finalise v2.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rdpack
 Type: Package
 Title: Update and Manipulate Rd Documentation Objects
-Version: 2.4.0.9000
+Version: 2.5
 Authors@R: c( person(given = c("Georgi", "N."),
                      family = "Boshnakov", 
                      role = c("aut", "cre"), 

NEWS.md

@@ -1,9 +1,19 @@
-# Rdpack 2.4.0.9000
+# Rdpack 2.5
 
 - Rd macros `insertCite` and friends were calling `insert_citeOnly` with
   argument `key` instead of `keys`. This was not an error since partial matching
   is ok here but not good practice. Fixes issue #28 reported by Marcel Ramos.
-
+
+- changed the saved value in "tests/testthat/dummyArticle.rds" used in
+  'test-bib.R' with a value obtained with R-devel r84896 n previu versins of R
+  there wasasuperfluous final ' .').
+
+- in some cases when square brackets were requested, rather than round ones,
+  `insertCiteOnly` was using closing round parenthesis.
+
+- in some cases `insertCiteOnly` was not handling well the last cite when it was
+  followed by free text.
+
 
 # Rdpack 2.4
 
@@ -13,7 +23,7 @@
   since the preceding `\insertCited`. Prompted by issue #27 to allow separate
   references lists for each method and the class in R6 documentation.
 
-- It is no longer necessary to remove backslashes from `\&` in similar in bibtex
+- It is no longer necessary to remove backslashes from `\&` and similar in bibtex
   files (e.g. in "John Wiley \& Sons"). The backslash was appearing in the
   rendered pdf manual but R-devel's checks started to warn about it recently
   with something like `checkRd: (-1) pcts-package.Rd:287: Escaped LaTeX

R/bib.R

@@ -691,6 +691,9 @@ makeVignetteReference <- function(package, vig = 1, verbose = TRUE,
 }
 
 ## 2018-03-13 new
+
+## 2023-08-19 TODO: this function was patched and its functionality extended via patches so
+##     many times that it needs consolidation.
 insert_citeOnly <- function(keys, package = NULL, before = NULL, after = NULL,
                             bibpunct = NULL, ..., 
                             cached_env = NULL, cite_only = FALSE, dont_cite = FALSE) {
@@ -765,14 +768,23 @@ insert_citeOnly <- function(keys, package = NULL, before = NULL, after = NULL,
         keys <- substr(keys, 2, nchar(keys)) # drop refch
         ## TODO: check if there are still @'s at this point
 
-        refpat <- paste0("(", refch, "[^;,()[:space:]]+)")  #  "(@[^;,[:space:]]+)"
+        refpat  <- paste0("(", refch, "[^;,()[:space:]]+)")  #  "(@[^;,[:space:]]+)"
+        refpat2 <- paste0(     refch, "[^;,()[:space:]]+\\)")
         if(textual){
             wrkkeys <- strsplit(keys, "@")[[1]] # note [[1]] !!!
 
-            ## the last key is special, since there is none after it
+            ## 2023-08-19 Note:
+            ##
+            ##     The code until the assignment to 'keys' puts a ')' at the end of each key.
+            ##     presumably to designate the end of the key for gregexpr below. But these ')'
+            ##     need to be removed later. 
+            ##
+            ## first process the last key - it is special, since there is none after it
             nk <- length(wrkkeys)
             wrkkeys[nk] <- if(grepl("[;,]$", wrkkeys[nk]))
                                sub("([;,])$", ")\\1", wrkkeys[nk])
+                           else if(grepl("[;,]", wrkkeys[nk]))
+                               sub("([;,][^;,]*)$", ")\\1" , wrkkeys[nk])
                            else
                                paste0(wrkkeys[nk], ")")
 
@@ -789,6 +801,7 @@ insert_citeOnly <- function(keys, package = NULL, before = NULL, after = NULL,
             keys <- paste0(wrkkeys, collapse = refch)
         }
 
+        ## find the positions of the keys (used further below to replace them with the cites
         m <- gregexpr(refpat, keys)
         allkeys <- regmatches(keys, m)[[1]] # note: [[1]]
         allkeys <- gsub(refch, "", allkeys)
@@ -814,16 +827,20 @@ insert_citeOnly <- function(keys, package = NULL, before = NULL, after = NULL,
                            safe_cite(key, bibs, textual = textual, bibpunct = bibpunct,
                                      from.package = package)
                        )
-#print(refs)
+
         if(textual){
-            ## drop ")" - strong assumption that that is the last char
-            refs <- sapply(refs, function(s) substr(s, 1, nchar(s) - 1))
+            ## 2023-08-19 Note: need to drop the ')' added above. The commented out solution
+            ##    below drop the last symbol in the prepared cites instead, which is
+            ##    equivalent but only if bibpunct is missing or specifies ')' as closing for
+            ##    the likes of Boshnakov (2020). The new solution matches again with a
+            ##    pattern including the ')' at the end of the key, so that ')' gets replaced
+            ##    along with the key.
+            ## was: refs <- sapply(refs, function(s) substr(s, 1, nchar(s) - 1))
+            m <- gregexpr(refpat2, keys)
         }
-#print(refs)
         ## replace keys with citations
         text <- keys
         regmatches(text, m) <- list(refs)
-
         ## parentheses around the whole cite; 2022-02-05: also if !nobrackets
         if(!textual && !nobrackets) # 2018-03-28 don't put parentheses in textual mode
             text <- paste0("(", text, ")")
@@ -850,7 +867,7 @@ insert_citeOnly <- function(keys, package = NULL, before = NULL, after = NULL,
 
     ## 2022-06-05: was: toRd(text)
     ##    workaround for issue #25; effectively assumes that citation text
-    ##    doesn't contain braces that need escaping 
+    ##    doesn't contain braces that need escaping
     .toRd_cite(text)
 }
 

tests/testthat/initialize-methods.Rd

@@ -91,7 +91,7 @@
   \code{\link{setMethod}} of the form:
 
 \preformatted{    setMethod("initialize", "traceable",
-      function(.Object, def, tracer, exit, at, print) \dots
+      function(.Object, def, tracer, exit, at, print) \{ .... \}
     )
 }
 

tests/testthat/test-bib.R

@@ -41,10 +41,9 @@ test_that("bib works fine", {
         "@see also @Rpackage:rbibutils and @parseRd;textual", package = "Rdpack"),
         "see also Boshnakov and Putman (2020) and Murdoch (2010)")
 
-    ## commenting out since not sure if the ')' is on purpose after  "among others" (:TODO:)
-    ##
-    ## expect_equal(insert_citeOnly("@see also @Rpackage:rbibutils and @parseRd, among others;textual", package = "Rdpack"),
-    ##              "see also Boshnakov and Putman (2020) and Murdoch (2010, among others)")
+    expect_equal(insert_citeOnly(
+        "@see also @Rpackage:rbibutils and @parseRd, among others;textual", package = "Rdpack"),
+        "see also Boshnakov and Putman (2020) and Murdoch (2010), among others")
 
     expect_equal(insert_citeOnly(
         "@see also @Rpackage:rbibutils and @parseRd", package = "Rdpack"),
@@ -53,22 +52,10 @@ test_that("bib works fine", {
         "@see also @Rpackage:rbibutils and @parseRd;textual", package = "Rdpack"),
         "see also Boshnakov and Putman (2020) and Murdoch (2010)")
 
-    insert_citeOnly(
+    expect_equal(insert_citeOnly(
         "@see also @Rpackage:rbibutils and @parseRd;textual", package = "Rdpack",
-                                                              bibpunct = c("[", "]"))
-
-    ## TODO: bug here:
-    ##
-    ## expect_equal(insert_citeOnly(
-    ##     "@see also @Rpackage:rbibutils and @parseRd;textual", package = "Rdpack",
-    ##                                                           bibpunct = c("[", "]")),
-    ##     "see also Boshnakov and Putman [2020] and Murdoch [2010]")
-    ##
-    ## produces:
-    ##   "see also Boshnakov and Putman [2020) and Murdoch [2010)"
-    ## (note the closing parentheses)
-    ## Uncomment the print comments in insertCite() to see more details.
-
+                                                              bibpunct = c("[", "]")),
+        "see also Boshnakov and Putman [2020] and Murdoch [2010]")
 
     expect_equal(insert_citeOnly(
         "@see also @Rpackage:rbibutils and @parseRd;nobrackets", package = "Rdpack"),
@@ -127,11 +114,29 @@ test_that("bib works fine", {
     expect_false(grepl("\\\\", insert_citeOnly("DiaLop2020ejor;textual", "Rdpack")))
 
 
-    ## after fix of issue #26
+    ## after fix of issue #26:
     ##     before the fix it was necessary to manually remove the backslash from \&, \_, etc.
     ##     in the bib file. Now the backslashes are removed by Rdpack
-    expect_known_value(insert_all_ref(matrix(c("dummyArticle", "Rdpack"), ncol = 2)),
-                       "dummyArticle.rds", update = FALSE)
+    ##
+    ## fix in August 2023 for a change in R-devel (citation.R):
+    ##     resaved 'dummyArticle.rds' and conditioned on R-devel r84986.
+    ##
+    ##     Previously the rendered version of the 'note' field contained a superfluous ' .'.
+    ##     This was fixed in R-devel r84986 (or somewhat earlier). 
+    ##     After the change in R-devel, we get with the old dummyArticle.rds:
+    ##       > waldo::compare(readRDS("tests/testthat/dummyArticle.rds"),
+    ##                        insert_all_ref(matrix(c("dummyArticle", "Rdpack"), ncol = 2)))
+    ##      lines(old) vs lines(new)
+    ##      "A. ZZZ (2018)."
+    ##      "\\dQuote{A relation between several fundamental constants: \\eqn{e^{i\\pi}=-1}.}"
+    ##      "\\emph{A non-existent journal with the formula \\eqn{L_2} in its name & an ampersand which is preceded by a backslash in the bib file.}."
+    ##      - "This reference does not exist. It is a test/demo that simple formulas in BibTeX files are OK. A formula in field 'note': \\eqn{c^2 = a^2 + b^2}. ."
+    ##      + "This reference does not exist. It is a test/demo that simple formulas in BibTeX files are OK. A formula in field 'note': \\eqn{c^2 = a^2 + b^2}."
+    ##
+    ##     (notice '. .' at the end of the old string)
+    if(is.numeric(svnrev <- R.Version()$'svn rev')  &&  svnrev >= 84986)
+        expect_known_value(insert_all_ref(matrix(c("dummyArticle", "Rdpack"), ncol = 2)),
+                           "dummyArticle.rds", update = FALSE)
 
     ## makeVignetteReference("Rdpack", 1)