Linting

Author: csgillespie

.lintr

@@ -0,0 +1,6 @@
+linters: with_defaults(
+    assignment_linter = NULL,
+    object_name_linter = NULL,
+    line_length_linter(100),
+    commented_code_linter = NULL
+  )

R/actions.R

@@ -1,7 +1,7 @@
 #' Update the status of an article.
 #'
 #' \code{reject}, \code{accept} and \code{withdraw} update the status,
-#' move the file to the correct directory and draft an email from a 
+#' move the file to the correct directory and draft an email from a
 #' template of the corresponding name.
 #'
 #' @rdname action
@@ -23,7 +23,7 @@ update_status <- function(article, status, comments = "", date = Sys.Date()) {
 #' @export
 reject <- function(article, comments = "", date = Sys.Date()) {
   article <- as.article(article)
-  
+
   cli::cli_h1(paste("Rejecting paper", format(article$id)))
   cli::cli_alert_info("Updating DESCRIPTION file")
   update_status(article, "rejected", comments = comments, date = date)

R/article.R

@@ -10,22 +10,22 @@
 #' @export
 article <- function(..., quiet = FALSE) {
   tryCatch(make_article(...),
-    error = function(e) {
-      article <- unparsed(...)
-      if (!quiet) {
-        message("Failed to parse: ")
-        print(article)
-        message(e, "\n")
-      }
-      article
-    }
+           error = function(e) {
+             article <- unparsed(...)
+             if (!quiet) {
+               message("Failed to parse: ")
+               print(article)
+               message(e, "\n")
+             }
+             article
+           }
   )
 }
 
 #' Convert input into an article.
 #'
-#' @param id a path to a DESCRIPTION, a path to a directory containing 
-#'   DESCRIPTION, or a article name, found in a sub-directory rejected, 
+#' @param id a path to a DESCRIPTION, a path to a directory containing
+#'   DESCRIPTION, or a article name, found in a sub-directory rejected,
 #'   accepted or submissions
 #' @export
 #' @examples
@@ -65,7 +65,7 @@ load_article <- function(path, quiet = FALSE) {
   if (nrow(dcf) != 1) stop("DCF parsing error: ", path, call. = FALSE)
 
   # Remove field names that keep.white incorrectly preserves
-  for(field in fields) {
+  for (field in fields) {
     dcf[, field] <- gsub(paste(field, ": ?", sep = ""), "", dcf[, field])
   }
   # Convert missing values to empty strings
@@ -75,7 +75,7 @@ load_article <- function(path, quiet = FALSE) {
   dcf <- as.list(as.data.frame(dcf, stringsAsFactors = FALSE))
   # Only should be manually set in tests
   if (is.null(dcf$id) || identical(dcf$id, "")) {
-    dcf$id <- basename(dirname(path))  
+    dcf$id <- basename(dirname(path))
   }
   dcf$path <- dirname(path)
   do.call(article, dcf)
@@ -101,7 +101,9 @@ make_article <- function(id, slug = "", authors = "", title = "", editor = "",
 parse_supplementaries <- function(suppl) {
   x <- str_trim(str_split(suppl, "\n")[[1]])
   x <- x[str_length(x) > 0]
-  xs <-lapply(x, function(y) {class(y) <- "supplfile"; y})
+  xs <- lapply(x, function(y) {
+    class(y) <- "supplfile"; y
+  })
   class(xs) <- "supplfile_list"
   xs
 }

R/assignments.R

@@ -1,3 +1,4 @@
+globalVariables("titles")
 # XXX: Repetition below. But I intend to split out the different
 # sections in the future
 #' @export
@@ -13,7 +14,6 @@ summarise_articles = function(editor = NULL) {
   all_articles = get_assignments(editor)
   latest = get_latest_assignments(all_articles)
 
-
   cli::cli_h1("Submitted")
   art = latest[latest$status_status == "submitted", ]
   titles = str_trunc(art$title, 30)

R/convert_landing.R

@@ -17,7 +17,7 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
   has_slug_ptr <- character(length(has_slug))
   has_slug_ptr[has_slug] <- sapply(conf_articles[has_slug], function(x) x$slug)
 
-  if (!dir.exists(file.path(web_path, "archive", yr_id)) 
+  if (!dir.exists(file.path(web_path, "archive", yr_id))
     && action == "report_and_commit")
     dir.create(file.path(web_path, "archive", yr_id))
   i <- 0L
@@ -26,7 +26,7 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
     fls0 <- list.files(file.path(web_path, "archive", issue))
     fls <- fls0[str_detect(fls0, "^RJournal_")]
     strings <- "[A-Z][a-z][a-z]*"
-    nms0 <- str_subset(str_replace_all(str_sub(fls, 17L, str_length(fls)-4L),
+    nms0 <- str_subset(str_replace_all(str_sub(fls, 17L, str_length(fls) - 4L),
       "[_\\+\\~]", " "), strings)
     nms <- str_replace(nms0, " et al", "")
   }
@@ -84,9 +84,9 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
         i <- ifelse(length(current_dirs) > 0,
           as.integer(max(as.integer(str_sub(current_dirs, 9L, 11L)))) + 1L, 1L)
       }
-      next_dir <- formatC(i, format="d", flag="0", width=3L)
+      next_dir <- formatC(i, format = "d", flag = "0", width = 3L)
       slug <- paste0("RJ-", yr_id, "-", next_dir)
-      if (action == "report_and_commit") 
+      if (action == "report_and_commit")
         dir.create(file.path(web_path, "archive", yr_id, slug))
     } else{
       slug <- article$slug
@@ -116,7 +116,7 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
         refs_list$CTV_rev <- rev_dep_ctv(refs_list$CRANpkgs)
 
 #      print(refs_list)
-       
+
       metadata <- c(list(
         title = pdf_list$title,
         bibtitle = pdf_list$bibtitle,
@@ -127,22 +127,22 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
         ), refs_list[!sapply(refs_list, is.null)])
       metadata <- c(metadata, list(landing = str_sub(slug, 4L, 7L)))
 
-      aus <- unlist(str_split(paste(metadata$author, collapse=" "), " "))
-      if ("R\xc3\xb6nneg\xc3\xa5rd" %in% aus) 
+      aus <- unlist(str_split(paste(metadata$author, collapse = " "), " "))
+      if ("R\xc3\xb6nneg\xc3\xa5rd" %in% aus)
         aus <- str_replace(str_replace(aus, "[\xc3\xb6]", "oe"), "[\xc3\xa5]", "aa")
-      if ("S\xc3\xb3lymos" %in% aus) 
+      if ("S\xc3\xb3lymos" %in% aus)
         aus <- str_replace(aus, "[\xc3\xb3]", "o")
-      if ("Herv\xc3\xa9" %in% aus) 
+      if ("Herv\xc3\xa9" %in% aus)
         aus <- str_replace(aus, "[\xc3\xa9]", "e")
-      if ("B\xc3\xa5\xc3\xa5th" %in% aus) 
+      if ("B\xc3\xa5\xc3\xa5th" %in% aus)
         aus <- str_replace_all(aus, "[\xc3\xa5]", "aa")
       pub_file <- NULL
       if (issue == "2009-2" && art == "2009-07") aus <- "Coeurjolly"
       if (issue == "2012-2" && art == "2011-22")
         pub_file <- "RJournal_2012-2_Murrell+Ly.pdf"
       if (issue == "2012-2" && art == "2011-32")
         pub_file <- "RJournal_2012-2_Murrell.pdf"
-      if (issue == "2012-2" && art == "2011-35") 
+      if (issue == "2012-2" && art == "2011-35")
         pub_file <- "RJournal_2012-2_Murrell2.pdf"
 
       if (is.null(pub_file)) pub_file <- fls[which(sapply(lapply(nms,
@@ -151,10 +151,10 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
 
       if (length(pub_file) == 0) {
         cat(nms, "\n")
-        cat(metadata$author, collapse=" ", "\n")
+        cat(metadata$author, collapse = " ", "\n")
         stop(issue, " ", art, " no match")
       }
-      
+
 #      cat(issue, art, paste(metadata$author, collapse=" "), "\n")
 #      cat(pub_file, "\n")
 
@@ -163,7 +163,7 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
         stop("published file :", pub_file, "not found in ", issue)
 
       metadata <- c(metadata, list(old_slug = str_sub(pub_file, 17L,
-        str_length(pub_file)-4L)))
+        str_length(pub_file) - 4L)))
 #      cat(from, "\n")
 
     } else {
@@ -178,7 +178,7 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
         refs_list$CTV_rev <- rev_dep_ctv(refs_list$CRANpkgs)
 
 #      print(refs_list)
-       
+
       sl <- as.data.frame(article$status)
       metadata <- c(list(
         title = pdf_list$title,
@@ -220,18 +220,18 @@ convert_proofs <- function(issue, action="report_only", clean=TRUE) {
     }
 
     article_config_content <- list(
-        slug=metadata$slug,
-        old_slug=metadata$old_slug,
-        title=metadata$title,
-        bibtitle=metadata$bibtitle,
-        author=metadata$author,
-        bibauthor=metadata$bibauthor,
-        landing=metadata$landing,
-        abstract=metadata$abstract
+        slug = metadata$slug,
+        old_slug = metadata$old_slug,
+        title = metadata$title,
+        bibtitle = metadata$bibtitle,
+        author = metadata$author,
+        bibauthor = metadata$bibauthor,
+        landing = metadata$landing,
+        abstract = metadata$abstract
     )
     if (!is.null(conf_articles[[conf_art]]$pages))
         article_config_content <- c(article_config_content,
-          list(pages=conf_articles[[conf_art]]$pages))
+          list(pages = conf_articles[[conf_art]]$pages))
     if (!is.null(metadata$acknowledged))
         article_config_content <- c(article_config_content,
           list(acknowledged=metadata$acknowledged))

R/crossref.R

@@ -28,11 +28,11 @@ journal_metadata = list(
 doi_batch_id_tpl = "<doi_batch_id>{{ID}}</doi_batch_id>\n"
 print_doi_batch_id <- function(file) {
     x <- as.POSIXlt(Sys.time())
-    mon <- if(nchar(x$mon) == 1) paste("0", x$mon, sep="") else x$mon
-    mday <- if(nchar(x$mday) == 1) paste("0", x$mday, sep="") else x$mday
-    hour <-  if(nchar(x$hour) == 1) paste("0", x$hour, sep="") else x$hour
-    min <-  if(nchar(x$min) == 1) paste("0", x$min, sep="") else x$min
-    sec <-  if(nchar(round(x$sec)) == 1) paste("0", round(x$sec), sep="") else round(x$sec)
+    mon <- if (nchar(x$mon) == 1) paste("0", x$mon, sep="") else x$mon
+    mday <- if (nchar(x$mday) == 1) paste("0", x$mday, sep="") else x$mday
+    hour <- if (nchar(x$hour) == 1) paste("0", x$hour, sep="") else x$hour
+    min <- if (nchar(x$min) == 1) paste("0", x$min, sep="") else x$min
+    sec <- if(nchar(round(x$sec)) == 1) paste("0", round(x$sec), sep="") else round(x$sec)
     ID = paste(x$year, mon, mday, hour, min, sec, sep="")
     txt = whisker.render(doi_batch_id_tpl, list(ID=ID))
     cat(txt, file=file, append=TRUE)
@@ -255,7 +255,7 @@ newDeposit = function(x, out="") {
     cat("<registrant>CrossRef</registrant> \n </head>\n
 	<body>\n", file=out, append=TRUE)
     ## this generates xml for all bib items stored in a bib file
-    for(i in 1:length(x$articles)) {
+    for (i in 1:length(x$articles)) {
         cat("<journal>\n", file=out, append=TRUE)
         print_journal_metadata(out)
         print_journal_issue(x, out)

R/email.R

@@ -56,7 +56,7 @@ email_text <- function(text) {
 
   url <- paste0("mailto:", to, "?",
     paste0(names(fields), "=", unlist(fields), collapse = "&"))
-  
+
   browseURL(url)
 }
 

R/path.R

@@ -9,11 +9,12 @@ set_articles_path <- function(path) {
   .articles$path <- path
 }
 
-get_articles_path <- function(){
+get_articles_path <- function() {
   dir <- .articles$path %||% getwd()
   if (!(basename(dir) %in% c("articles", "articles_test"))) {
     abort(
-      sprintf("The current articles path is not correct. Set the path to the articles repository with `set_articles_path()`",
+      sprintf("The current articles path is not correct.
+              Set the path to the articles repository with `set_articles_path()`",
               dir)
     )
   }

R/report.R

@@ -15,14 +15,14 @@ report <- function(articles = active_articles()) {
 report_line <- function(x) {
   message(x$path) # to identify culprit when things go wrong
   stopifnot(is.article(x))
-  
+
   todo <- todo(x)
-  status <- last_status(x)
+  #status <- last_status(x)
   last_date <- last_status(x)$date
-  
+
   days_taken <- difftime(Sys.Date(), last_date, "days")
   stars <- sum(days_taken > deadlines(todo))
-  
+
   data.frame(
     status = todo,
     ed = editor_abbr(x$editor),
@@ -75,7 +75,7 @@ order_status <- function(x) {
   x <- unique(x)
   eic <- x[grepl("editor-in-chief", x)]
   editors <- setdiff(x[grepl("editor", x)], eic)
-  others <- setdiff(x, c(eic, editors)) 
+  others <- setdiff(x, c(eic, editors))
   c(eic, editors, others)
 }
 

R/reviewers.R

@@ -147,4 +147,3 @@ add_review = function(article, reviewer_id, review, recommend = NULL) {
                        comment = recommend)
   return(invisible(NULL))
 }
-

R/rfc822.R

@@ -79,4 +79,3 @@ parse_address <- function(x) {
 
   address(email, name, comment)
 }
-

R/status.R

@@ -207,7 +207,7 @@ parse_status <- function(x) {
   re <- "^(\\d{4}-\\d{2}-\\d{2}) ([^\\[]*)(?: \\[([^\\[]+)\\])?$"
   if (!str_detect(x, re)) {
     # NM added line
-    cat('bad status:',x,'\n')
+    cat("bad status:", x, "\n")
     stop("Status must have form 'yyyy-mm-dd status [optional comments]'",
       call. = FALSE)
   }
@@ -226,7 +226,7 @@ parse_status <- function(x) {
 
 as.data.frame.status_list <- function(status_list) {
   message("DF")
-  ml <- vector(mode="list", length=length(status_list))
-  for (i in seq(along=ml)) ml[[i]] <- as.data.frame(unclass(status_list[[i]]))
+  ml <- vector(mode = "list", length = length(status_list))
+  for (i in seq(along = ml)) ml[[i]] <- as.data.frame(unclass(status_list[[i]]))
   do.call("rbind", ml)
 }