = ", ", which(bad)),
" are not!",
call. = FALSE)
}
names(x)[unnamed] <- x[unnamed]
x[unnamed] <- Inf
}
}
if (!is.null(path)) {
names(x) <- file.path(path, names(x))
}
names(x) <- normalize_path(names(x))
remove_line_duplicates(
remove_file_duplicates(
compact(x)
)
)
}
remove_file_duplicates <- function(x) {
unique_names <- unique(names(x))
## check for duplicate files
if (length(unique_names) < length(names(x))) {
x <- lapply(unique_names,
function(name) {
vals <- unname(unlist(x[names(x) == name]))
if (any(vals == Inf)) {
Inf
} else {
vals
}
})
names(x) <- unique_names
}
x
}
remove_line_duplicates <- function(x) {
x[] <- lapply(x, unique)
x
}
parse_covr_ignore <- function(file = getOption("covr.covrignore", Sys.getenv("COVR_COVRIGNORE", ".covrignore"))) {
if (!file.exists(file)) {
return(NULL)
}
lines <- readLines(file)
paths <- Sys.glob(lines, dirmark = TRUE)
files <- unlist(
lapply(paths, function(x) {
if (dir.exists(x)) {
list.files(recursive = TRUE, all.files = TRUE, path = x, full.names = TRUE)
} else {
x
}
}))
}