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

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revision 97, Mon May 3 16:07:46 2010 UTC revision 308, Fri Oct 21 12:08:39 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 <- 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      toup <- names(y)[!toadd]
17      x[names(y)[toadd]] <- y[toadd]
18      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
19      x
20    ### A list, same type as x, but with added elements from y.
21    }
22    
23    
24    getSource <- function
25    ### Extract a function's source code.
26    (fun.obj
27    ### A function.
28     ) {
29          srcref <- attr(fun.obj, "srcref")
30          if (!is.null(srcref)) {
31            ##unlist(strsplit(as.character(srcref), "\n"))
32            as.character(srcref)
33          }
34          else attr(fun.obj, "source")
35    ### Source code lines as a character vector.
36    }
37    
38    ### Prefix for code comments used with grep and gsub.
39    prefix <- "^[ \t]*###[ \t]*"
40    
41    decomment <- function
42    ### Remove comment prefix and join lines of code to form a
43    ### documentation string.
44    (comments
45    ### Character vector of prefixed comment lines.
46     ){
47      gsub(prefix,"",comments)
48    ### String without prefixes or newlines.
49    }
50    
51    forall <- function
52  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
53  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
54  ### documentation list.  ### documentation list.
 forall <- function  
55  (FUN,  (FUN,
56  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
57   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 9  Line 59 
59  ### 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
60  ### the result will be returned.  ### the result will be returned.
61   ){   ){
62    function(objs,docs,...){    FUN <- FUN
63      f <- function(objs,docs,...){
64        if(length(objs)==0)return(list())
65      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
66      L <- list()      L <- list()
67      for(N in names(docs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
68        for(N in union(names(docs),names(objs))){
69        o <- objs[[N]]        o <- objs[[N]]
70        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
71                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
72      }      }
73        on.exit()## remove warning message
74      L      L
75    }    }
76      class(f) <- c("allfun","function")
77      f
78  ### A Parser Function.  ### A Parser Function.
79  }  }
80    
81  ### For each function in the package, do something.  ### Print method for functions constructed using forall.
82  forfun <- function(FUN)forall(FUN,is.function)  print.allfun <- function(x,...){
83      e <- environment(x)
84  ### Default parsers to use with package.skeleton.dx    cat("Function to apply to every element.\nselector:")
85  forall.parsers <-    print(e$subfun)
86    list(## Extract lots of info from normal functions.    cat("processor:")
87         parsefun=list(forfun,function(src,name,...){    print(e$FUN)
          extract.docs.fun(src,name)  
        }),  
        ## Fill in author from DESCRIPTION and titles.  
        author.from.description=list(forall,function(desc,...){  
          list(author=desc[,"Maintainer"])  
        }),  
        ## The format section sometimes causes problems, so erase it.  
        erase.format=list(forall,function(...){  
          list(format="")  
        }),  
        ## Convert the function name to a title.  
        title.from.name=list(forall,function(name,doc,...){  
          if("title"%in%names(doc))list() else  
          list(title=gsub("[._]"," ",name))  
        }),  
        ## Get examples for FUN from the file test/FUN.R  
        examples.from.testfile=list(forfun,function(name,...){  
          tfile <- file.path("..","tests",paste(name,".R",sep=""))  
          if(file.exists(tfile))  
            list(examples=paste(readLines(tfile),collapse="\n"))  
          else list()  
        }),  
        ## Get examples from inline definitions after return()  
        examples.after.return=list(forfun,function(name,src,...){  
          coll <- paste(src,collapse="\n")  
          thispre <- gsub("^[\\^]","",prefix)  
          FIND <- paste("(return|UseMethod)[(][^\\n]*\\n",thispre,sep="")  
          m <- regexpr(FIND,coll)  
          if(m[1]==-1)return(list())  
          after <- substr(coll,m[1],nchar(coll))  
          FIND <-  
            paste("[^\\n]*",# rest of the return line  
                  "((?:\\n###[^\\n]*)+)",#comment value lines \\1  
                  "([\\w\\W]*)[}]",#examples \\2  
                  sep="")  
          SEP <- "----------"  
          REP <- paste("\\1",SEP,"\\2",sep="")  
          r <- strsplit(gsub(FIND,REP,after,perl=TRUE),split=SEP)[[1]]  
          l <- strsplit(r,split="\n")  
          ##if(name=="dl.combine")browser()  
          excode <- c(l[[2]],"")  
          prefixes <- gsub("(\\s*).*","\\1",excode,perl=TRUE)[grep("\\w",excode)]  
          FIND <- prefixes[which.min(nchar(prefixes))]  
          list(examples=paste(sub(FIND,"",excode),collapse="\n"),  
               value=decomment(l[[1]][-1]))  
        }))  
   
 ### List of parser functions that operate on single objects. This list  
 ### is useful for testing these functions, ie  
 ### lonely$parsefuns(attr(extract.docs.file,"src"),"extract.docs.file")  
 lonely <- sapply(forall.parsers,function(L)L[[2]])  
   
 extract.docs.file <- function # Extract documentation from a file  
 ### 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().  
 (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 ){  
           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.  
88  }  }
89    
90  ### List of parsers to use by default with package.skeleton.dx.  ### For each function in the package, do something.
91  default.parsers <- c(extract.docs.file=extract.docs.file,  forfun <- function(FUN)forall(FUN,is.function)
                      sapply(forall.parsers,function(L)L[[1]](L[[2]])))  
92    
93  extract.docs.fun <- function # Extract documentation from a function  kill.prefix.whitespace <- function
94  ### Given source code of a function, return a list describing inline  ### Figure out what the whitespace preceding the example code is, and
95  ### documentation in that source code.  ### then delete that from every line.
96  (code,  (ex
97  ### The function to examine.  ### character vector of example code lines.
  name.fun  
 ### The name of the function/chunk to use in warning messages.  
98   ){   ){
99    res <- list()    tlines <- gsub("\\s*","",ex)
100    clines <- grep(prefix,code)    ##tlines <- gsub("#.*","",tlines)
101    if(length(grep("#",code[1]))){    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
102      res$title <- gsub("[^#]*#\\s*(.*)","\\1",code[1],perl=TRUE)    FIND <- prefixes[which.min(nchar(prefixes))]
103    }    ## Eliminate leading tabulations or 2/4 spaces
104    if(length(clines) > 0){    sub(FIND, "", ex)
105      ##details<<  ### Character vector of code lines with preceding whitespace removed.
106      ## The primary mechanism is that consecutive groups of lines matching  }
107      ## the specified prefix regular expression "\code{^### }" (i.e. lines  
108      ## beginning with "\code{### }") are collected  prefixed.lines <- structure(function(src,...){
109      ## as follows into documentation sections:\describe{  ### The primary mechanism of inline documentation is via consecutive
110      ## \item{description}{group starting at line 2 in the code}  ### groups of lines matching the specified prefix regular expression
111      ## \item{arguments}{group following each function argument}  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
112      ## \item{value}{group ending at the penultimate line of the code}}  ### collected as follows into documentation sections:\describe{
113      ## These may be added to by use of the \code{##<<} constructs described  ### \item{description}{group starting at line 2 in the code}
114      ## below.  ### \item{arguments}{group following each function argument}
115    ### \item{value}{group ending at the penultimate line of the code}}
116    ### These may be added to by use of the \code{##<<} constructs
117    ### described below.
118      clines <- grep(prefix,src)
119      if(length(clines)==0)return(list())
120      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
121      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
122      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
123      ## detect body of function using paren matching
124      code <- gsub("#.*","",src)
125      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
126      parens <- f("(")-f(")")
127      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
128      if(length(body.begin)==0)body.begin <- 1 ## rare cases
129      is.arg <- function(){
130        gres <- grep("^\\s*#",src[start-1],perl=TRUE)
131        0 == length(gres) && start<=body.begin
132      }
133      res <- list()
134      for(i in seq_along(starts)){      for(i in seq_along(starts)){
135        start <- clines[starts[i]]        start <- clines[starts[i]]
136        end <- clines[ends[i]]        end <- clines[ends[i]]
137        lab <- if(end+1==length(code))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
138        lab <- if(all(processed==""))"value"
139        else if(start==2)"description"        else if(start==2)"description"
140        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
141           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
142           #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 ,  
143                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
144                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
145          arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
146                   arg <- gsub("...", "\\dots", arg, fix = TRUE)                   arg <- gsub("...", "\\dots", arg, fix = TRUE)
147           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
148         } else {         } else {
149           next;           next;
150         }         }
151        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
     }  
152    }    }
153      res
154    },ex=function(){
155    test <- function
156    ### the description
157    (x,
158    ### the first argument
159     y ##<< another argument
160     ){
161      5
162    ### the return value
163    ##seealso<< foobar
164    }
165    src <- getSource(test)
166    prefixed.lines(src)
167    extract.xxx.chunks(src)
168    })
169    
170    extract.xxx.chunks <- function # Extract documentation from a function
171    ### Given source code of a function, return a list describing inline
172    ### documentation in that source code.
173    (src,
174    ### The source lines of the function to examine, as a character
175    ### vector.
176     name.fun="(unnamed function)",
177    ### The name of the function/chunk to use in warning messages.
178     ...
179    ### ignored.
180     ){
181      res <- list()
182    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
183    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
184    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 315  Line 251 
251          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
252        }        }
253        chunk.res <- NULL        chunk.res <- NULL
254        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
255          chunk.res <-          chunk.res <-
256            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
257            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
258        invisible(chunk.res)        invisible(chunk.res)
259      }      }
260    while ( k <= length(code) ){    while ( k <= length(src) ){
261      line <- code[k]      line <- src[k]
262      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      ##print(line)
263        ##if(grepl("^$",line))browser()
264        if ( grepl(extra.regexp,line,perl=TRUE) ){
265        ## 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
266        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
267        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
268          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
269        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
270        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
271        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 336  Line 274 
274        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
275        if ( "describe" == new.field ){        if ( "describe" == new.field ){
276          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
277          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
278          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
279          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
280            ## \code{##describe<<} comments.
281          if ( first.describe ){          if ( first.describe ){
282            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
283          } else {          } else {
# Line 398  Line 337 
337            first.describe <- TRUE;            first.describe <- TRUE;
338          }          }
339        }        }
340      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
341        ## append this line to current chunk        ## append this line to current chunk
342        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
343          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
344          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
345          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 413  Line 352 
352            payload <- stripped            payload <- stripped
353          }          }
354        }        }
355      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
356        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
357        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
358          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 422  Line 361 
361        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
362        in.chunk <- TRUE        in.chunk <- TRUE
363        if ( not.describe ){        if ( not.describe ){
364            ## TDH 2010-06-18 For item{}s in the documentation list names,
365            ## we don't need to have a backslash before, so delete it.
366            arg <- gsub("^[\\]+","",arg)
367          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
368          payload <- comment          payload <- comment
369        } else {        } else {
# Line 472  Line 414 
414  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
415  }  }
416    
417    leadingS3generic <- function # check whether function name is an S3 generic
418    ### Determines whether a function name looks like an S3 generic function
419    (name,                     ##<< name of function
420     env,                      ##<< environment to search for additional generics
421     ...)                      ##<< ignored here
422    {
423      ##details<< This function is one of the default parsers, but exposed as
424      ## possibly of more general interest. Given a function name of the form
425      ## x.y.z it looks for the generic function x applying to objects of class
426      ## y.z and also for generic function x.y applying to objects of class z.
427      ##
428      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
429      l <- length(parts)
430      if (l > 1) {
431        for (i in 1:(l - 1)) {
432          ## Look for a generic function (known by the system or defined
433          ## in the package) that matches that part of the function name
434          generic <- paste(parts[1:i], collapse = ".")
435          if (any(generic %in% utils:::getKnownS3generics()) ||
436              utils:::findGeneric(generic, env) != "") {
437            object <- paste(parts[(i + 1):l], collapse = ".")
438            ##details<< Assumes that the first name which matches any known
439            ## generics is the target generic function, so if both x and x.y
440            ## are generic functions, will assume generic x applying to objects
441            ## of class y.z
442            ##value<< If a matching generic found returns a list with a single component:
443            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
444          }
445        }
446      }
447      ##value<< If no matching generic functions are found, returns an empty list.
448      list()
449    }
450    
451    ### Parsers for each function that are constructed automatically. This
452    ### is a named list, and each element is a parser function for an
453    ### individual object.
454    forfun.parsers <-
455      list(prefixed.lines=prefixed.lines,
456           extract.xxx.chunks=extract.xxx.chunks,
457           ## title from first line of function def
458           title.from.firstline=function(src,...){
459             first <- src[1]
460             if(!is.character(first))return(list())
461             if(!grepl("#",first))return(list())
462             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
463           },
464           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
465           ## please, let me choose which dir to use for examples!
466           ## Get examples for FUN from the file tests/FUN.R
467           examples.from.testfile=function(name,...){
468             tsubdir <- getOption("inlinedocs.exdir")
469             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
470             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
471             if(file.exists(tfile))
472               list(examples=readLines(tfile))
473             else list()
474           },
475           definition.from.source=function(doc,src,...){
476             def <- doc$definition
477             is.empty <- function(x)is.null(x)||x==""
478             if(is.empty(def) && !is.empty(src))
479               list(definition=src)
480             else list()
481           })
482    
483    ### List of Parser Functions that can be applied to any object.
484    forall.parsers <-
485      list(## Fill in author from DESCRIPTION and titles.
486           author.from.description=function(desc,...){
487             list(author=desc[,"Author"])
488           },
489           ## The format section sometimes causes problems, so erase it.
490           erase.format=function(...){
491             list(format="")
492           },
493           ## Convert the function name to a title.
494           title.from.name=function(name,doc,...){
495             if("title"%in%names(doc))list() else
496             list(title=gsub("[._]"," ",name))
497           },
498           ## PhG: here is what I propose for examples code in the 'ex' attribute
499           examples.in.attr =  function (name, o, ...) {
500             ex <- attr(o, "ex")
501             if (!is.null(ex)) {
502               ## Special case for code contained in a function
503               if (inherits(ex, "function")) {
504                 ## If source is available, start from there
505                 src <- getSource(ex)
506                 if (!is.null(src)) {
507                   ex <- src
508                 } else { ## Use the body of the function
509                   ex <- deparse(body(ex))
510                 }
511                 ## Eliminate leading and trailing code
512                 ex <- ex[-c(1, length(ex))]
513                 if(ex[1]=="{")ex <- ex[-1]
514                 ## all the prefixes
515                 ex <- kill.prefix.whitespace(ex)
516                 ## Add an empty line before and after example
517                 ex <- c("", ex, "")
518               }
519               list(examples = ex)
520             } else list()
521           },collapse=function(doc,...){
522             L <- lapply(doc,paste,collapse="\n")
523             L$.overwrite <- TRUE
524             L
525           },tag.s3methods=leadingS3generic
526           )
527    
528    ### List of parser functions that operate on single objects. This list
529    ### is useful for testing these functions.
530    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
531      f <- function # title
532    ### description
533      (x, ##<< arg x
534       y
535    ### arg y
536       ){
537        ##value<< a list with elements
538        list(x=x, ##<< original x value
539             y=y, ##<< original y value
540             sum=x+y) ##<< their sum
541        ##end<<
542      }
543      src <- getSource(f)
544      lonely$extract.xxx.chunks(src)
545      lonely$prefixed.lines(src)
546    })
547    
548    extra.code.docs <- function # Extract documentation from code chunks
549    ### Parse R code to extract inline documentation from comments around
550    ### each function. These are not able to be retreived simply by
551    ### looking at the "source" attribute. This is a Parser Function that
552    ### can be used in the parser list of package.skeleton.dx(). TODO:
553    ### Modularize this into separate Parsers Functions for S4 classes,
554    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
555    (code,
556    ### Code lines in a character vector containing multiple R objects to
557    ### parse for documentation.
558     objs,
559    ### The objects defined in the code.
560     ...
561    ### ignored
562     ){
563      parsed <- extract.file.parse(code)
564      extract.docs.try <- function(o,on)
565        {
566          ## Note: we could use parsed information here too, but that
567          ## would produce different results for setMethodS3 etc.
568          doc <- list()
569          if ( !is.null(parsed[[on]]) ){
570            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
571              doc$definition <- paste(parsed[[on]]@code)
572            }
573            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
574              doc$description <- parsed[[on]]@description
575            }
576            ## if ( "setMethodS3" == parsed[[on]]@created ){
577            ##   gen <- leadingS3generic(on,topenv())
578            ##   if ( 0 < length(gen) ){
579            ##     doc$.s3method <- gen$.s3method
580            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
581            ##   }
582            ## }
583          }
584          if("title" %in% names(doc) && !"description" %in% names(doc) ){
585            ## For short functions having both would duplicate, but a
586            ## description is required. Therefore automatically copy title
587            ## across to avoid errors at package build time.
588            doc$description <- doc$title
589          }
590          doc
591        }
592      extract.docs <- function(on){
593        res <- try({o <- objs[[on]]
594                    extract.docs.try(o, on)},FALSE)
595        if(class(res)=="try-error"){
596          cat("Failed to extract docs for: ",on,"\n\n")
597          list()
598        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
599          NULL
600        } else if(0 == length(res) && "function" %in% class(o)
601                  && 1 == length(osource <- getSource(o))
602                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
603                  ){
604          ## phew - this should only pick up R.oo S3 generic definitions like:
605          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
606          NULL
607        } else res
608      }
609      doc.names <- names(objs)
610      res <- sapply(doc.names,extract.docs,simplify=FALSE)
611      ## Special processing for S4 classes as they do not appear in normal ls()
612      for ( nn in names(parsed) ){
613        if ( parsed[[nn]]@created == "setClass" ){
614          S4class.docs <- extract.docs.setClass(parsed[[nn]])
615          docname <- paste(nn,"class",sep="-")
616          if ( is.null(res[[docname]]) ){
617            res[[docname]] <- S4class.docs
618            doc.names <- c(doc.names,docname)
619          } else {
620            stop(nn," appears as both S4 class and some other definition")
621          }
622        }
623      }
624      inherit.docs <- function(on){
625        in.res <- res[[on]]
626        if ( !is.null(parsed[[on]]) ){
627          for ( parent in parsed[[on]]@parent ){
628            if ( !is.na(parent) ){
629              if ( is.null(in.res) ){
630                in.res <- res[[parent]]
631              } else if ( parent %in% names(res) ){
632                parent.docs <- res[[parent]]
633                for ( nn in names(parent.docs) ){
634                  if ( !nn %in% names(in.res) ){
635                    in.res[[nn]] <- parent.docs[[nn]]
636                  }
637                }
638              }
639            }
640          }
641        }
642        invisible(in.res)
643      }
644      all.done <- FALSE
645      while ( !all.done ){
646        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
647        all.done <- identical(res1,res)
648        res <- res1
649      }
650      ## now strip out any generics (which have value NULL in res):
651      res.not.null <- sapply(res,function(x){!is.null(x)})
652      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
653        res <- res[res.not.null]
654      }
655      res
656    ### named list of lists, one for each object to document.
657    }
658    
659    ### List of parsers to use by default with package.skeleton.dx.
660    default.parsers <-
661      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
662        sapply(forfun.parsers,forfun),
663        edit.package.file=function(desc,...){
664          in.details <- setdiff(colnames(desc),"Description")
665          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
666          L <-
667            list(list(title=desc[,"Title"],
668                      description=desc[,"Description"],
669                      `tabular{ll}`=details))
670          names(L) <- paste(desc[,"Package"],"-package",sep="")
671          L
672        },
673        sapply(forall.parsers,forall)
674        )
675    
676  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
677  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
678  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
679  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
680    ### the parent class.
681           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
682                          created="character", ##<< how created                          created="character", ##<< how created
683                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 510  Line 712 
712      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
713      default.description <- NULL      default.description <- NULL
714      while ( start > last.end+1      while ( start > last.end+1
715             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
716        start <- start-1        start <- start-1
717      }      }
718      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 537  Line 739 
739        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
740        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
741        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
742        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
743          parent <- chars[3]          parent <- chars[3]
744        }        }
745        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 569  Line 771 
771        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
772        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
773        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
774        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
775          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
776        }        }
777        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 610  Line 812 
812    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
813    ## following line.    ## following line.
814    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
815    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
816      ## also apply source parsing functions that I separated out into
817      ## separate functions
818      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
819      docs$title <- lonely$title.from.firstline(chunk.source)
820      ##details<<
821      ## If there is no explicit title on the first line of setClass, then
822      ## one is made up from the class name.
823      if ( 0 == length(docs$title) ){
824        docs$title <- list(title=paste(class.name,"S4 class"))
825      }
826    ##details<<    ##details<<
827    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
828    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 634  Line 846 
846    }    }
847    invisible(docs)    invisible(docs)
848  }  }
849    
850    apply.parsers <- function
851    ### Parse code to r objs, then run all the parsers and return the
852    ### documentation list.
853    (code,
854    ### Character vector of code lines.
855     parsers=default.parsers,
856    ### List of Parser Functions.
857     verbose=FALSE,
858    ### Echo names of Parser Functions?
859     ...
860    ### Additional arguments to pass to Parser Functions.
861     ){
862      e <- new.env()
863      ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
864      ## Error in assignClassDef(Class, classDef, where) :
865      ##   Class "DocLink" has a locked definition in package "inlinedocs"
866      ## Traced to "where" argument in setClassDef which defaults to topenv()
867      ## which in turn is inlinedocs when processing inlinedocs package, hence
868      ## the clash. The following works (under R 2.12.2), so that the topenv()
869      ## now finds e before finding the inlinedocs environment.
870      old <- options(keep.source=TRUE,topLevelEnvironment=e)
871      on.exit(options(old))
872      exprs <- parse(text=code)
873      ## TDH 2011-04-07 set this so that no warnings about creating a fake
874      ## package when we try to process S4 classes defined in code
875      e$.packageName <- "inlinedocs.processor"
876      for (i in exprs){
877        ## TDH 2011-04-07 Disable this tryCatch since it makes it harder
878        ##to debug errors/warnings in the evaluated code
879    
880        ##tryCatch({
881          eval(i, e)
882        ##},error=function(e){
883          ##print(e)
884        ##})
885      }
886      objs <- sapply(ls(e),get,e,simplify=FALSE)
887    
888      docs <- list()
889    
890      ## apply parsers in sequence to code and objs
891      for(i in seq_along(parsers)){
892        N <- names(parsers[i])
893        if(verbose){
894          if(is.character(N) && N!=""){
895            cat(N," ",sep="")
896          }else cat('. ')
897        }
898        p <- parsers[[i]]
899        ## This is the argument list that each parser receives:
900        L <- p(code=code,objs=objs,docs=docs,env=e,...)
901        docs <- combine(docs,L)
902      }
903      ## post-process to collapse all character vectors
904      for(i in seq_along(docs)){
905        for(j in seq_along(docs[[i]])){
906          if(names(docs[[i]])[j]!=".s3method")
907          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
908        }
909      }
910      if(verbose)cat("\n")
911      docs
912    ### A list of extracted documentation from code.
913    }
914    
915    ### Names of Parser Functions that operate on the desc arg.
916    descfile.names <- c("author.from.description","edit.package.file")
917    
918    ### Names of Parser Functions that do NOT use the desc arg.
919    non.descfile.names <-
920      names(default.parsers)[!names(default.parsers)%in%descfile.names]
921    
922    ### Parsers that operate only on R code, independently of the
923    ### description file.
924    nondesc.parsers <- default.parsers[non.descfile.names]
925    
926    extract.docs.file <- structure(function
927    ### Apply all parsers relevant to extract info from just 1 code file.
928    (f,
929    ### File name of R code to read and parse.
930     parsers=NULL,
931    ### Parser Functions to use to parse the code and extract
932    ### documentation.
933     ...
934    ### Other arguments to pass to Parser Functions.
935     ){
936      if(is.null(parsers))parsers <- nondesc.parsers
937      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
938    },ex=function(){
939      f <- system.file("silly","R","silly.R",package="inlinedocs")
940      extract.docs.file(f)
941    })
942    

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