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Diff of /pkg/inlinedocs/R/parsers.R

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revision 109, Mon Jun 7 08:42:15 2010 UTC revision 196, Fri Feb 18 12:52:48 2011 UTC
# Line 1  Line 1 
1    ### 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      toadd <- !names(y)%in%names(x)
11      toup <- names(y)[!toadd]
12      ##if("doc"%in%names(x))return(x$doc)
13      ##if("doc"%in%names(y))return(y$doc)
14      x[names(y)[toadd]] <- y[toadd]
15      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
16      return(x)
17    ### A list, same type as x, but with added elements from y.
18    }
19    
20    ### Prefix for code comments used with grep and gsub.
21    prefix <- "^[ \t]*###[ \t]"
22    
23    decomment <- function
24    ### Remove comment prefix and join lines of code to form a
25    ### documentation string.
26    (comments
27    ### Character vector of prefixed comment lines.
28     ){
29      gsub(prefix,"",comments)
30    ### String without prefixes or newlines.
31    }
32    
33    forall <- function
34  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
35  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
36  ### documentation list.  ### documentation list.
 forall <- function  
37  (FUN,  (FUN,
38  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
39   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 9  Line 41 
41  ### is.function. subfun(x)==TRUE means FUN will be applied to x and  ### is.function. subfun(x)==TRUE means FUN will be applied to x and
42  ### the result will be returned.  ### the result will be returned.
43   ){   ){
44    function(objs,docs,...){    FUN <- FUN
45      f <- function(objs,docs,...){
46      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
47      L <- list()      L <- list()
48        on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
49      for(N in names(docs)){      for(N in names(docs)){
50        o <- objs[[N]]        o <- objs[[N]]
51        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=attr(o,"source"),
52                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
53      }      }
54        on.exit()## remove warning message
55      L      L
56    }    }
57      class(f) <- c("allfun","function")
58      f
59  ### A Parser Function.  ### A Parser Function.
60  }  }
61    
62    ### Print method for functions constructed using forall.
63    print.allfun <- function(x,...){
64      e <- environment(x)
65      cat("Function to apply to every element.\nselector:")
66      print(e$subfun)
67      cat("processor:")
68      print(e$FUN)
69    }
70    
71  ### For each function in the package, do something.  ### For each function in the package, do something.
72  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
73    
74  ### Parsers for each object/function that are constructed  kill.prefix.whitespace <- function
75  ### automatically. This is a named list, each element is a list of 2  ### Figure out what the whitespace preceding the example code is, and
76  ### elements: forfun/forall, then a parser function for an individual  ### then delete that from every line.
77  ### object.  (ex
78  forall.parsers <-  ### character vector of example code lines.
79    list(## Extract lots of info from normal functions.   ){
80         parsefun=list(forfun,function(src,name,...){    tlines <- gsub("\\s*","",ex)
81           extract.docs.fun(src,name)    ##tlines <- gsub("#.*","",tlines)
82         }),    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
83         ## Fill in author from DESCRIPTION and titles.    FIND <- prefixes[which.min(nchar(prefixes))]
84         author.from.description=list(forall,function(desc,...){    ## Eliminate leading tabulations or 2/4 spaces
85           list(author=desc[,"Maintainer"])    sub(FIND, "", ex)
86         }),  ### Character vector of code lines with preceding whitespace removed.
87         ## The format section sometimes causes problems, so erase it.  }
88         erase.format=list(forall,function(...){  
89           list(format="")  examples.after.return <- function
90         }),  ### Get examples from inline definitions after return()
91         ## Convert the function name to a title.  ### PhG: this does not work well! Think of these situations:
92         title.from.name=list(forall,function(name,doc,...){  ### 1) You have multiple return() in the code of your function,
93           if("title"%in%names(doc))list() else  ### 2) You have return() appearing is some example code, ...
94           list(title=gsub("[._]"," ",name))  ### I can hardly propose a hack here. The whole code of the function
95         }),  ### must be parsed, and one must determine which one is the last line
96         # PhG: it is tests/FUN.R!!! I would like more flexibility here  ### of code that is actually executed.
97             # please, let me choose which dir to use for examples!  ###
98             ## Get examples for FUN from the file tests/FUN.R  ### I make two propositions here
99         examples.from.testfile=list(forfun,function(name,...){  ### 1) to keep the same mechanism that has the advantage of simplicity
100           tsubdir <- getOption("inlinedocs.exdir")  ###    but to use a special tag
101                   if (is.null(tsubdir)) tsubdir <- "tests"       # Default value  ###    ##examples<< or #{{{examples to separate
102                   tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))  ###    function code from examples explicitly, and
103           if(file.exists(tfile))  ### 2) to place the example in an "ex" attribute
104             list(examples=paste(readLines(tfile),collapse="\n"))  ###    attached to the function
105           else list()  ###    (see next parser). That solution will be also interesting for
106         }),  ###    documenting datasets, something not done yet by inlinedocs!
107         ## Get examples from inline definitions after return()  (src,name="",...) {
108             # PhG: this does not work well! Think at these situations:    ## Look for the examples mark
109             # 1) You have multiple return() in the code of your function,    m <- grep("^\\s*(##examples<<|#\\{\\{\\{examples)", src)
            # 2) You have return() appearing is some example code, ...  
            # I can hardly propose a hack here. The whole code of the function  
            # must be parsed, and one must determine which one is the last line  
            # of code that is actually executed.  
            #  
            # I make two propositions here  
            # 1) to keep the same mechanism that has the advantage of simplicity  
            #    but to use a special tag ##examples<< or #{{{examples to separate  
            #    function code from examples explicitly, and  
            # 2) to place the example in an "ex" attribute attached to the function  
            #    (see next parser). That solution will be also interesting for  
            #    documenting datasets, something not done yet by inlinedocs!  
            examples.after.return = list(forfun, function(name, src, ...) {  
                         # Look for the examples mark  
                         m <- grep("##examples<<|#\\{\\{\\{examples", src)  
110                          if (!length(m)) return(list())                          if (!length(m)) return(list())
111                          if (length(m) > 1)                          if (length(m) > 1)
112                                  warning("More than one examples tag for ", name, ". Taking the last one")      warning("More than one examples tag for ", name,
113                ". Taking the last one")
114                          m <- m[length(m)]                          m <- m[length(m)]
115                          # Look for the lines containing return value comments just before    ## Look for the lines containing return value comments just before
116                          r <- grep("\\s*### ", src[1:(m-1)])                          r <- grep("\\s*### ", src[1:(m-1)])
117                          if (!length(r)) {                          if (!length(r)) {
118                                  value <- NULL                                  value <- NULL
119                          } else {                          } else {
120                                  # Only take consecutive lines before the mark        ## Only take consecutive lines before the mark
121                                  keep <- rev((m - rev(r)) == 1:length(r))                                  keep <- rev((m - rev(r)) == 1:length(r))
122                                  if (!any(keep)) {                                  if (!any(keep)) {
123                                          value <- NULL                                          value <- NULL
# Line 93  Line 125 
125                                          value <- decomment(src[r[keep]])                                          value <- decomment(src[r[keep]])
126                                  }                                  }
127                          }                          }
128                          # Collect now the example code beneath the mark    ## Collect now the example code beneath the mark
129                          ex <- src[(m + 1):(length(src) - 1)]                          ex <- src[(m + 1):(length(src) - 1)]
130                          # Possibly eliminate a #}}} tag    ## Possibly eliminate a #}}} tag
131                          ex <- ex[!grepl("#}}}", ex)]                          ex <- ex[!grepl("#}}}", ex)]
132                          # Eliminate leading tabulations or four spaces    ## Eliminate leading tabulations or four spaces
133                          ex <- sub("^\t|    ", "", ex)    ex <- kill.prefix.whitespace(ex)
134                          # Add an empty line before and after example    ## Add an empty line before and after example
135                          ex <- c("", ex, "")                          ex <- c("", ex, "")
136                          # Return examples and value    ## Return examples and value
137                          list(examples = paste(ex, collapse = "\n"), value = value)    list(examples = ex, value = value)
            }),  
            # PhG: here is what I propose for examples code in the 'ex' attribute  
            examples.in.attr = list(forfun, function (name, o, ...) {  
                         ex <- attr(o, "ex")  
                         if (!is.null(ex)) {  
                                 # Special case for code contained in a function  
                                 if (inherits(ex, "function")) {  
                                         # If source is available, start from there  
                                         src <- attr(ex, "source")  
                                         if (!is.null(src)) {  
                                                 ex <- src  
                                         } else { # Use the body of the function  
                                                 ex <- deparse(body(ex))  
                                         }  
                                         # Eliminate leading and trailing code  
                                         ex <- ex[-c(1, length(ex))]  
                                         # Eliminate leading tabulations or four spaces  
                                         ex <- sub("^\t|    ", "", ex)  
                                         # Add an empty line before and after example  
                                         ex <- c("", ex, "")  
                                 }  
                                 list(examples = paste(ex, collapse = "\n"))  
                         } else list()  
            }))  
   
 ### List of parser functions that operate on single objects. This list  
 ### is useful for testing these functions, ie  
 ### lonely$parsefun(attr(extract.docs.file,"source"),"extract.docs.file")  
 lonely <- sapply(forall.parsers,function(L)L[[2]])  
   
 extra.code.docs <- function # Extract documentation from code chunks  
 ### Parse R code to extract inline documentation from comments around  
 ### each function. These are not able to be retreived simply by  
 ### looking at the "source" attribute. This is a Parser Function that  
 ### can be used in the parser list of package.skeleton.dx(). TODO:  
 ### Modularize this into separate Parsers Functions for S4 classes,  
 ### prefixes, ##<<blocks, etc. Right now it is not very clean!  
 (code,  
 ### Code lines in a character vector containing multiple R objects to  
 ### parse for documentation.  
  objs,  
 ### The objects defined in the code.  
  ...  
 ### ignored  
  ){  
   parsed <- extract.file.parse(code)  
   extract.docs.try <- function(o,on)  
     {  
       ## Note: we could use parsed information here too, but that  
       ## would produce different results for setMethodS3 etc.  
       doc <- list()  
       if ( !is.null(parsed[[on]]) ){  
         if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics  
           doc$definition <- paste(parsed[[on]]@code,collapse="\n")  
         }  
         if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){  
           doc$description <- parsed[[on]]@description  
         }  
         if ( "setMethodS3" == parsed[[on]]@created ){  
           # PhG: this may be wrong! It does not catch correctly how the method  
                   # must be splitted in case of methods containing dots. for instance,  
                   # as.data.frame.matrix must be split into: m1 = as.data.frame and  
                   # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!  
                   pattern <- "^([^\\.]+)\\.(.*)$"  
           doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),  
               m2 <- gsub(pattern,"\\2",on,perl=TRUE))  
           if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){  
                           m1 <- paste("`",m1,"`",sep="")  
           }  
           cat("S3method(",m1,",",m2,")\n",sep="")  
         }  
       }  
       if("title" %in% names(doc) && !"description" %in% names(doc) ){  
         ## For short functions having both would duplicate, but a  
         ## description is required. Therefore automatically copy title  
         ## across to avoid errors at package build time.  
         doc$description <- doc$title  
       }  
       doc  
     }  
   extract.docs <- function(on){  
     res <- try({o <- objs[[on]]  
                 extract.docs.try(o, on)},FALSE)  
     if(class(res)=="try-error"){  
       cat("Failed to extract docs for: ",on,"\n\n")  
       list()  
     } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){  
       NULL  
     } else if(0 == length(res) && "function" %in% class(o)  
               && 1 == length(osource <- attr(o,"source"))  
               && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))  
               ){  
       ## phew - this should only pick up R.oo S3 generic definitions like:  
       ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"  
       NULL  
     } else res  
   }  
   doc.names <- names(objs)  
   res <- sapply(doc.names,extract.docs,simplify=FALSE)  
   ## Special processing for S4 classes as they do not appear in normal ls()  
   for ( nn in names(parsed) ){  
     if ( parsed[[nn]]@created == "setClass" ){  
       S4class.docs <- extract.docs.setClass(parsed[[nn]])  
       docname <- paste(nn,"class",sep="-")  
       if ( is.null(res[[docname]]) ){  
         res[[docname]] <- S4class.docs  
         doc.names <- c(doc.names,docname)  
       } else {  
         stop(nn," appears as both S4 class and some other definition")  
       }  
     }  
   }  
   inherit.docs <- function(on){  
     in.res <- res[[on]]  
     if ( !is.null(parsed[[on]]) ){  
       for ( parent in parsed[[on]]@parent ){  
         if ( !is.na(parent) ){  
           if ( is.null(in.res) ){  
             in.res <- res[[parent]]  
           } else if ( parent %in% names(res) ){  
             parent.docs <- res[[parent]]  
             for ( nn in names(parent.docs) ){  
               if ( !nn %in% names(in.res) ){  
                 in.res[[nn]] <- parent.docs[[nn]]  
               }  
             }  
           }  
         }  
       }  
     }  
     invisible(in.res)  
   }  
   all.done <- FALSE  
   while ( !all.done ){  
     res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)  
     all.done <- identical(res1,res)  
     res <- res1  
   }  
   ## now strip out any generics (which have value NULL in res):  
   res.not.null <- sapply(res,function(x){!is.null(x)})  
   if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){  
     res <- res[res.not.null]  
   }  
   res  
 ### named list of lists, one for each object to document.  
138  }  }
139    
140  ### List of parsers to use by default with package.skeleton.dx.  prefixed.lines <- structure(function(src,...){
141  default.parsers <-  ### The primary mechanism of inline documentation is via consecutive
142    c(extra.code.docs=extra.code.docs,  ### groups of lines matching the specified prefix regular expression
143      sapply(forall.parsers,function(L)L[[1]](L[[2]])),  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
144      edit.package.file=function(desc,...){  ### collected as follows into documentation sections:\describe{
145        in.details <- setdiff(colnames(desc),"Description")  ### \item{description}{group starting at line 2 in the code}
146        details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",  ### \item{arguments}{group following each function argument}
147                               sep=""),collapse="\n")  ### \item{value}{group ending at the penultimate line of the code}}
148        L <-  ### These may be added to by use of the \code{##<<} constructs
149          list(list(title=desc[,"Title"],  ### described below.
150                    description=desc[,"Description"],    clines <- grep(prefix,src)
151                    `tabular{ll}`=details,    if(length(clines)==0)return(list())
                   author=desc[,"Maintainer"]))  
       names(L) <- paste(desc[,"Package"],"-package",sep="")  
       L  
     })  
   
 extract.docs.fun <- function # Extract documentation from a function  
 ### Given source code of a function, return a list describing inline  
 ### documentation in that source code.  
 (code,  
 ### The function to examine.  
  name.fun  
 ### The name of the function/chunk to use in warning messages.  
  ){  
   res <- list()  
   clines <- grep(prefix,code)  
   if(length(grep("#",code[1]))){  
     res$title <- gsub("[^#]*#\\s*(.*)","\\1",code[1],perl=TRUE)  
   }  
   if(length(clines) > 0){  
     ##details<<  
     ## The primary mechanism is that consecutive groups of lines matching  
     ## the specified prefix regular expression "\code{^### }" (i.e. lines  
     ## beginning with "\code{### }") are collected  
     ## as follows into documentation sections:\describe{  
     ## \item{description}{group starting at line 2 in the code}  
     ## \item{arguments}{group following each function argument}  
     ## \item{value}{group ending at the penultimate line of the code}}  
     ## These may be added to by use of the \code{##<<} constructs described  
     ## below.  
152      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
153      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
154      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
155      ## detect body of function using paren matching
156      code <- gsub("#.*","",src)
157      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
158      parens <- f("(")-f(")")
159      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
160      if(length(body.begin)==0)body.begin <- 1 ## rare cases
161      is.arg <- function(){
162        gres <- grep("^\\s*#",src[start-1],perl=TRUE)
163        0 == length(gres) && start<=body.begin
164      }
165      res <- list()
166      for(i in seq_along(starts)){      for(i in seq_along(starts)){
167        start <- clines[starts[i]]        start <- clines[starts[i]]
168        end <- clines[ends[i]]        end <- clines[ends[i]]
169        lab <- if(end+1==length(code))"value"      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"
170        else if(start==2)"description"        else if(start==2)"description"
171        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
172           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
173           #arg <- gsub("^([^=,]*)[=,].*","\\1",arg)        arg <- gsub("^[ \t(,]*", "", src[start - 1])
          #arg <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots  
                  arg <- gsub("^[ \t(,]*", "", code[start - 1])  #twutz: strip leading white spaces and brackets and ,  
174                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
175                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
176          arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
177                   arg <- gsub("...", "\\dots", arg, fix = TRUE)                   arg <- gsub("...", "\\dots", arg, fix = TRUE)
178           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
179         } else {         } else {
180           next;           next;
181         }         }
182        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
     }  
183    }    }
184      res
185    },ex=function(){
186    test <- function
187    ### the description
188    (x,
189    ### the first argument
190     y ##<< another argument
191     ){
192      5
193    ### the return value
194    ##seealso<< foobar
195    }
196    src <- attr(test,"source")
197    prefixed.lines(src)
198    extract.xxx.chunks(src)
199    })
200    
201    extract.xxx.chunks <- function # Extract documentation from a function
202    ### Given source code of a function, return a list describing inline
203    ### documentation in that source code.
204    (src,
205    ### The source lines of the function to examine, as a character
206    ### vector.
207     name.fun="(unnamed function)",
208    ### The name of the function/chunk to use in warning messages.
209     ...
210    ### ignored.
211     ){
212      res <- list()
213    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
214    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
215    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 386  Line 282 
282          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
283        }        }
284        chunk.res <- NULL        chunk.res <- NULL
285        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
286          chunk.res <-          chunk.res <-
287            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
288            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
289        invisible(chunk.res)        invisible(chunk.res)
290      }      }
291    while ( k <= length(code) ){    while ( k <= length(src) ){
292      line <- code[k]      line <- src[k]
293      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
294        ## we have a new extra chunk - first get field name and any payload        ## we have a new extra chunk - first get field name and any payload
295        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
296        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 469  Line 365 
365            first.describe <- TRUE;            first.describe <- TRUE;
366          }          }
367        }        }
368      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
369        ## append this line to current chunk        ## append this line to current chunk
370        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
371          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
372          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
373          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 484  Line 380 
380            payload <- stripped            payload <- stripped
381          }          }
382        }        }
383      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
384        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
385        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
386          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 493  Line 389 
389        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
390        in.chunk <- TRUE        in.chunk <- TRUE
391        if ( not.describe ){        if ( not.describe ){
392            ## TDH 2010-06-18 For item{}s in the documentation list names,
393            ## we don't need to have a backslash before, so delete it.
394            arg <- gsub("^[\\]+","",arg)
395          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
396          payload <- comment          payload <- comment
397        } else {        } else {
# Line 543  Line 442 
442  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
443  }  }
444    
445    ### Parsers for each function that are constructed automatically. This
446    ### is a named list, and each element is a parser function for an
447    ### individual object.
448    forfun.parsers <-
449      list(prefixed.lines=prefixed.lines,
450           examples.after.return=examples.after.return,
451           extract.xxx.chunks=extract.xxx.chunks,
452           ## title from first line of function def
453           title.from.firstline=function(src,...){
454             first <- src[1]
455             if(!is.character(first))return(list())
456             if(!grepl("#",first))return(list())
457             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
458           },
459           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
460           ## please, let me choose which dir to use for examples!
461           ## Get examples for FUN from the file tests/FUN.R
462           examples.from.testfile=function(name,...){
463             tsubdir <- getOption("inlinedocs.exdir")
464             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
465             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
466             if(file.exists(tfile))
467               list(examples=readLines(tfile))
468             else list()
469           },
470           definition.from.source=function(doc,src,...){
471             def <- doc$definition
472             is.empty <- function(x)is.null(x)||x==""
473             if(is.empty(def) && !is.empty(src))
474               list(definition=src)
475             else list()
476           })
477    
478    ### List of Parser Functions that can be applied to any object.
479    forall.parsers <-
480      list(## Fill in author from DESCRIPTION and titles.
481           author.from.description=function(desc,...){
482             list(author=desc[,"Maintainer"])
483           },
484           ## The format section sometimes causes problems, so erase it.
485           erase.format=function(...){
486             list(format="")
487           },
488           ## Convert the function name to a title.
489           title.from.name=function(name,doc,...){
490             if("title"%in%names(doc))list() else
491             list(title=gsub("[._]"," ",name))
492           },
493           ## PhG: here is what I propose for examples code in the 'ex' attribute
494           examples.in.attr =  function (name, o, ...) {
495             ex <- attr(o, "ex")
496             if (!is.null(ex)) {
497               ## Special case for code contained in a function
498               if (inherits(ex, "function")) {
499                 ## If source is available, start from there
500                 src <- attr(ex, "source")
501                 if (!is.null(src)) {
502                   ex <- src
503                 } else { ## Use the body of the function
504                   ex <- deparse(body(ex))
505                 }
506                 ## Eliminate leading and trailing code
507                 ex <- ex[-c(1, length(ex))]
508                 ## all the prefixes
509                 ex <- kill.prefix.whitespace(ex)
510                 ## Add an empty line before and after example
511                 ex <- c("", ex, "")
512               }
513               list(examples = ex)
514             } else list()
515           }
516           )
517    
518    ### List of parser functions that operate on single objects. This list
519    ### is useful for testing these functions.
520    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
521      f <- function # title
522    ### description
523      (x, ##<< arg x
524       y
525    ### arg y
526       ){
527        ##value<< a list with elements
528        list(x=x, ##<< original x value
529             y=y, ##<< original y value
530             sum=x+y) ##<< their sum
531        ##end<<
532      }
533      src <- attr(f,"source")
534      lonely$extract.xxx.chunks(src)
535      lonely$prefixed.lines(src)
536    })
537    
538    extra.code.docs <- function # Extract documentation from code chunks
539    ### Parse R code to extract inline documentation from comments around
540    ### each function. These are not able to be retreived simply by
541    ### looking at the "source" attribute. This is a Parser Function that
542    ### can be used in the parser list of package.skeleton.dx(). TODO:
543    ### Modularize this into separate Parsers Functions for S4 classes,
544    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
545    (code,
546    ### Code lines in a character vector containing multiple R objects to
547    ### parse for documentation.
548     objs,
549    ### The objects defined in the code.
550     ...
551    ### ignored
552     ){
553      parsed <- extract.file.parse(code)
554      extract.docs.try <- function(o,on)
555        {
556          ## Note: we could use parsed information here too, but that
557          ## would produce different results for setMethodS3 etc.
558          doc <- list()
559          if ( !is.null(parsed[[on]]) ){
560            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
561              doc$definition <- paste(parsed[[on]]@code)
562            }
563            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
564              doc$description <- parsed[[on]]@description
565            }
566            if ( "setMethodS3" == parsed[[on]]@created ){
567              # PhG: this may be wrong! It does not catch correctly how the method
568              # must be splitted in case of methods containing dots. for instance,
569              # as.data.frame.matrix must be split into: m1 = as.data.frame and
570              # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!
571                      pattern <- "^([^\\.]+)\\.(.*)$"
572              doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),
573                  m2 <- gsub(pattern,"\\2",on,perl=TRUE))
574              if ( grepl("\\W",m1,perl=TRUE) ){
575                              m1 <- paste("`",m1,"`",sep="")
576              }
577              cat("S3method(",m1,",",m2,")\n",sep="")
578            }
579          }
580          if("title" %in% names(doc) && !"description" %in% names(doc) ){
581            ## For short functions having both would duplicate, but a
582            ## description is required. Therefore automatically copy title
583            ## across to avoid errors at package build time.
584            doc$description <- doc$title
585          }
586          doc
587        }
588      extract.docs <- function(on){
589        res <- try({o <- objs[[on]]
590                    extract.docs.try(o, on)},FALSE)
591        if(class(res)=="try-error"){
592          cat("Failed to extract docs for: ",on,"\n\n")
593          list()
594        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
595          NULL
596        } else if(0 == length(res) && "function" %in% class(o)
597                  && 1 == length(osource <- attr(o,"source"))
598                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
599                  ){
600          ## phew - this should only pick up R.oo S3 generic definitions like:
601          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
602          NULL
603        } else res
604      }
605      doc.names <- names(objs)
606      res <- sapply(doc.names,extract.docs,simplify=FALSE)
607      ## Special processing for S4 classes as they do not appear in normal ls()
608      for ( nn in names(parsed) ){
609        if ( parsed[[nn]]@created == "setClass" ){
610          S4class.docs <- extract.docs.setClass(parsed[[nn]])
611          docname <- paste(nn,"class",sep="-")
612          if ( is.null(res[[docname]]) ){
613            res[[docname]] <- S4class.docs
614            doc.names <- c(doc.names,docname)
615          } else {
616            stop(nn," appears as both S4 class and some other definition")
617          }
618        }
619      }
620      inherit.docs <- function(on){
621        in.res <- res[[on]]
622        if ( !is.null(parsed[[on]]) ){
623          for ( parent in parsed[[on]]@parent ){
624            if ( !is.na(parent) ){
625              if ( is.null(in.res) ){
626                in.res <- res[[parent]]
627              } else if ( parent %in% names(res) ){
628                parent.docs <- res[[parent]]
629                for ( nn in names(parent.docs) ){
630                  if ( !nn %in% names(in.res) ){
631                    in.res[[nn]] <- parent.docs[[nn]]
632                  }
633                }
634              }
635            }
636          }
637        }
638        invisible(in.res)
639      }
640      all.done <- FALSE
641      while ( !all.done ){
642        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
643        all.done <- identical(res1,res)
644        res <- res1
645      }
646      ## now strip out any generics (which have value NULL in res):
647      res.not.null <- sapply(res,function(x){!is.null(x)})
648      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
649        res <- res[res.not.null]
650      }
651      res
652    ### named list of lists, one for each object to document.
653    }
654    
655    ### List of parsers to use by default with package.skeleton.dx.
656    default.parsers <-
657      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
658        sapply(forfun.parsers,forfun),
659        sapply(forall.parsers,forall),
660        edit.package.file=function(desc,...){
661          in.details <- setdiff(colnames(desc),"Description")
662          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
663          L <-
664            list(list(title=desc[,"Title"],
665                      description=desc[,"Description"],
666                      `tabular{ll}`=details))
667          names(L) <- paste(desc[,"Package"],"-package",sep="")
668          L
669        }
670        )
671    
672  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
673  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
674  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
# Line 581  Line 707 
707      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
708      default.description <- NULL      default.description <- NULL
709      while ( start > last.end+1      while ( start > last.end+1
710             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
711        start <- start-1        start <- start-1
712      }      }
713      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 608  Line 734 
734        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
735        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
736        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
737        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
738          parent <- chars[3]          parent <- chars[3]
739        }        }
740        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 640  Line 766 
766        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
767        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
768        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
769        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
770          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
771        }        }
772        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 681  Line 807 
807    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
808    ## following line.    ## following line.
809    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
810    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
811      ## also apply source parsing functions that I separated out into
812      ## separate functions
813      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
814      docs$title <- lonely$title.from.firstline(chunk.source)
815    ##details<<    ##details<<
816    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
817    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 719  Line 849 
849  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
850   ){   ){
851    e <- new.env()    e <- new.env()
852    old <- options(keep.source.pkgs=TRUE)    old <- options(keep.source=TRUE)
853    on.exit(options(old))    on.exit(options(old))
   ##tryCatch({  
854      exprs <- parse(text=code)      exprs <- parse(text=code)
855      for (i in exprs) eval(i, e)    for (i in exprs){
856  ##   },error=function(err){      tryCatch(eval(i, e),error=function(e){
857  ##     print(i)        ##print(e)
858  ##     stop("eval or parse failed with error:\n",err)      })
859  ##   })    }
860    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
861    
862    docs <- list()    docs <- list()
# Line 763  Line 892 
892      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,...)
893      docs <- combine(docs,L)      docs <- combine(docs,L)
894    }    }
895      ## post-process to collapse all character vectors
896      for(i in seq_along(docs)){
897        for(j in seq_along(docs[[i]])){
898          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
899        }
900      }
901    if(verbose)cat("\n")    if(verbose)cat("\n")
902    docs    docs
903  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
904  }  }
905    
906    ### Names of Parser Functions that operate on the desc arg.
907    descfile.names <- c("author.from.description","edit.package.file")
908    
909    ### Names of Parser Functions that do NOT use the desc arg.
910    non.descfile.names <-
911      names(default.parsers)[!names(default.parsers)%in%descfile.names]
912    
913    ### Parsers that operate only on R code, independently of the
914    ### description file.
915    nondesc.parsers <- default.parsers[non.descfile.names]
916    
917  extract.docs.file <- function  extract.docs.file <- function
918  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
919  (f,  (f,
920  ### File name of R code to read and parse.  ### File name of R code to read and parse.
921   parsers=list(extra.code.docs,default.parsers$parsefun),   parsers=nondesc.parsers,
922  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
923  ### documentation.  ### documentation.
924   ...   ...

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