Format R code with air

R/gn_debug.R

@@ -5,5 +5,5 @@
 #' @export
 #' @param ... ignored
 gn_debug <- function(...) {
-  .Defunct(msg="gn_debug is defunct, functionality was removed from gnparser")
+  .Defunct(msg = "gn_debug is defunct, functionality was removed from gnparser")
 }

R/gn_parse.R

@@ -44,15 +44,24 @@ gn_parse <- function(
   cultivar = FALSE,
   capitalize = FALSE,
   diaereses = FALSE,
-  details = FALSE) {
-
+  details = FALSE
+) {
   gnparser_exists()
   ver_check(1)
   assert(x, "character")
   file <- tempfile(fileext = ".txt")
   on.exit(unlink(file))
   cat(x, file = file, sep = "\n")
-  res <- parse_one(file, "compact", threads, batch_size,
-    ignore_tags, cultivar, capitalize, diaereses, details)
+  res <- parse_one(
+    file,
+    "compact",
+    threads,
+    batch_size,
+    ignore_tags,
+    cultivar,
+    capitalize,
+    diaereses,
+    details
+  )
   lapply(strsplit(res, "\n")[[1]], jsonlite::fromJSON)
 }

R/gn_parse_tidy.R

@@ -22,8 +22,8 @@ gn_parse_tidy <- function(
   cultivar = FALSE,
   capitalize = FALSE,
   diaereses = FALSE,
-  ignore_tags = FALSE) {
-
+  ignore_tags = FALSE
+) {
   gnparser_exists()
   ver_check(1)
   assert(x, "character")

R/gn_version.R

@@ -1,10 +1,10 @@
 #' gn_version
-#' 
+#'
 #' get gnparser version information
-#' 
+#'
 #' @export
 #' @return named list, with `version` and `build`
-#' @examples 
+#' @examples
 #' trys <- function(x) try(x, silent=TRUE)
 #' if (interactive()) {
 #' trys(gn_version())
@@ -13,7 +13,9 @@ gn_version <- function() {
   gnparser_exists()
   # z <- gnparser_cmd("-V", error = FALSE)
   z <- gnparser_cmd("-V", error = FALSE)
-  if (z$status != 0) z <- gnparser_cmd("-v", error = FALSE)
+  if (z$status != 0) {
+    z <- gnparser_cmd("-v", error = FALSE)
+  }
   err_chk(z)
   process_version_string(z$stdout)
   # txt <- rawToChar(z$stdout)

R/gnparser.R

@@ -1,44 +1,65 @@
 #' @noRd
 #' @param ... Arguments to be passed to `sys::exec_internal('gnparser', ...)`
-gnparser_cmd = function(...) {
+gnparser_cmd <- function(...) {
   sys::exec_internal(find_gnparser(), ...)
 }
 
 # find an executable from PATH, APPDATA, system.file(), ~/bin, etc
-find_exec = function(cmd, dir, info = '') {
+find_exec <- function(cmd, dir, info = '') {
   for (d in bin_paths(dir)) {
-    exec = if (is_windows()) paste0(cmd, ".exe") else cmd
-    path = file.path(d, exec)
-    if (utils::file_test("-x", path)) break else path = ''
+    exec <- if (is_windows()) paste0(cmd, ".exe") else cmd
+    path <- file.path(d, exec)
+    if (utils::file_test("-x", path)) break else path <- ''
   }
-  path2 = Sys.which(cmd)
+  path2 <- Sys.which(cmd)
   if (path == '' || same_path(path, path2)) {
-    if (path2 == '') stop(cmd, ' not found. ', info, call. = FALSE)
-    return(cmd)  # do not use the full path of the command
+    if (path2 == '') {
+      stop(cmd, ' not found. ', info, call. = FALSE)
+    }
+    return(cmd) # do not use the full path of the command
   } else {
-    if (path2 != '') warning(
-      'Found ', cmd, ' at "', path, '" and "', path2, '". The former will be used. ',
-      "If you don't need both copies, you may delete/uninstall one."
-    )
+    if (path2 != '') {
+      warning(
+        'Found ',
+        cmd,
+        ' at "',
+        path,
+        '" and "',
+        path2,
+        '". The former will be used. ',
+        "If you don't need both copies, you may delete/uninstall one."
+      )
+    }
   }
   normalizePath(path)
 }
 
 gnpenv <- new.env()
-find_gnparser = local({
-  gnpenv$path = NULL  # cache the path to gnparser
+find_gnparser <- local({
+  gnpenv$path <- NULL # cache the path to gnparser
   function() {
-    if (is.null(gnpenv$path)) gnpenv$path <- find_exec(
-      'gnparser', 'gnparser', 'You need to install gnparser'
-    )
+    if (is.null(gnpenv$path)) {
+      gnpenv$path <- find_exec(
+        'gnparser',
+        'gnparser',
+        'You need to install gnparser'
+      )
+    }
     gnpenv$path
   }
 })
 
-parse_one <- function(x, format = NULL, threads = NULL, 
-  batch_size = NULL, ignore_tags = NULL, cultivar = FALSE,
-  capitalize = FALSE, diaereses = FALSE, details = FALSE) {
-
+parse_one <- function(
+  x,
+  format = NULL,
+  threads = NULL,
+  batch_size = NULL,
+  ignore_tags = NULL,
+  cultivar = FALSE,
+  capitalize = FALSE,
+  diaereses = FALSE,
+  details = FALSE
+) {
   assert(format, "character")
   assert(threads, c("integer", "numeric")) # NULL OK
   assert(batch_size, c("integer", "numeric"))
@@ -49,32 +70,53 @@ parse_one <- function(x, format = NULL, threads = NULL,
   assert(details, "logical")
 
   args <- character(0)
-  if (!is.null(format)) args <- c(args, "--format", format)
-  if (!is.null(threads)) args <- c(args, "--jobs", threads)
-  if (!is.null(batch_size)) args <- c(args, "--batch_size", batch_size)
-  if (ignore_tags) args <- c(args, "--ignore_tags")
-  if (cultivar) args <- c(args, "--cultivar")
-  if (capitalize) args <- c(args, "--capitalize")
-  if (diaereses) args <- c(args, "--diaereses")
-  if (details) args <- c(args, "--details")
+  if (!is.null(format)) {
+    args <- c(args, "--format", format)
+  }
+  if (!is.null(threads)) {
+    args <- c(args, "--jobs", threads)
+  }
+  if (!is.null(batch_size)) {
+    args <- c(args, "--batch_size", batch_size)
+  }
+  if (ignore_tags) {
+    args <- c(args, "--ignore_tags")
+  }
+  if (cultivar) {
+    args <- c(args, "--cultivar")
+  }
+  if (capitalize) {
+    args <- c(args, "--capitalize")
+  }
+  if (diaereses) {
+    args <- c(args, "--diaereses")
+  }
+  if (details) {
+    args <- c(args, "--details")
+  }
   z <- gnparser_cmd(c(args, x), error = FALSE)
   err_chk(z)
   return(rawToChar(z$stdout))
 }
 
 gnparser_exists <- function() {
   check_gnp <- gnparser_cmd()
-  if (check_gnp$status != 0) stop("You need to install gnparser")
+  if (check_gnp$status != 0) {
+    stop("You need to install gnparser")
+  }
   return(TRUE)
 }
 
 process_version_string <- function(x) {
   txt <- rawToChar(x)
   txt <- strsplit(txt, "\n")[[1]]
-  unlist(lapply(txt[nzchar(txt)], function(w) {
-    tmp <- gsub("\\s", "", strsplit(w, ":\\s")[[1]])
-    stats::setNames(list(tmp[2]), tmp[1])
-  }), FALSE)
+  unlist(
+    lapply(txt[nzchar(txt)], function(w) {
+      tmp <- gsub("\\s", "", strsplit(w, ":\\s")[[1]])
+      stats::setNames(list(tmp[2]), tmp[1])
+    }),
+    FALSE
+  )
 }
 
 ver_check <- function(version) {
@@ -83,7 +125,9 @@ ver_check <- function(version) {
   # ver <- process_version_string(ver$stdout)
   ver <- gn_version()
   ver_first_num <- as.numeric(substring(gsub("v|\\.", "", ver$version), 1, 1))
-  if (ver_first_num < version) stop("you need to install `gnparser` v1 or greater")
+  if (ver_first_num < version) {
+    stop("you need to install `gnparser` v1 or greater")
+  }
   return(TRUE)
 }
 
@@ -93,7 +137,9 @@ same_path <- function(p1, p2, ...) {
 }
 # from xfun::normalize_path
 normalize_path <- function(path, winslash = "/", must_work = FALSE) {
-  res = normalizePath(path, winslash = winslash, mustWork = must_work)
-  if (is_windows()) res[is.na(path)] = NA
+  res <- normalizePath(path, winslash = winslash, mustWork = must_work)
+  if (is_windows()) {
+    res[is.na(path)] <- NA
+  }
   res
 }

R/install_gnparser.R

@@ -27,9 +27,10 @@
 #' installed. This may be useful when upgrading gnparser.
 #' @export
 
-install_gnparser = function(version, force) {
-   lifecycle::deprecate_stop(
-      when = "0.3.0",
-      what = "install_gnparser()",
-      details = "Please see help page for deprecation reason and solution.")
+install_gnparser <- function(version, force) {
+  lifecycle::deprecate_stop(
+    when = "0.3.0",
+    what = "install_gnparser()",
+    details = "Please see help page for deprecation reason and solution."
+  )
 }

R/zzz.R

@@ -1,9 +1,12 @@
-
 assert <- function(x, y) {
   if (!is.null(x)) {
     if (!inherits(x, y)) {
-      stop(deparse(substitute(x)), " must be of class ",
-        paste0(y, collapse = ", "), call. = FALSE)
+      stop(
+        deparse(substitute(x)),
+        " must be of class ",
+        paste0(y, collapse = ", "),
+        call. = FALSE
+      )
     }
   }
 }
@@ -29,7 +32,7 @@ readcsv <- function(x) {
 is_windows <- function() .Platform$OS.type == "windows"
 is_macos <- function() unname(Sys.info()["sysname"] == "Darwin")
 dir_exists <- function(x) utils::file_test("-d", x)
-pkg_file = function(..., mustWork = TRUE) {
+pkg_file <- function(..., mustWork = TRUE) {
   system.file(..., package = 'rgnparser', mustWork = mustWork)
 }
 

inst/precompile.R

@@ -9,4 +9,4 @@ load_all()
 
 knit("vignettes/rgnparser.Rmd.orig", "vignettes/rgnparser.Rmd")
 
-build_vignettes()
+build_vignettes()

tests/testthat/test-gn_parse.R

@@ -2,14 +2,19 @@ skip_on_cran()
 skip_on_ci()
 
 test_that("gn_parse", {
-  x <- c("Quadrella steyermarkii (Standl.) Iltis &amp; Cornejo",
-    "Parus major Linnaeus, 1788", "Helianthus annuus var. texanus")
+  x <- c(
+    "Quadrella steyermarkii (Standl.) Iltis &amp; Cornejo",
+    "Parus major Linnaeus, 1788",
+    "Helianthus annuus var. texanus"
+  )
   w <- gn_parse(x)
   vapply(w, "[[", "", "normalized")
 
   expect_is(w, "list")
-  for (i in w) expect_is(i, "list")
-
+  for (i in w) {
+    expect_is(i, "list")
+  }
+
   expect_is(w[[1]]$parsed, "logical")
   expect_is(w[[1]]$verbatim, "character")
   expect_is(w[[1]]$normalized, "character")
@@ -22,33 +27,41 @@ test_that("cultivar arg works", {
   with_cult <- gn_parse("Sarracenia flava 'Maxima'", cultivar = TRUE)
   without_cult <- gn_parse("Sarracenia flava 'Maxima'", cultivar = FALSE)
   expect_equal(
-    with_cult[[1]]$canonical$simple, "Sarracenia flava ‘Maxima’"
+    with_cult[[1]]$canonical$simple,
+    "Sarracenia flava ‘Maxima’"
   )
   expect_equal(
-    without_cult[[1]]$canonical$simple, "Sarracenia flava"
+    without_cult[[1]]$canonical$simple,
+    "Sarracenia flava"
   )
 })
 
 test_that("capitalize arg works", {
   with_capital <- gn_parse("parus major", capitalize = TRUE)
   without_capital <- gn_parse(
-    "parus major", capitalize = FALSE)
+    "parus major",
+    capitalize = FALSE
+  )
   expect_equal(
-    with_capital[[1]]$canonical$simple, "Parus major"
+    with_capital[[1]]$canonical$simple,
+    "Parus major"
   )
   # Without capitalization, name cannot be parsed
   expect_equal(
-    without_capital[[1]]$parsed, FALSE
+    without_capital[[1]]$parsed,
+    FALSE
   )
 })
 
 test_that("diaereses arg works", {
   with_dia <- gn_parse("Leptochloöpsis virgata", diaereses = TRUE)
   without_dia <- gn_parse("Leptochloöpsis virgata", diaereses = FALSE)
   expect_equal(
-    with_dia[[1]]$canonical$simple, "Leptochloöpsis virgata"
+    with_dia[[1]]$canonical$simple,
+    "Leptochloöpsis virgata"
   )
   expect_equal(
-    without_dia[[1]]$canonical$simple, "Leptochlooepsis virgata"
+    without_dia[[1]]$canonical$simple,
+    "Leptochlooepsis virgata"
   )
 })

tests/testthat/test-gn_parse_tidy.R

@@ -2,8 +2,11 @@ skip_on_cran()
 skip_on_ci()
 
 test_that("gn_parse_tidy", {
-  x <- c("Quadrella steyermarkii (Standl.) Iltis & Cornejo",
-    "Parus major Linnaeus, 1788", "Helianthus annuus var. texanus")
+  x <- c(
+    "Quadrella steyermarkii (Standl.) Iltis & Cornejo",
+    "Parus major Linnaeus, 1788",
+    "Helianthus annuus var. texanus"
+  )
   z <- gn_parse_tidy(x)
 
   expect_is(z, "data.frame")