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[inlinedocs] Annotation of /pkg/inlinedocs/R/parsers.R
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Annotation of /pkg/inlinedocs/R/parsers.R

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1 : tdhock 110 ### combine lists or character strings
2 :     combine <- function(x,y)UseMethod("combine")
3 :    
4 :     ### combine character strings by pasting them together
5 :     combine.character <- function(x,y)
6 :     paste(x,y,sep="\n")
7 :    
8 :     ### combine lists by adding elements or adding to existing elements
9 :     combine.list <- function(x,y){
10 : tdhock 200 toadd <- if(".overwrite"%in%names(y)){
11 :     y <- y[names(y)!=".overwrite"]
12 :     rep(TRUE,length(y))
13 :     }else{
14 :     !names(y)%in%names(x)
15 :     }
16 : tdhock 185 toup <- names(y)[!toadd]
17 : tdhock 110 x[names(y)[toadd]] <- y[toadd]
18 :     for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
19 : tdhock 200 x
20 : tdhock 110 ### A list, same type as x, but with added elements from y.
21 :     }
22 :    
23 :     ### Prefix for code comments used with grep and gsub.
24 : tdhock 257 prefix <- "^[ \t]*###[ \t]*"
25 : tdhock 110
26 :     decomment <- function
27 :     ### Remove comment prefix and join lines of code to form a
28 :     ### documentation string.
29 :     (comments
30 :     ### Character vector of prefixed comment lines.
31 :     ){
32 : tdhock 185 gsub(prefix,"",comments)
33 : tdhock 110 ### String without prefixes or newlines.
34 :     }
35 :    
36 : tdhock 162 forall <- function
37 : tdhock 158 ### For each object in the package that satisfies the criterion
38 :     ### checked by subfun, parse source using FUN and return the resulting
39 : tdhock 87 ### documentation list.
40 :     (FUN,
41 :     ### Function to apply to each element in the package.
42 :     subfun=function(x)TRUE
43 :     ### Function to select subsets of elements of the package, such as
44 :     ### is.function. subfun(x)==TRUE means FUN will be applied to x and
45 :     ### the result will be returned.
46 :     ){
47 : tdhock 138 FUN <- FUN
48 :     f <- function(objs,docs,...){
49 : tdhock 300 if(length(objs)==0)return(list())
50 : tdhock 87 objs <- objs[sapply(objs,subfun)]
51 :     L <- list()
52 : tdhock 162 on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
53 : tdhock 204 for(N in union(names(docs),names(objs))){
54 : tdhock 87 o <- objs[[N]]
55 : tdhock 89 L[[N]] <- FUN(src=attr(o,"source"),
56 :     name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
57 : tdhock 87 }
58 : tdhock 162 on.exit()## remove warning message
59 : tdhock 87 L
60 :     }
61 : tdhock 138 class(f) <- c("allfun","function")
62 :     f
63 : tdhock 87 ### A Parser Function.
64 :     }
65 :    
66 : tdhock 138 ### Print method for functions constructed using forall.
67 :     print.allfun <- function(x,...){
68 :     e <- environment(x)
69 :     cat("Function to apply to every element.\nselector:")
70 :     print(e$subfun)
71 :     cat("processor:")
72 :     print(e$FUN)
73 :     }
74 :    
75 : tdhock 87 ### For each function in the package, do something.
76 :     forfun <- function(FUN)forall(FUN,is.function)
77 :    
78 : tdhock 163 kill.prefix.whitespace <- function
79 :     ### Figure out what the whitespace preceding the example code is, and
80 :     ### then delete that from every line.
81 :     (ex
82 :     ### character vector of example code lines.
83 :     ){
84 :     tlines <- gsub("\\s*","",ex)
85 :     ##tlines <- gsub("#.*","",tlines)
86 :     prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
87 :     FIND <- prefixes[which.min(nchar(prefixes))]
88 :     ## Eliminate leading tabulations or 2/4 spaces
89 :     sub(FIND, "", ex)
90 :     ### Character vector of code lines with preceding whitespace removed.
91 :     }
92 :    
93 : tdhock 175 prefixed.lines <- structure(function(src,...){
94 : tdhock 138 ### The primary mechanism of inline documentation is via consecutive
95 :     ### groups of lines matching the specified prefix regular expression
96 :     ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
97 :     ### collected as follows into documentation sections:\describe{
98 :     ### \item{description}{group starting at line 2 in the code}
99 :     ### \item{arguments}{group following each function argument}
100 :     ### \item{value}{group ending at the penultimate line of the code}}
101 :     ### These may be added to by use of the \code{##<<} constructs
102 :     ### described below.
103 :     clines <- grep(prefix,src)
104 :     if(length(clines)==0)return(list())
105 :     bounds <- which(diff(clines)!=1)
106 :     starts <- c(1,bounds+1)
107 :     ends <- c(bounds,length(clines))
108 :     ## detect body of function using paren matching
109 : tdhock 159 code <- gsub("#.*","",src)
110 :     f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
111 : tdhock 138 parens <- f("(")-f(")")
112 :     body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
113 : tdhock 175 if(length(body.begin)==0)body.begin <- 1 ## rare cases
114 : tdhock 138 is.arg <- function(){
115 : tdhock 159 gres <- grep("^\\s*#",src[start-1],perl=TRUE)
116 :     0 == length(gres) && start<=body.begin
117 :     }
118 : tdhock 138 res <- list()
119 :     for(i in seq_along(starts)){
120 :     start <- clines[starts[i]]
121 :     end <- clines[ends[i]]
122 : tdhock 175 lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"
123 : tdhock 138 else if(start==2)"description"
124 :     else if(is.arg()){
125 :     ##twutz: strip leading white spaces and brackets and ,
126 :     arg <- gsub("^[ \t(,]*", "", src[start - 1])
127 :     arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
128 :     ##twutz: remove trailing whitespaces
129 :     arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
130 :     arg <- gsub("...", "\\dots", arg, fix = TRUE)
131 :     paste("item{",arg,"}",sep="")
132 :     } else {
133 :     next;
134 :     }
135 :     res[[lab]] <- decomment(src[start:end])
136 :     }
137 :     res
138 : tdhock 175 },ex=function(){
139 :     test <- function
140 : tdhock 191 ### the description
141 : tdhock 175 (x,
142 :     ### the first argument
143 :     y ##<< another argument
144 :     ){
145 :     5
146 :     ### the return value
147 :     ##seealso<< foobar
148 : tdhock 138 }
149 : tdhock 175 src <- attr(test,"source")
150 :     prefixed.lines(src)
151 :     extract.xxx.chunks(src)
152 :     })
153 : tdhock 138
154 : tdhock 154 extract.xxx.chunks <- function # Extract documentation from a function
155 : tdhock 87 ### Given source code of a function, return a list describing inline
156 :     ### documentation in that source code.
157 : tdhock 154 (src,
158 :     ### The source lines of the function to examine, as a character
159 :     ### vector.
160 :     name.fun="(unnamed function)",
161 : tdhock 87 ### The name of the function/chunk to use in warning messages.
162 : tdhock 154 ...
163 :     ### ignored.
164 : tdhock 95 ){
165 : tdhock 87 res <- list()
166 :     ##details<< For simple functions/arguments, the argument may also be
167 :     ## documented by appending \code{##<<} comments on the same line as the
168 :     ## argument name. Mixing this mechanism with \code{###} comment lines for
169 :     ## the same argument is likely to lead to confusion, as the \code{###}
170 :     ## lines are processed first.
171 :     #arg.pat <- paste("^[^=,#]*?([\\w\\.]+)\\s*([=,].*|\\)\\s*)?",
172 :     # "<<\\s*(\\S.*?)\\s*$",
173 :     # sep="##") # paste avoids embedded trigger fooling the system
174 :     #tw: removed first comma
175 :     arg.pat <- paste("^[^=#]*?([\\w\\.]+)\\s*([=,].*|\\)\\s*)?",
176 :     "<<\\s*(\\S.*?)\\s*$",
177 :     sep="##") # paste avoids embedded trigger fooling the system
178 :    
179 :     skeleton.fields <- c("alias","details","keyword","references","author",
180 :     "note","seealso","value","title","description",
181 :     "describe","end")
182 :     ##details<< Additionally, consecutive sections of \code{##} comment
183 :     ## lines beginning with \code{##}\emph{xxx}\code{<<} (where
184 :     ## \emph{xxx} is one of the fields: \code{alias}, \code{details},
185 :     ## \code{keyword}, \code{references}, \code{author}, \code{note},
186 :     ## \code{seealso}, \code{value}, \code{title} or \code{description})
187 :     ## are accumulated and inserted in the relevant part of the .Rd
188 :     ## file.
189 :     ##
190 :     ## For \code{value}, \code{title}, \code{description} and function
191 :     ## arguments, these \emph{append} to any text from "prefix"
192 :     ## (\code{^### }) comment lines, irrespective of the order in the
193 :     ## source.
194 :     ##
195 :     ## When documenting S4 classes, documentation from \code{details}
196 :     ## sections will appear under a section \code{Objects from the Class}. That
197 :     ## section typically includes information about construction methods
198 :     ## as well as other description of class objects (but note that the
199 :     ## class Slots are documented in a separate section).
200 :    
201 :     ## but this should not appear, because separated by a blank line
202 :     extra.regexp <- paste("^\\s*##(",paste(skeleton.fields,collapse="|"),
203 :     ")<<\\s*(.*)$",sep="")
204 :     cont.re <- "^\\s*##\\s*"
205 :     in.describe <- 0
206 :     first.describe <- FALSE
207 :     k <- 1
208 :     in.chunk <- FALSE
209 :     end.chunk <- function(field,payload)
210 :     {
211 :     if ( "alias" == field ){
212 :     ##note<< \code{alias} extras are automatically split at new lines.
213 :     payload <- gsub("\\n+","\\}\n\\\\alias\\{",payload,perl=TRUE)
214 :     chunk.sep <- "}\n\\alias{"
215 :     } else if ( "keyword" == field ){
216 :     ##keyword<< documentation utilities
217 :     ##note<< \code{keyword} extras are automatically split at white space,
218 :     ## as all the valid keywords are single words.
219 :     payload <- gsub("\\s+","\\}\n\\\\keyword\\{",payload,perl=TRUE)
220 :     chunk.sep <- "}\n\\keyword{"
221 :     } else if ( "title" == field ){
222 :     chunk.sep <- " "
223 :     } else if ( "description" == field ){
224 :     chunk.sep <- "\n"
225 :     } else {
226 :     ##details<< Each separate extra section appears as a new
227 :     ## paragraph except that: \itemize{\item empty sections (no
228 :     ## matter how many lines) are ignored;\item \code{alias} and
229 :     ## \code{keyword} sections have special rules;\item
230 :     ## \code{description} should be brief, so all such sections
231 :     ## are concatenated as one paragraph;\item \code{title} should
232 :     ## be one line, so any extra \code{title} sections are
233 :     ## concatenated as a single line with spaces separating the
234 :     ## sections.}
235 :     chunk.sep <- "\n\n"
236 :     }
237 :     chunk.res <- NULL
238 : tdhock 191 if ( !grepl("^\\s*$",payload,perl=TRUE) )
239 : tdhock 87 chunk.res <-
240 :     if ( is.null(res[[field]]) ) payload
241 :     else paste(res[[field]], payload, sep=chunk.sep)
242 :     invisible(chunk.res)
243 :     }
244 : tdhock 154 while ( k <= length(src) ){
245 :     line <- src[k]
246 : tdhock 191 if ( grepl(extra.regexp,line,perl=TRUE) ){
247 : tdhock 87 ## we have a new extra chunk - first get field name and any payload
248 :     new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
249 :     new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
250 :    
251 :     ##details<< As a special case, the construct \code{##describe<<} causes
252 :     ## similar processing to the main function arguments to be
253 :     ## applied in order to construct a describe block within the
254 :     ## documentation, for example to describe the members of a
255 :     ## list. All subsequent "same line" \code{##<<} comments go into that
256 :     ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
257 :     if ( "describe" == new.field ){
258 :     ##details<< Such regions may be nested, but not in such a way
259 :     ## that the first element in a \code{describe} is another \code{describe}.
260 :     ## Thus there must be at least one \code{##<<} comment between each
261 :     ## pair of \code{##describe<<} comments.
262 :     if ( first.describe ){
263 :     stop("consecutive ##describe<< at line",k,"in",name.fun)
264 :     } else {
265 :     if ( nzchar(new.contents) ){
266 :     if ( is.null(payload) || 0 == nzchar(payload) ){
267 :     payload <- new.contents
268 :     } else {
269 :     payload <- paste(payload,new.contents,sep="\n\n")
270 :     }
271 :     }
272 :     first.describe <- TRUE
273 :     }
274 :     } else if ( "end" == new.field ){
275 :     ##details<< When nested \code{describe} blocks are used, a comment-only
276 :     ## line with \code{##end<<} terminates the current level only; any
277 :     ## other valid \code{##}\emph{xxx}\code{<<} line terminates
278 :     ## all open describe blocks.
279 :     if ( in.describe>0 ){
280 :     ## terminate current \item and \describe block only
281 :     if ( "value" == cur.field && 1 == in.describe ){
282 :     payload <- paste(payload,"}",sep="")
283 :     } else {
284 :     payload <- paste(payload,"}\n}",sep="")
285 :     }
286 :     in.describe <- in.describe-1;
287 :     } else {
288 :     warning("mismatched ##end<< at line ",k," in ",name.fun)
289 :     }
290 :     if ( nzchar(new.contents) ){
291 :     if ( nzchar(payload) ){
292 :     payload <- paste(payload,new.contents,sep="\n")
293 :     } else {
294 :     payload <- new.contents
295 :     }
296 :     }
297 :     } else {
298 :     ## terminate all open \describe blocks (+1 because of open item)
299 :     if ( 0 < in.describe ){
300 :     if ( "value" != cur.field ){ # value is implicit describe block
301 :     payload <- paste(payload,"}",sep="")
302 :     }
303 :     while ( in.describe>0 ){
304 :     payload <- paste(payload,"}",sep="\n")
305 :     in.describe <- in.describe-1;
306 :     }
307 :     }
308 :     ## finishing any existing payload
309 :     if ( in.chunk ) res[[cur.field]] <- end.chunk(cur.field,payload)
310 :     in.chunk <- TRUE
311 :     cur.field <- new.field
312 :     payload <- new.contents
313 :     ##note<< The "value" section of a .Rd file is implicitly a describe
314 :     ## block and \code{##}\code{value}\code{<<} acts accordingly. Therefore
315 :     ## it automatically enables the describe block itemization (##<< after
316 :     ## list entries).
317 :     if ( "value" == new.field ){
318 :     first.describe <- TRUE;
319 :     }
320 :     }
321 : tdhock 191 } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
322 : tdhock 87 ## append this line to current chunk
323 : tdhock 191 if ( !grepl(prefix,line,perl=TRUE) ){
324 : tdhock 87 ##describe<< Any lines with "\code{### }" at the left hand
325 :     ## margin within the included chunks are handled separately,
326 :     ## so if they appear in the documentation they will appear
327 :     ## before the \code{##}\emph{xxx}\code{<}\code{<} chunks.
328 :     ### This one should not appear.
329 :     stripped <- gsub(cont.re,"",line,perl=TRUE)
330 :     if ( nzchar(payload) ){
331 :     payload <- paste(payload,stripped,sep="\n")
332 :     } else {
333 :     payload <- stripped
334 :     }
335 :     }
336 : tdhock 191 } else if ( grepl(arg.pat,line,perl=TRUE) ){
337 : tdhock 87 not.describe <- (0==in.describe && !first.describe)
338 :     if ( in.chunk && not.describe){
339 :     res[[cur.field]] <- end.chunk(cur.field,payload)
340 :     }
341 :     comment <- gsub(arg.pat,"\\3",line,perl=TRUE);
342 :     arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
343 :     in.chunk <- TRUE
344 :     if ( not.describe ){
345 : tdhock 115 ## TDH 2010-06-18 For item{}s in the documentation list names,
346 :     ## we don't need to have a backslash before, so delete it.
347 :     arg <- gsub("^[\\]+","",arg)
348 : tdhock 87 cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
349 :     payload <- comment
350 :     } else {
351 :     ## this is a describe block, so we need to paste with existing
352 :     ## payload as a new \item.
353 :     if ( first.describe ){
354 :     ## for first item, need to add describe block starter
355 :     if ( "value" == cur.field ){
356 :     payload <- paste(payload,"\n",arg,"{",sep="")
357 :     } else {
358 :     payload <- paste(payload,"\\describe{\n",arg,"{",sep="")
359 :     }
360 :     first.describe <- FALSE
361 :     in.describe <- in.describe+1
362 :     } else {
363 :     ## subsequent item - terminate existing and start new
364 :     payload <- paste(payload,"}\n",arg,"{",sep="")
365 :     }
366 :     if ( nzchar(comment) ){
367 :     payload <- paste(payload,comment,sep="")
368 :     }
369 :     }
370 :     } else if ( in.chunk ){
371 :     if ( 0 == in.describe && !first.describe ){
372 :     ## reached an end to current field, but need to wait if in.describe
373 :     res[[cur.field]] <- end.chunk(cur.field,payload)
374 :     in.chunk <- FALSE
375 :     cur.field <- NULL
376 :     payload <- NULL
377 :     }
378 :     }
379 :     k <- k+1
380 :     }
381 :     ## finishing any existing payload
382 :     if ( 0 < in.describe ){
383 :     if ( "value" != cur.field ){ # value is implicit describe block
384 :     payload <- paste(payload,"}",sep="")
385 :     }
386 :     while ( in.describe>0 ){
387 :     payload <- paste(payload,"}",sep="\n")
388 :     in.describe <- in.describe-1;
389 :     }
390 :     }
391 :     if ( in.chunk ) res[[cur.field]] <- end.chunk(cur.field,payload)
392 :     res
393 :     ### Named list of character strings extracted from comments. For each
394 :     ### name N we will look for N\{...\} in the Rd file and replace it
395 :     ### with the string in this list (implemented in modify.Rd.file).
396 :     }
397 :    
398 : kmpont 212 leadingS3generic <- function # check whether function name is an S3 generic
399 :     ### Determines whether a function name looks like an S3 generic function
400 :     (name, ##<< name of function
401 :     env, ##<< environment to search for additional generics
402 :     ...) ##<< ignored here
403 :     {
404 :     ##details<< This function is one of the default parsers, but exposed as
405 :     ## possibly of more general interest. Given a function name of the form
406 :     ## x.y.z it looks for the generic function x applying to objects of class
407 :     ## y.z and also for generic function x.y applying to objects of class z.
408 :     ##
409 :     parts <- strsplit(name, ".", fixed = TRUE)[[1]]
410 :     l <- length(parts)
411 :     if (l > 1) {
412 :     for (i in 1:(l - 1)) {
413 :     ## Look for a generic function (known by the system or defined
414 :     ## in the package) that matches that part of the function name
415 :     generic <- paste(parts[1:i], collapse = ".")
416 :     if (any(generic %in% utils:::getKnownS3generics()) ||
417 :     utils:::findGeneric(generic, env) != "") {
418 :     object <- paste(parts[(i + 1):l], collapse = ".")
419 :     ##details<< Assumes that the first name which matches any known
420 :     ## generics is the target generic function, so if both x and x.y
421 :     ## are generic functions, will assume generic x applying to objects
422 :     ## of class y.z
423 :     ##value<< If a matching generic found returns a list with a single component:
424 :     return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
425 :     }
426 :     }
427 :     }
428 :     ##value<< If no matching generic functions are found, returns an empty list.
429 :     list()
430 :     }
431 :    
432 : tdhock 154 ### Parsers for each function that are constructed automatically. This
433 :     ### is a named list, and each element is a parser function for an
434 :     ### individual object.
435 :     forfun.parsers <-
436 :     list(prefixed.lines=prefixed.lines,
437 :     extract.xxx.chunks=extract.xxx.chunks,
438 :     ## title from first line of function def
439 : tdhock 191 title.from.firstline=function(src,...){
440 : tdhock 195 first <- src[1]
441 :     if(!is.character(first))return(list())
442 :     if(!grepl("#",first))return(list())
443 :     list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
444 : tdhock 154 },
445 :     ## PhG: it is tests/FUN.R!!! I would like more flexibility here
446 :     ## please, let me choose which dir to use for examples!
447 :     ## Get examples for FUN from the file tests/FUN.R
448 :     examples.from.testfile=function(name,...){
449 :     tsubdir <- getOption("inlinedocs.exdir")
450 :     if (is.null(tsubdir)) tsubdir <- "tests" # Default value
451 :     tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
452 :     if(file.exists(tfile))
453 : tdhock 185 list(examples=readLines(tfile))
454 : tdhock 154 else list()
455 :     },
456 :     definition.from.source=function(doc,src,...){
457 :     def <- doc$definition
458 :     is.empty <- function(x)is.null(x)||x==""
459 :     if(is.empty(def) && !is.empty(src))
460 : tdhock 185 list(definition=src)
461 : tdhock 154 else list()
462 :     })
463 :    
464 :     ### List of Parser Functions that can be applied to any object.
465 :     forall.parsers <-
466 :     list(## Fill in author from DESCRIPTION and titles.
467 :     author.from.description=function(desc,...){
468 :     list(author=desc[,"Maintainer"])
469 :     },
470 :     ## The format section sometimes causes problems, so erase it.
471 :     erase.format=function(...){
472 :     list(format="")
473 :     },
474 :     ## Convert the function name to a title.
475 :     title.from.name=function(name,doc,...){
476 :     if("title"%in%names(doc))list() else
477 :     list(title=gsub("[._]"," ",name))
478 :     },
479 :     ## PhG: here is what I propose for examples code in the 'ex' attribute
480 :     examples.in.attr = function (name, o, ...) {
481 :     ex <- attr(o, "ex")
482 :     if (!is.null(ex)) {
483 :     ## Special case for code contained in a function
484 :     if (inherits(ex, "function")) {
485 :     ## If source is available, start from there
486 :     src <- attr(ex, "source")
487 :     if (!is.null(src)) {
488 :     ex <- src
489 :     } else { ## Use the body of the function
490 :     ex <- deparse(body(ex))
491 :     }
492 :     ## Eliminate leading and trailing code
493 :     ex <- ex[-c(1, length(ex))]
494 : tdhock 163 ## all the prefixes
495 :     ex <- kill.prefix.whitespace(ex)
496 : tdhock 154 ## Add an empty line before and after example
497 :     ex <- c("", ex, "")
498 :     }
499 : tdhock 185 list(examples = ex)
500 : tdhock 154 } else list()
501 : tdhock 200 },collapse=function(doc,...){
502 :     L <- lapply(doc,paste,collapse="\n")
503 :     L$.overwrite <- TRUE
504 :     L
505 : kmpont 212 },tag.s3methods=leadingS3generic
506 : tdhock 196 )
507 : tdhock 154
508 :     ### List of parser functions that operate on single objects. This list
509 :     ### is useful for testing these functions.
510 : tdhock 196 lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
511 : tdhock 154 f <- function # title
512 :     ### description
513 :     (x, ##<< arg x
514 :     y
515 :     ### arg y
516 :     ){
517 :     ##value<< a list with elements
518 :     list(x=x, ##<< original x value
519 :     y=y, ##<< original y value
520 :     sum=x+y) ##<< their sum
521 :     ##end<<
522 :     }
523 :     src <- attr(f,"source")
524 :     lonely$extract.xxx.chunks(src)
525 :     lonely$prefixed.lines(src)
526 : tdhock 196 })
527 : tdhock 154
528 :     extra.code.docs <- function # Extract documentation from code chunks
529 :     ### Parse R code to extract inline documentation from comments around
530 :     ### each function. These are not able to be retreived simply by
531 :     ### looking at the "source" attribute. This is a Parser Function that
532 :     ### can be used in the parser list of package.skeleton.dx(). TODO:
533 :     ### Modularize this into separate Parsers Functions for S4 classes,
534 :     ### prefixes, ##<<blocks, etc. Right now it is not very clean!
535 :     (code,
536 :     ### Code lines in a character vector containing multiple R objects to
537 :     ### parse for documentation.
538 :     objs,
539 :     ### The objects defined in the code.
540 :     ...
541 :     ### ignored
542 :     ){
543 :     parsed <- extract.file.parse(code)
544 :     extract.docs.try <- function(o,on)
545 :     {
546 :     ## Note: we could use parsed information here too, but that
547 :     ## would produce different results for setMethodS3 etc.
548 :     doc <- list()
549 :     if ( !is.null(parsed[[on]]) ){
550 :     if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
551 : tdhock 185 doc$definition <- paste(parsed[[on]]@code)
552 : tdhock 154 }
553 :     if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
554 :     doc$description <- parsed[[on]]@description
555 :     }
556 : kmpont 212 ## if ( "setMethodS3" == parsed[[on]]@created ){
557 :     ## gen <- leadingS3generic(on,topenv())
558 :     ## if ( 0 < length(gen) ){
559 :     ## doc$.s3method <- gen$.s3method
560 :     ## cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
561 :     ## }
562 :     ## }
563 : tdhock 154 }
564 :     if("title" %in% names(doc) && !"description" %in% names(doc) ){
565 :     ## For short functions having both would duplicate, but a
566 :     ## description is required. Therefore automatically copy title
567 :     ## across to avoid errors at package build time.
568 :     doc$description <- doc$title
569 :     }
570 :     doc
571 :     }
572 :     extract.docs <- function(on){
573 :     res <- try({o <- objs[[on]]
574 :     extract.docs.try(o, on)},FALSE)
575 :     if(class(res)=="try-error"){
576 :     cat("Failed to extract docs for: ",on,"\n\n")
577 :     list()
578 :     } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
579 :     NULL
580 :     } else if(0 == length(res) && "function" %in% class(o)
581 :     && 1 == length(osource <- attr(o,"source"))
582 : tdhock 191 && grepl(paste("UseMethod(",on,")",sep="\""),osource)
583 : tdhock 154 ){
584 :     ## phew - this should only pick up R.oo S3 generic definitions like:
585 :     ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
586 :     NULL
587 :     } else res
588 :     }
589 :     doc.names <- names(objs)
590 :     res <- sapply(doc.names,extract.docs,simplify=FALSE)
591 :     ## Special processing for S4 classes as they do not appear in normal ls()
592 :     for ( nn in names(parsed) ){
593 :     if ( parsed[[nn]]@created == "setClass" ){
594 :     S4class.docs <- extract.docs.setClass(parsed[[nn]])
595 :     docname <- paste(nn,"class",sep="-")
596 :     if ( is.null(res[[docname]]) ){
597 :     res[[docname]] <- S4class.docs
598 :     doc.names <- c(doc.names,docname)
599 :     } else {
600 :     stop(nn," appears as both S4 class and some other definition")
601 :     }
602 :     }
603 :     }
604 :     inherit.docs <- function(on){
605 :     in.res <- res[[on]]
606 :     if ( !is.null(parsed[[on]]) ){
607 :     for ( parent in parsed[[on]]@parent ){
608 :     if ( !is.na(parent) ){
609 :     if ( is.null(in.res) ){
610 :     in.res <- res[[parent]]
611 :     } else if ( parent %in% names(res) ){
612 :     parent.docs <- res[[parent]]
613 :     for ( nn in names(parent.docs) ){
614 :     if ( !nn %in% names(in.res) ){
615 :     in.res[[nn]] <- parent.docs[[nn]]
616 :     }
617 :     }
618 :     }
619 :     }
620 :     }
621 :     }
622 :     invisible(in.res)
623 :     }
624 :     all.done <- FALSE
625 :     while ( !all.done ){
626 :     res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
627 :     all.done <- identical(res1,res)
628 :     res <- res1
629 :     }
630 :     ## now strip out any generics (which have value NULL in res):
631 :     res.not.null <- sapply(res,function(x){!is.null(x)})
632 :     if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
633 :     res <- res[res.not.null]
634 :     }
635 :     res
636 :     ### named list of lists, one for each object to document.
637 :     }
638 :    
639 :     ### List of parsers to use by default with package.skeleton.dx.
640 :     default.parsers <-
641 :     c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
642 :     sapply(forfun.parsers,forfun),
643 :     edit.package.file=function(desc,...){
644 :     in.details <- setdiff(colnames(desc),"Description")
645 : tdhock 185 details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
646 : tdhock 154 L <-
647 :     list(list(title=desc[,"Title"],
648 :     description=desc[,"Description"],
649 : tdhock 195 `tabular{ll}`=details))
650 : tdhock 154 names(L) <- paste(desc[,"Package"],"-package",sep="")
651 :     L
652 : tdhock 197 },
653 :     sapply(forall.parsers,forall)
654 : tdhock 186 )
655 : tdhock 154
656 : tdhock 87 setClass("DocLink", # Link documentation among related functions
657 :     ### The \code{.DocLink} class provides the basis for hooking together
658 :     ### documentation of related classes/functions/objects. The aim is that
659 : kmpont 212 ### documentation sections missing from the child are inherited from
660 :     ### the parent class.
661 : tdhock 87 representation(name="character", ##<< name of object
662 :     created="character", ##<< how created
663 :     parent="character", ##<< parent class or NA
664 :     code="character", ##<< actual source lines
665 :     description="character") ##<< preceding description block
666 :     )
667 :    
668 :     extract.file.parse <- function # File content analysis
669 :     ### Using the base \code{\link{parse}} function, analyse the file to link
670 :     ### preceding "prefix" comments to each active chunk. Those comments form
671 :     ### the default description for that chunk. The analysis also looks for
672 :     ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
673 :     ### calls in order to link the documentation of those properly.
674 :     (code
675 :     ### Lines of R source code in a character vector - note that any
676 :     ### nested \code{source} statements are \emph{ignored} when scanning
677 :     ### for class definitions.
678 :     ){
679 :     res <- list()
680 :     old.opt <- options(keep.source=TRUE)
681 :     parsed <- try(parse(text=code))
682 :     options(old.opt)
683 :     if ( inherits(parsed,"try-error") ){
684 :     stop("parse failed with error:\n",parsed)
685 :     }
686 :     chunks <- attr(parsed,"srcref")
687 :     last.end <- 0
688 :     for ( k in 1:length(parsed) ){
689 :     start <- chunks[[k]][1]
690 :     ##details<< If the definition chunk does not contain a
691 :     ## description, any immediately preceding sequence consecutive
692 :     ## "prefix" lines will be used instead.
693 :     default.description <- NULL
694 :     while ( start > last.end+1
695 : tdhock 191 && grepl(prefix,code[start-1],perl=TRUE) ){
696 : tdhock 87 start <- start-1
697 :     }
698 :     if ( start < chunks[[k]][1] ){
699 :     default.description <- decomment(code[start:(chunks[[k]][1]-1)])
700 :     } else {
701 :     default.description <- NA_character_;
702 :     }
703 :     ##details<< Class and method definitions can take several forms,
704 :     ## determined by expression type: \describe{
705 :     ## \item{assignment (<-)}{Ordinary assignment of value/function;}
706 :     ## \item{setClass}{Definition of S4 class;}
707 :     ## \item{setConstructorS3}{Definition of S3 class using R.oo package;}
708 :     ## \item{setMethodS3}{Definition of method for S3 class using R.oo package.}}
709 :     ## Additionally, the value may be a name of a function defined elsewhere,
710 :     ## in which case the documentation should be copied from that other definition.
711 :     ## This is handled using the concept of documentation links.
712 :     lang <- parsed[[k]]
713 :     chars <- as.character(lang)
714 :     expr.type <- chars[1]
715 :     parent <- NA_character_
716 :    
717 :     if ( expr.type == "<-" || expr.type == "setConstructorS3" || expr.type == "setClass" ){
718 :     object.name <- chars[2]
719 :     ## If the function definition is not embedded within the call, then
720 :     ## the parent is that function. Test whether the the third value
721 :     ## looks like a name and add it to parents if so.
722 : tdhock 191 if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
723 : tdhock 87 parent <- chars[3]
724 :     }
725 :     res[[object.name]] <- new("DocLink",name=object.name,
726 :     created=expr.type,
727 :     parent=parent,
728 :     code=paste(chunks[[k]],sep=""),
729 :     description=default.description)
730 :     } else if ( expr.type == "setMethodS3" ){
731 :     ##details<< The \code{setMethodS3} calls introduce additional
732 :     ## complexity: they will define an additional S3 generic (which
733 :     ## needs documentation to avoid warnings at package build time)
734 :     ## unless one already exists. This also is handled by "linking"
735 :     ## documentation. A previously unseen generic is linked to the
736 :     ## first defining instances, subsequent definitions of that generic
737 :     ## also link back to the first defining instance.
738 :     generic.name <- chars[2]
739 :     object.name <- paste(generic.name,chars[3],sep=".")
740 :     if ( is.null(res[[generic.name]]) ){
741 :     generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")
742 :     res[[generic.name]] <- new("DocLink",
743 :     name=generic.name,
744 :     created=expr.type,
745 :     parent=object.name,
746 :     code=NA_character_,
747 :     description=generic.desc)
748 :     } else {
749 :     parent <- res[[generic.name]]@parent
750 :     }
751 :     ## If the function definition is not embedded within the call, then
752 :     ## the parent is that function. Test whether the the fourth value
753 :     ## looks like a name and add it to parents if so.
754 : tdhock 191 if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
755 : tdhock 87 parent <- c(chars[4],parent)
756 :     }
757 :     res[[object.name]] <- new("DocLink",name=object.name,
758 :     created=expr.type,
759 :     parent=parent,
760 :     code=paste(chunks[[k]],sep=""),
761 :     description=default.description)
762 :     } else {
763 :     ## Not sure what to do with these yet. Need to deal with setMethod, setAs etc.
764 :     }
765 :     }
766 :     invisible(res)
767 :     ### Returns an invisible list of .DocLink objects.
768 :     }
769 :    
770 :     extract.docs.setClass <- function # S4 class inline documentation
771 :     ### Using the same conventions as for functions, definitions of S4 classes
772 :     ### in the form \code{setClass("classname",\dots)} are also located and
773 :     ### scanned for inline comments.
774 : tdhock 93 (doc.link
775 : tdhock 87 ### DocLink object as created by \code{\link{extract.file.parse}}.
776 :     ### Note that \code{source} statements are \emph{ignored} when scanning for
777 :     ### class definitions.
778 : tdhock 93 ){
779 : tdhock 87 chunk.source <- doc.link@code
780 :     ##details<<
781 :     ## Extraction of S4 class documentation is currently limited to expressions
782 :     ## within the source code which have first line starting with
783 :     ## \code{setClass("classname"}. These are located from the source file
784 :     ## (allowing also for white space around the \code{setClass} and \code{(}).
785 :     ## Note that \code{"classname"} must be a quoted character string;
786 :     ## expressions returning such a string are not matched.
787 :     class.name <- doc.link@name
788 :    
789 :     ##details<< For class definitions, the slots (elements of the
790 :     ## \code{representation} list) fill the role of function
791 :     ## arguments, so may be documented by \code{##<<} comments on
792 :     ## the same line or \code{### } comments at the beginning of the
793 :     ## following line.
794 :     f.n <- paste(class.name,"class",sep="-")
795 : tdhock 154 docs <- extract.xxx.chunks(chunk.source,f.n)
796 : tdhock 138 ## also apply source parsing functions that I separated out into
797 :     ## separate functions
798 :     docs <- combine(docs,lonely$prefixed.lines(chunk.source))
799 :     docs$title <- lonely$title.from.firstline(chunk.source)
800 : tdhock 87 ##details<<
801 :     ## The class definition skeleton includes an \code{Objects from the Class}
802 :     ## section, to which any \code{##details<<} documentation chunks are
803 :     ## written. It is given a vanilla content if there are no specific
804 :     ## \code{##details<<} documentation chunks.
805 :     if ( is.null(docs[["details"]]) ){
806 :     docs[["details"]] <-
807 :     paste("Objects can be created by calls of the form \\code{new(",
808 :     class.name," ...)}",sep="")
809 :     }
810 :     docs[["section{Objects from the Class}"]] <- docs[["details"]]
811 :     ## seealso has a skeleton line not marked by ~ .. ~, so have to suppress
812 :     if ( is.null(docs[["seealso"]]) ){
813 :     docs[["seealso"]] <- ""
814 :     }
815 :     if ( is.null(docs[["alias"]]) ){
816 :     docs[["alias"]] <- class.name
817 :     }
818 :     if ( is.null(docs[["description"]]) ){
819 :     docs[["description"]] <- doc.link@description
820 :     }
821 :     invisible(docs)
822 :     }
823 : tdhock 105
824 : tdhock 109 apply.parsers <- function
825 :     ### Parse code to r objs, then run all the parsers and return the
826 :     ### documentation list.
827 : tdhock 105 (code,
828 :     ### Character vector of code lines.
829 : tdhock 109 parsers=default.parsers,
830 : tdhock 105 ### List of Parser Functions.
831 : tdhock 109 verbose=FALSE,
832 : tdhock 105 ### Echo names of Parser Functions?
833 :     ...
834 :     ### Additional arguments to pass to Parser Functions.
835 :     ){
836 :     e <- new.env()
837 : kmpont 212 ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
838 :     ## Error in assignClassDef(Class, classDef, where) :
839 :     ## Class "DocLink" has a locked definition in package "inlinedocs"
840 :     ## Traced to "where" argument in setClassDef which defaults to topenv()
841 :     ## which in turn is inlinedocs when processing inlinedocs package, hence
842 :     ## the clash. The following works (under R 2.12.2), so that the topenv()
843 :     ## now finds e before finding the inlinedocs environment.
844 : kmpont 213 old <- options(keep.source=TRUE,topLevelEnvironment=e)
845 : tdhock 109 on.exit(options(old))
846 : tdhock 110 exprs <- parse(text=code)
847 : tdhock 248 ## TDH 2011-04-07 set this so that no warnings about creating a fake
848 :     ## package when we try to process S4 classes defined in code
849 :     e$.packageName <- "inlinedocs.processor"
850 : tdhock 152 for (i in exprs){
851 : tdhock 248 ## TDH 2011-04-07 Disable this tryCatch since it makes it harder
852 :     ##to debug errors/warnings in the evaluated code
853 :    
854 :     ##tryCatch({
855 :     eval(i, e)
856 :     ##},error=function(e){
857 : tdhock 152 ##print(e)
858 : tdhock 248 ##})
859 : tdhock 152 }
860 : tdhock 105 objs <- sapply(ls(e),get,e,simplify=FALSE)
861 :    
862 :     docs <- list()
863 : phgrosjean 108
864 : tdhock 109 ## apply parsers in sequence to code and objs
865 : tdhock 105 for(i in seq_along(parsers)){
866 :     N <- names(parsers[i])
867 :     if(verbose){
868 :     if(is.character(N) && N!=""){
869 :     cat(N," ",sep="")
870 :     }else cat('. ')
871 :     }
872 :     p <- parsers[[i]]
873 :     ## This is the argument list that each parser receives:
874 : tdhock 200 L <- p(code=code,objs=objs,docs=docs,env=e,...)
875 : tdhock 105 docs <- combine(docs,L)
876 :     }
877 : tdhock 196 ## post-process to collapse all character vectors
878 :     for(i in seq_along(docs)){
879 :     for(j in seq_along(docs[[i]])){
880 : tdhock 198 if(names(docs[[i]])[j]!=".s3method")
881 : tdhock 196 docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
882 :     }
883 :     }
884 : tdhock 105 if(verbose)cat("\n")
885 :     docs
886 :     ### A list of extracted documentation from code.
887 :     }
888 : tdhock 109
889 : tdhock 138 ### Names of Parser Functions that operate on the desc arg.
890 :     descfile.names <- c("author.from.description","edit.package.file")
891 :    
892 :     ### Names of Parser Functions that do NOT use the desc arg.
893 :     non.descfile.names <-
894 :     names(default.parsers)[!names(default.parsers)%in%descfile.names]
895 :    
896 : tdhock 118 ### Parsers that operate only on R code, independently of the
897 :     ### description file.
898 : tdhock 138 nondesc.parsers <- default.parsers[non.descfile.names]
899 : tdhock 118
900 : tdhock 209 extract.docs.file <- structure(function
901 : tdhock 109 ### Apply all parsers relevant to extract info from just 1 code file.
902 :     (f,
903 :     ### File name of R code to read and parse.
904 : tdhock 203 parsers=NULL,
905 : tdhock 109 ### Parser Functions to use to parse the code and extract
906 :     ### documentation.
907 :     ...
908 :     ### Other arguments to pass to Parser Functions.
909 :     ){
910 : tdhock 203 if(is.null(parsers))parsers <- nondesc.parsers
911 : tdhock 109 apply.parsers(readLines(f),parsers,verbose=FALSE,...)
912 : tdhock 209 },ex=function(){
913 :     f <- system.file("silly","R","silly.R",package="inlinedocs")
914 : tdhock 248 extract.docs.file(f)
915 : tdhock 209 })
916 : tdhock 248

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