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

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revision 87, Sat May 1 12:21:27 2010 UTC revision 300, Fri Jun 17 07:37:46 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    ### Prefix for code comments used with grep and gsub.
24    prefix <- "^[ \t]*###[ \t]*"
25    
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      gsub(prefix,"",comments)
33    ### String without prefixes or newlines.
34    }
35    
36    forall <- function
37  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
38  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
39  ### documentation list.  ### documentation list.
 forall <- function  
40  (FUN,  (FUN,
41  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
42   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 9  Line 44 
44  ### 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
45  ### the result will be returned.  ### the result will be returned.
46   ){   ){
47    function(objs,docs,...){    FUN <- FUN
48      f <- function(objs,docs,...){
49        if(length(objs)==0)return(list())
50      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
51      L <- list()      L <- list()
52      for(N in names(objs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
53        for(N in union(names(docs),names(objs))){
54        o <- objs[[N]]        o <- objs[[N]]
55        L[[N]] <- FUN(src=attr(o,"source"),name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)        L[[N]] <- FUN(src=attr(o,"source"),
56                        name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
57      }      }
58        on.exit()## remove warning message
59      L      L
60    }    }
61      class(f) <- c("allfun","function")
62      f
63  ### A Parser Function.  ### A Parser Function.
64  }  }
65    
66    ### 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  ### For each function in the package, do something.  ### For each function in the package, do something.
76  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
77    
78  ### Get last line (test)  kill.prefix.whitespace <- function
79  parsefuns <- forfun(function(src,name,...){  ### Figure out what the whitespace preceding the example code is, and
80    extract.docs.fun(src,name)  ### then delete that from every line.
81  })  (ex
82    ### character vector of example code lines.
 ### Fill in author from DESCRIPTION and titles.  
 author.from.description <- forall(function(desc,...){  
   list(author=desc[,"Maintainer"])  
 })  
   
 ### The format section sometimes causes problems, so erase it.  
 erase.format <- forall(function(...){  
   list(format="")  
 })  
   
 ### Convert the function name to a title.  
 title.from.name <- forall(function(name,...){  
   list(title=gsub("[._]"," ",name))  
 })  
   
 ### Get examples for FUN from the file test/FUN.R  
 examples.from.testfile <- 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 <- forfun(function(src,...){  
   rline <- grep("return([^)]*)",src)  
   if(length(rline)==0)return(list())  
   rline <- rline[length(rline)]  
   comment.line.nums <- grep(prefix,src)  
   if(!(comment.end <- rline+1)%in%comment.line.nums)return(list())  
   while(comment.end%in%comment.line.nums)comment.end <- comment.end+1  
   excode <- src[comment.end:(length(src)-1)]  
   list(examples=paste(gsub("^\\W*","",excode),collapse="\n"))  
 })  
   
 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  
83   ){   ){
84    parsed <- extract.file.parse(code)    tlines <- gsub("\\s*","",ex)
85    extract.docs.try <- function(o,on)    ##tlines <- gsub("#.*","",tlines)
86      {    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
87        ## Note: we could use parsed information here too, but that    FIND <- prefixes[which.min(nchar(prefixes))]
88        ## would produce different results for setMethodS3 etc.    ## Eliminate leading tabulations or 2/4 spaces
89        doc <- list()    sub(FIND, "", ex)
90        if ( !is.null(parsed[[on]]) ){  ### Character vector of code lines with preceding whitespace removed.
91          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics  }
92            doc$definition <- paste(parsed[[on]]@code,collapse="\n")  
93          }  prefixed.lines <- structure(function(src,...){
94          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){  ### The primary mechanism of inline documentation is via consecutive
95            doc$description <- parsed[[on]]@description  ### groups of lines matching the specified prefix regular expression
96          }  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
97          if ( "setMethodS3" == parsed[[on]]@created ){  ### collected as follows into documentation sections:\describe{
98            pattern <- "^([^\\.]+)\\.(.*)$"  ### \item{description}{group starting at line 2 in the code}
99            doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),  ### \item{arguments}{group following each function argument}
100                m2 <- gsub(pattern,"\\2",on,perl=TRUE))  ### \item{value}{group ending at the penultimate line of the code}}
101            if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){  ### These may be added to by use of the \code{##<<} constructs
102              m1 <- paste("`",m1,"`",sep="")  ### described below.
103            }    clines <- grep(prefix,src)
104            cat("S3method(",m1,",",m2,")\n",sep="")    if(length(clines)==0)return(list())
         }  
       }  
       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.  
 }  
   
 ### Default parsers to use with package.skeleton.dx  
 default.parsers <- list("parsefuns","extract.docs.file",  
                         "examples.after.return","examples.from.testfile",  
                         "author.from.description","erase.format","title.from.name")  
   
 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.  
105      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
106      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
107      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
108      ## detect body of function using paren matching
109      code <- gsub("#.*","",src)
110      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
111      parens <- f("(")-f(")")
112      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
113      if(length(body.begin)==0)body.begin <- 1 ## rare cases
114      is.arg <- function(){
115        gres <- grep("^\\s*#",src[start-1],perl=TRUE)
116        0 == length(gres) && start<=body.begin
117      }
118      res <- list()
119      for(i in seq_along(starts)){      for(i in seq_along(starts)){
120        start <- clines[starts[i]]        start <- clines[starts[i]]
121        end <- clines[ends[i]]        end <- clines[ends[i]]
122        lab <- if(end+1==length(code))"value"      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"
123        else if(start==2)"description"        else if(start==2)"description"
124        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
125           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
126           #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 ,  
127                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
128                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
129          arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
130                   arg <- gsub("...", "\\dots", arg, fix = TRUE)                   arg <- gsub("...", "\\dots", arg, fix = TRUE)
131           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
132         } else {         } else {
133           next;           next;
134         }         }
135        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
     }  
136    }    }
137      res
138    },ex=function(){
139    test <- function
140    ### the description
141    (x,
142    ### the first argument
143     y ##<< another argument
144     ){
145      5
146    ### the return value
147    ##seealso<< foobar
148    }
149    src <- attr(test,"source")
150    prefixed.lines(src)
151    extract.xxx.chunks(src)
152    })
153    
154    extract.xxx.chunks <- function # Extract documentation from a function
155    ### Given source code of a function, return a list describing inline
156    ### documentation in that source code.
157    (src,
158    ### The source lines of the function to examine, as a character
159    ### vector.
160     name.fun="(unnamed function)",
161    ### The name of the function/chunk to use in warning messages.
162     ...
163    ### ignored.
164     ){
165      res <- list()
166    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
167    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
168    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 300  Line 235 
235          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
236        }        }
237        chunk.res <- NULL        chunk.res <- NULL
238        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
239          chunk.res <-          chunk.res <-
240            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
241            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
242        invisible(chunk.res)        invisible(chunk.res)
243      }      }
244    while ( k <= length(code) ){    while ( k <= length(src) ){
245      line <- code[k]      line <- src[k]
246      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
247        ## 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
248        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
249        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 383  Line 318 
318            first.describe <- TRUE;            first.describe <- TRUE;
319          }          }
320        }        }
321      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
322        ## append this line to current chunk        ## append this line to current chunk
323        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
324          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
325          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
326          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 398  Line 333 
333            payload <- stripped            payload <- stripped
334          }          }
335        }        }
336      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
337        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
338        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
339          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 407  Line 342 
342        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
343        in.chunk <- TRUE        in.chunk <- TRUE
344        if ( not.describe ){        if ( not.describe ){
345            ## 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          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
349          payload <- comment          payload <- comment
350        } else {        } else {
# Line 457  Line 395 
395  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
396  }  }
397    
398    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    ### 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           title.from.firstline=function(src,...){
440             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           },
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               list(examples=readLines(tfile))
454             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               list(definition=src)
461             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                 ## all the prefixes
495                 ex <- kill.prefix.whitespace(ex)
496                 ## Add an empty line before and after example
497                 ex <- c("", ex, "")
498               }
499               list(examples = ex)
500             } else list()
501           },collapse=function(doc,...){
502             L <- lapply(doc,paste,collapse="\n")
503             L$.overwrite <- TRUE
504             L
505           },tag.s3methods=leadingS3generic
506           )
507    
508    ### List of parser functions that operate on single objects. This list
509    ### is useful for testing these functions.
510    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
511      f <- function # title
512    ### description
513      (x, ##<< arg x
514       y
515    ### arg y
516       ){
517        ##value<< a list with elements
518        list(x=x, ##<< original x value
519             y=y, ##<< original y value
520             sum=x+y) ##<< their sum
521        ##end<<
522      }
523      src <- attr(f,"source")
524      lonely$extract.xxx.chunks(src)
525      lonely$prefixed.lines(src)
526    })
527    
528    extra.code.docs <- function # Extract documentation from code chunks
529    ### Parse R code to extract inline documentation from comments around
530    ### each function. These are not able to be retreived simply by
531    ### looking at the "source" attribute. This is a Parser Function that
532    ### can be used in the parser list of package.skeleton.dx(). TODO:
533    ### Modularize this into separate Parsers Functions for S4 classes,
534    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
535    (code,
536    ### Code lines in a character vector containing multiple R objects to
537    ### parse for documentation.
538     objs,
539    ### The objects defined in the code.
540     ...
541    ### ignored
542     ){
543      parsed <- extract.file.parse(code)
544      extract.docs.try <- function(o,on)
545        {
546          ## Note: we could use parsed information here too, but that
547          ## would produce different results for setMethodS3 etc.
548          doc <- list()
549          if ( !is.null(parsed[[on]]) ){
550            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
551              doc$definition <- paste(parsed[[on]]@code)
552            }
553            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
554              doc$description <- parsed[[on]]@description
555            }
556            ## if ( "setMethodS3" == parsed[[on]]@created ){
557            ##   gen <- leadingS3generic(on,topenv())
558            ##   if ( 0 < length(gen) ){
559            ##     doc$.s3method <- gen$.s3method
560            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
561            ##   }
562            ## }
563          }
564          if("title" %in% names(doc) && !"description" %in% names(doc) ){
565            ## For short functions having both would duplicate, but a
566            ## description is required. Therefore automatically copy title
567            ## across to avoid errors at package build time.
568            doc$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                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
583                  ){
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          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
646          L <-
647            list(list(title=desc[,"Title"],
648                      description=desc[,"Description"],
649                      `tabular{ll}`=details))
650          names(L) <- paste(desc[,"Package"],"-package",sep="")
651          L
652        },
653        sapply(forall.parsers,forall)
654        )
655    
656  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
657  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
658  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
659  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
660    ### the parent class.
661           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
662                          created="character", ##<< how created                          created="character", ##<< how created
663                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 495  Line 692 
692      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
693      default.description <- NULL      default.description <- NULL
694      while ( start > last.end+1      while ( start > last.end+1
695             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
696        start <- start-1        start <- start-1
697      }      }
698      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 522  Line 719 
719        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
720        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
721        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
722        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
723          parent <- chars[3]          parent <- chars[3]
724        }        }
725        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 554  Line 751 
751        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
752        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
753        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
754        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
755          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
756        }        }
757        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 574  Line 771 
771  ### Using the same conventions as for functions, definitions of S4 classes  ### Using the same conventions as for functions, definitions of S4 classes
772  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
773  ### scanned for inline comments.  ### scanned for inline comments.
774  (doc.link)  (doc.link
775  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{\link{extract.file.parse}}.
776  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
777  ### class definitions.  ### class definitions.
778  {   ){
779    chunk.source <- doc.link@code    chunk.source <- doc.link@code
780    ##details<<    ##details<<
781    ## Extraction of S4 class documentation is currently limited to expressions    ## Extraction of S4 class documentation is currently limited to expressions
# Line 595  Line 792 
792    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
793    ## following line.    ## following line.
794    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
795    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
796      ## also apply source parsing functions that I separated out into
797      ## separate functions
798      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
799      docs$title <- lonely$title.from.firstline(chunk.source)
800    ##details<<    ##details<<
801    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
802    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 619  Line 820 
820    }    }
821    invisible(docs)    invisible(docs)
822  }  }
823    
824    apply.parsers <- function
825    ### Parse code to r objs, then run all the parsers and return the
826    ### documentation list.
827    (code,
828    ### Character vector of code lines.
829     parsers=default.parsers,
830    ### List of Parser Functions.
831     verbose=FALSE,
832    ### Echo names of Parser Functions?
833     ...
834    ### Additional arguments to pass to Parser Functions.
835     ){
836      e <- new.env()
837      ## 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      old <- options(keep.source=TRUE,topLevelEnvironment=e)
845      on.exit(options(old))
846      exprs <- parse(text=code)
847      ## 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      for (i in exprs){
851        ## 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          ##print(e)
858        ##})
859      }
860      objs <- sapply(ls(e),get,e,simplify=FALSE)
861    
862      docs <- list()
863    
864      ## apply parsers in sequence to code and objs
865      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        L <- p(code=code,objs=objs,docs=docs,env=e,...)
875        docs <- combine(docs,L)
876      }
877      ## post-process to collapse all character vectors
878      for(i in seq_along(docs)){
879        for(j in seq_along(docs[[i]])){
880          if(names(docs[[i]])[j]!=".s3method")
881          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
882        }
883      }
884      if(verbose)cat("\n")
885      docs
886    ### A list of extracted documentation from code.
887    }
888    
889    ### 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    ### Parsers that operate only on R code, independently of the
897    ### description file.
898    nondesc.parsers <- default.parsers[non.descfile.names]
899    
900    extract.docs.file <- structure(function
901    ### 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     parsers=NULL,
905    ### Parser Functions to use to parse the code and extract
906    ### documentation.
907     ...
908    ### Other arguments to pass to Parser Functions.
909     ){
910      if(is.null(parsers))parsers <- nondesc.parsers
911      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
912    },ex=function(){
913      f <- system.file("silly","R","silly.R",package="inlinedocs")
914      extract.docs.file(f)
915    })
916    

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