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

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revision 142, Wed Oct 20 09:21:53 2010 UTC revision 376, Mon Jan 28 01:08:01 2013 UTC
# Line 1  Line 1 
1    do.not.generate <- structure(function
2    ### Make a Parser Function used to indicate that certain Rd files
3    ### should not be generated.
4    (...
5    ### Character strings indicating Rd files without the .Rd suffix.
6     ){
7      filenames <- c(...)
8      function(docs,...){
9        for(fn in filenames){
10          docs[[fn]] <- list()
11        }
12        docs$.overwrite <- TRUE
13        docs
14      }
15    ### A Parser Function that will delete items from the outer
16    ### Documentation List.
17    },ex=function(){
18      silly.pkg <- system.file("silly",package="inlinedocs")
19      owd <- setwd(tempdir())
20      file.copy(silly.pkg,".",recursive=TRUE)
21    
22      ## define a custom Parser Function that will not generate some Rd
23      ## files
24      custom <- do.not.generate("silly-package","Silly-class")
25      parsers <- c(default.parsers,list(exclude=custom))
26    
27      ## At first, no Rd files in the man subdirectory.
28      man.dir <- file.path("silly","man")
29      dir(man.dir)
30    
31      ## Running package.skeleton.dx will generate bare-bones files for
32      ## those specified in do.not.generate, if they do not exist.
33      package.skeleton.dx("silly",parsers)
34      Rd.files <- c("silly-package.Rd","Silly-class.Rd","silly.example.Rd")
35      Rd.paths <- file.path(man.dir,Rd.files)
36      stopifnot(all(file.exists(Rd.paths)))
37    
38      ## Save the modification times of the Rd files
39      old <- file.info(Rd.paths)$mtime
40    
41      ## make sure there is at least 2 seconds elapsed, which is the
42      ## resolution for recording times on windows file systems.
43      Sys.sleep(4)
44    
45      ## However, it will NOT generate Rd for files specified in
46      ## do.not.generate, if they DO exist already.
47      package.skeleton.dx("silly",parsers)
48      mtimes <- data.frame(old,new=file.info(Rd.paths)$mtime)
49      rownames(mtimes) <- Rd.files
50      mtimes$changed <- mtimes$old != mtimes$new
51      print(mtimes)
52      stopifnot(mtimes["silly-package.Rd","changed"]==FALSE)
53      stopifnot(mtimes["Silly-class.Rd","changed"]==FALSE)
54      stopifnot(mtimes["silly.example.Rd","changed"]==TRUE)
55    
56      unlink("silly",recursive=TRUE)
57      setwd(owd)
58    })
59    
60    ### combine NULL objects.
61    combine.NULL<-function(x,y){
62        if (class(x) == "NULL"){
63            # print(paste("mm x=",x))
64            # print(paste("mm class(x)=",class(x)))
65            x=list("")
66        }
67        if (class(y) == "NULL"){
68            # print(paste("mm y=",y))
69            # print(paste("mm class(y)=",class(y)))
70            y=list("")
71        }
72        return(combine(x,y))
73    }
74    
75  ### combine lists or character strings  ### combine lists or character strings
76  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y){
77        UseMethod("combine")
78    }
79    
80  ### combine character strings by pasting them together  ### combine character strings by pasting them together
81  combine.character <- function(x,y)  combine.character <- function(x,y)
# Line 7  Line 83 
83    
84  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
85  combine.list <- function(x,y){  combine.list <- function(x,y){
86    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
87    toup <- names(y)[names(y)%in%names(x)]      y <- y[names(y)!=".overwrite"]
88        rep(TRUE,length(y))
89      }else{
90        !names(y)%in%names(x)
91      }
92      toup <- names(y)[!toadd]
93    x[names(y)[toadd]] <- y[toadd]    x[names(y)[toadd]] <- y[toadd]
94    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
95    return(x)    x
96  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
97  }  }
98    
99    
100    getSource <- function
101    ### Extract a function's source code.
102    (fun.obj
103    ### A function.
104     ) {
105          srcref <- attr(fun.obj, "srcref")
106          if (!is.null(srcref)) {
107            ##unlist(strsplit(as.character(srcref), "\n"))
108            as.character(srcref)
109          }
110          else attr(fun.obj, "source")
111    ### Source code lines as a character vector.
112    }
113    
114  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
115  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
116    
117  decomment <- function  decomment <- function
118  ### Remove comment prefix and join lines of code to form a  ### Remove comment prefix and join lines of code to form a
# Line 24  Line 120 
120  (comments  (comments
121  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
122   ){   ){
123    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
124  ### String without prefixes or newlines.  ### String without prefixes or newlines.
125  }  }
126    
 ### For each object in the package that satisfies the criterion#  
 ## checked by subfun, parse source using FUN and return the resulting  
 ### documentation list.  
127  forall <- function  forall <- function
128    ### For each object in the package that satisfies the criterion
129    ### checked by subfun, parse source using FUN and return the resulting
130    ### documentation list.
131  (FUN,  (FUN,
132  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
133   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 41  Line 137 
137   ){   ){
138    FUN <- FUN    FUN <- FUN
139    f <- function(objs,docs,...){    f <- function(objs,docs,...){
140        if(length(objs)==0)return(list())
141      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
142      L <- list()      L <- list()
143      for(N in names(docs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
144        for(N in union(names(docs),names(objs))){
145        o <- objs[[N]]        o <- objs[[N]]
146        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
147                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
148      }      }
149        on.exit()## remove warning message
150      L      L
151    }    }
152    class(f) <- c("allfun","function")    class(f) <- c("allfun","function")
# Line 67  Line 166 
166  ### For each function in the package, do something.  ### For each function in the package, do something.
167  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
168    
169  examples.after.return <- function  kill.prefix.whitespace <- function
170  ### Get examples from inline definitions after return()  ### Figure out what the whitespace preceding the example code is, and
171  ### PhG: this does not work well! Think of these situations:  ### then delete that from every line.
172  ### 1) You have multiple return() in the code of your function,  (ex
173  ### 2) You have return() appearing is some example code, ...  ### character vector of example code lines.
174  ### I can hardly propose a hack here. The whole code of the function   ){
175  ### must be parsed, and one must determine which one is the last line    tlines <- gsub("\\s*","",ex)
176  ### of code that is actually executed.    ##tlines <- gsub("#.*","",tlines)
177  ###    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
 ### 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!  
 (src,name="",...) {  
   ## Look for the examples mark  
   m <- grep("^\\s*(##examples<<|#\\{\\{\\{examples)", src)  
   if (!length(m)) return(list())  
   if (length(m) > 1)  
     warning("More than one examples tag for ", name,  
             ". Taking the last one")  
   m <- m[length(m)]  
   ## Look for the lines containing return value comments just before  
   r <- grep("\\s*### ", src[1:(m-1)])  
     if (!length(r)) {  
       value <- NULL  
     } else {  
       ## Only take consecutive lines before the mark  
       keep <- rev((m - rev(r)) == 1:length(r))  
       if (!any(keep)) {  
         value <- NULL  
       } else {  
         value <- decomment(src[r[keep]])  
       }  
     }  
   ## Collect now the example code beneath the mark  
   ex <- src[(m + 1):(length(src) - 1)]  
   ## Possibly eliminate a #}}} tag  
   ex <- ex[!grepl("#}}}", ex)]  
   ## Eliminate leading tabulations or four spaces  
   prefixes <- gsub("(\\s*).*","\\1",ex,perl=TRUE)[grep("\\w",ex)]  
178    FIND <- prefixes[which.min(nchar(prefixes))]    FIND <- prefixes[which.min(nchar(prefixes))]
179    ex <- sub(FIND,"",ex)    ## Eliminate leading tabulations or 2/4 spaces
180    ## Add an empty line before and after example    sub(FIND, "", ex)
181    ex <- c("", ex, "")  ### Character vector of code lines with preceding whitespace removed.
   ## Return examples and value  
   list(examples = paste(ex, collapse = "\n"), value = value)  
182  }  }
183    
184  prefixed.lines <- function(src,...){  prefixed.lines <- structure(function(src,...){
185  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
186  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
187  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 136  Line 197 
197    starts <- c(1,bounds+1)    starts <- c(1,bounds+1)
198    ends <- c(bounds,length(clines))    ends <- c(bounds,length(clines))
199    ## detect body of function using paren matching    ## detect body of function using paren matching
200    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",src)))    code <- gsub("#.*","",src)
201      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
202    parens <- f("(")-f(")")    parens <- f("(")-f(")")
203    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
204      if(length(body.begin)==0)body.begin <- 1 ## rare cases
205    is.arg <- function(){    is.arg <- function(){
206      0 == length(grep("^\\s*#",src[start-1],perl=TRUE)) &&      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
207        start<=body.begin      0 == length(gres) && start<=body.begin
208      }      }
209    res <- list()    res <- list()
210    for(i in seq_along(starts)){    for(i in seq_along(starts)){
211      start <- clines[starts[i]]      start <- clines[starts[i]]
212      end <- clines[ends[i]]      end <- clines[ends[i]]
213      lab <- if(end+1==length(src))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
214        lab <- if(all(processed==""))"value"
215      else if(start==2)"description"      else if(start==2)"description"
216      else if(is.arg()){      else if(is.arg()){
217        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 155  Line 219 
219        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
220        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
221        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
222        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
223        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
224      } else {      } else {
225        next;        next;
# Line 163  Line 227 
227      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
228    }    }
229    res    res
230  }  },ex=function(){
231    test <- function
232  ### Parsers for each object/function that are constructed  ### the description
233  ### automatically. This is a named list, each element is a list of 2  (x,
234  ### elements: forfun/forall, then a parser function for an individual  ### the first argument
235  ### object.   y ##<< another argument
 forfun.parsers <-  
   list(prefixed.lines=prefixed.lines,  
        examples.after.return=examples.after.return,  
        ## Extract lots of info from normal functions.  
        parsefun=function(src,name,...){  
          extract.docs.fun(src,name)  
        },  
        ## title from first line of function def  
        title.from.firstline=function(src,name,code,...){  
          if(length(grep("#",src[1]))){  
            list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))  
          } else list()  
        },  
        ## PhG: it is tests/FUN.R!!! I would like more flexibility here  
        ## please, let me choose which dir to use for examples!  
        ## Get examples for FUN from the file tests/FUN.R  
        examples.from.testfile=function(name,...){  
          tsubdir <- getOption("inlinedocs.exdir")  
          if (is.null(tsubdir)) tsubdir <- "tests"       # Default value  
          tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))  
          if(file.exists(tfile))  
            list(examples=paste(readLines(tfile),collapse="\n"))  
          else list()  
        },  
        definition.from.source=function(doc,src,...){  
          def <- doc$definition  
          if(is.null(def)||def=="")  
            list(definition=paste(src,collapse="\n"))  
          else list()  
        })  
   
 ### List of Parser Functions that can be applied to any object.  
 forall.parsers <-  
   list(## Fill in author from DESCRIPTION and titles.  
        author.from.description=function(desc,...){  
          list(author=desc[,"Maintainer"])  
        },  
        ## The format section sometimes causes problems, so erase it.  
        erase.format=function(...){  
          list(format="")  
        },  
        ## Convert the function name to a title.  
        title.from.name=function(name,doc,...){  
          if("title"%in%names(doc))list() else  
          list(title=gsub("[._]"," ",name))  
        },  
        ## PhG: here is what I propose for examples code in the 'ex' attribute  
        examples.in.attr =  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 2/4 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.  
 lonely <- c(forall.parsers,forfun.parsers)  
 attr(lonely,"ex") <- function(){  
   lonely$parsefun(attr(extract.docs.file,"source"),"extract.docs.file")  
 }  
   
 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))  
236                ){                ){
237        ## phew - this should only pick up R.oo S3 generic definitions like:    5
238        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"  ### the return value
239        NULL  ##seealso<< foobar
240      } else res  }
241    }  src <- getSource(test)
242    doc.names <- names(objs)  prefixed.lines(src)
243    res <- sapply(doc.names,extract.docs,simplify=FALSE)  extract.xxx.chunks(src)
   ## 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.  
 }  
   
 ### List of parsers to use by default with package.skeleton.dx.  
 default.parsers <-  
   c(extra.code.docs=extra.code.docs, ## TODO: cleanup!  
     sapply(forfun.parsers,forfun),  
     sapply(forall.parsers,forall),  
     edit.package.file=function(desc,...){  
       in.details <- setdiff(colnames(desc),"Description")  
       details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",  
                              sep=""),collapse="\n")  
       L <-  
         list(list(title=desc[,"Title"],  
                   description=desc[,"Description"],  
                   `tabular{ll}`=details,  
                   author=desc[,"Maintainer"]))  
       names(L) <- paste(desc[,"Package"],"-package",sep="")  
       L  
244      })      })
245    
246  extract.docs.fun <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
247  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
248  ### documentation in that source code.  ### documentation in that source code.
249  (code,  (src,
250  ### The function to examine.  ### The source lines of the function to examine, as a character
251   name.fun  ### vector.
252     name.fun="(unnamed function)",
253  ### The name of the function/chunk to use in warning messages.  ### The name of the function/chunk to use in warning messages.
254     ...
255    ### ignored.
256   ){   ){
257    res <- list()    res <- list()
258    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
# Line 462  Line 327 
327          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
328        }        }
329        chunk.res <- NULL        chunk.res <- NULL
330        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
331          chunk.res <-          chunk.res <-
332            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
333            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
334        invisible(chunk.res)        invisible(chunk.res)
335      }      }
336    while ( k <= length(code) ){    while ( k <= length(src) ){
337      line <- code[k]      line <- src[k]
338      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      ##print(line)
339        ##if(grepl("^$",line))browser()
340        if ( grepl(extra.regexp,line,perl=TRUE) ){
341        ## 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
342        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
343        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
344          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
345        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
346        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
347        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 483  Line 350 
350        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
351        if ( "describe" == new.field ){        if ( "describe" == new.field ){
352          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
353          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
354          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
355          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
356            ## \code{##describe<<} comments.
357          if ( first.describe ){          if ( first.describe ){
358            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
359          } else {          } else {
# Line 545  Line 413 
413            first.describe <- TRUE;            first.describe <- TRUE;
414          }          }
415        }        }
416      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
417        ## append this line to current chunk        ## append this line to current chunk
418        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
419          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
420          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
421          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 560  Line 428 
428            payload <- stripped            payload <- stripped
429          }          }
430        }        }
431      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
432        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
433        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
434          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 572  Line 440 
440          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
441          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
442          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
443          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
444          payload <- comment          payload <- comment
445        } else {        } else {
446          ## this is a describe block, so we need to paste with existing          ## this is a describe block, so we need to paste with existing
# Line 622  Line 490 
490  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
491  }  }
492    
493    leadingS3generic <- function # check whether function name is an S3 generic
494    ### Determines whether a function name looks like an S3 generic function
495    (name,                     ##<< name of function
496     env,                      ##<< environment to search for additional generics
497     ...)                      ##<< ignored here
498    {
499      ##details<< This function is one of the default parsers, but exposed as
500      ## possibly of more general interest. Given a function name of the form
501      ## x.y.z it looks for the generic function x applying to objects of class
502      ## y.z and also for generic function x.y applying to objects of class z.
503      ##
504      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
505      l <- length(parts)
506      if (l > 1) {
507        for (i in 1:(l - 1)) {
508          ## Look for a generic function (known by the system or defined
509          ## in the package) that matches that part of the function name
510          generic <- paste(parts[1:i], collapse = ".")
511          if (any(generic %in% utils:::getKnownS3generics()) ||
512              utils:::findGeneric(generic, env) != "") {
513            object <- paste(parts[(i + 1):l], collapse = ".")
514            ##details<< Assumes that the first name which matches any known
515            ## generics is the target generic function, so if both x and x.y
516            ## are generic functions, will assume generic x applying to objects
517            ## of class y.z
518            ##value<< If a matching generic found returns a list with a single component:
519            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
520          }
521        }
522      }
523      ##value<< If no matching generic functions are found, returns an empty list.
524      list()
525    }
526    
527    ### Parsers for each function that are constructed automatically. This
528    ### is a named list, and each element is a parser function for an
529    ### individual object.
530    forfun.parsers <-
531      list(prefixed.lines=prefixed.lines,
532           extract.xxx.chunks=extract.xxx.chunks,
533           ## title from first line of function def
534           title.from.firstline=function(src,...){
535             first <- src[1]
536             if(!is.character(first))return(list())
537             if(!grepl("#",first))return(list())
538             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
539           },
540           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
541           ## please, let me choose which dir to use for examples!
542           ## Get examples for FUN from the file tests/FUN.R
543           examples.from.testfile=function(name,...){
544             tsubdir <- getOption("inlinedocs.exdir")
545             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
546             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
547             if(file.exists(tfile))
548               list(examples=readLines(tfile))
549             else list()
550           },
551           definition.from.source=function(doc,src,...){
552             def <- doc$definition
553             is.empty <- function(x)is.null(x)||x==""
554             if(is.empty(def) && !is.empty(src))
555               list(definition=src)
556             else list()
557           })
558    
559    ### List of Parser Functions that can be applied to any object.
560    forall.parsers <-
561      list(## Fill in author from DESCRIPTION and titles.
562           author.from.description=function(desc,...){
563             list(author=desc[,"Author"])
564           },
565           ## The format section sometimes causes problems, so erase it.
566           erase.format=function(...){
567             list(format="")
568           },
569           ## Convert the function name to a title.
570           title.from.name=function(name,doc,...){
571             if("title"%in%names(doc))list() else
572             list(title=gsub("[._]"," ",name))
573           },
574           ## PhG: here is what I propose for examples code in the 'ex' attribute
575           examples.in.attr =  function (name, o, ...) {
576             ex <- attr(o, "ex")
577             if (!is.null(ex)) {
578               ## Special case for code contained in a function
579               if (inherits(ex, "function")) {
580                 ## If source is available, start from there
581                 src <- getSource(ex)
582                 if (!is.null(src)) {
583                   ex <- src
584                 } else { ## Use the body of the function
585                   ex <- deparse(body(ex))
586                 }
587                 ## Eliminate leading and trailing code
588                 ex <- ex[-c(1, length(ex))]
589                 if(ex[1]=="{")ex <- ex[-1]
590                 ## all the prefixes
591                 ex <- kill.prefix.whitespace(ex)
592                 ## Add an empty line before and after example
593                 ex <- c("", ex, "")
594               }
595               list(examples = ex)
596             } else list()
597           },collapse=function(doc,...){
598             L <- lapply(doc,paste,collapse="\n")
599             L$.overwrite <- TRUE
600             L
601           },tag.s3methods=leadingS3generic
602           )
603    
604    ### List of parser functions that operate on single objects. This list
605    ### is useful for testing these functions.
606    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
607      f <- function # title
608    ### description
609      (x, ##<< arg x
610       y
611    ### arg y
612       ){
613        ##value<< a list with elements
614        list(x=x, ##<< original x value
615             y=y, ##<< original y value
616             sum=x+y) ##<< their sum
617        ##end<<
618      }
619      src <- getSource(f)
620      lonely$extract.xxx.chunks(src)
621      lonely$prefixed.lines(src)
622    })
623    
624    extra.code.docs <- function # Extract documentation from code chunks
625    ### Parse R code to extract inline documentation from comments around
626    ### each function. These are not able to be retreived simply by
627    ### looking at the "source" attribute. This is a Parser Function that
628    ### can be used in the parser list of package.skeleton.dx(). TODO:
629    ### Modularize this into separate Parsers Functions for S4 classes,
630    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
631    (code,
632    ### Code lines in a character vector containing multiple R objects to
633    ### parse for documentation.
634     objs,
635    ### The objects defined in the code.
636     ...
637    ### ignored
638     ){
639      parsed <- extract.file.parse(code)
640      extract.docs.try <- function(o,on)
641        {
642          ## Note: we could use parsed information here too, but that
643          ## would produce different results for setMethodS3 etc.
644          doc <- list()
645          if ( !is.null(parsed[[on]]) ){
646            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
647              doc$definition <- paste(parsed[[on]]@code)
648            }
649            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
650              doc$description <- parsed[[on]]@description
651            }
652            ## if ( "setMethodS3" == parsed[[on]]@created ){
653            ##   gen <- leadingS3generic(on,topenv())
654            ##   if ( 0 < length(gen) ){
655            ##     doc$.s3method <- gen$.s3method
656            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
657            ##   }
658            ## }
659          }
660          if("title" %in% names(doc) && !"description" %in% names(doc) ){
661            ## For short functions having both would duplicate, but a
662            ## description is required. Therefore automatically copy title
663            ## across to avoid errors at package build time.
664            doc$description <- doc$title
665          }
666          doc
667        }
668      extract.docs <- function(on){
669        res <- try({o <- objs[[on]]
670                    extract.docs.try(o, on)},FALSE)
671        if(class(res)=="try-error"){
672          cat("Failed to extract docs for: ",on,"\n\n")
673          list()
674        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
675          NULL
676        } else if(0 == length(res) && "function" %in% class(o)
677                  && 1 == length(osource <- getSource(o))
678                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
679                  ){
680          ## phew - this should only pick up R.oo S3 generic definitions like:
681          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
682          NULL
683        } else res
684      }
685      doc.names <- names(objs)
686      res <- sapply(doc.names,extract.docs,simplify=FALSE)
687      ## Special processing for S4 classes as they do not appear in normal ls()
688      for ( nn in names(parsed) ){
689        if ( parsed[[nn]]@created == "setClass" ){
690          S4class.docs <- extract.docs.setClass(parsed[[nn]])
691          docname <- paste(nn,"class",sep="-")
692          if ( is.null(res[[docname]]) ){
693            res[[docname]] <- S4class.docs
694            doc.names <- c(doc.names,docname)
695          } else {
696            stop(nn," appears as both S4 class and some other definition")
697          }
698        }
699      }
700      inherit.docs <- function(on){
701        in.res <- res[[on]]
702        if ( !is.null(parsed[[on]]) ){
703          for ( parent in parsed[[on]]@parent ){
704            if ( !is.na(parent) ){
705              if ( is.null(in.res) ){
706                in.res <- res[[parent]]
707              } else if ( parent %in% names(res) ){
708                parent.docs <- res[[parent]]
709                for ( nn in names(parent.docs) ){
710                  if ( !nn %in% names(in.res) ){
711                    in.res[[nn]] <- parent.docs[[nn]]
712                  }
713                }
714              }
715            }
716          }
717        }
718        invisible(in.res)
719      }
720      all.done <- FALSE
721      while ( !all.done ){
722        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
723        all.done <- identical(res1,res)
724        res <- res1
725      }
726      ## now strip out any generics (which have value NULL in res):
727      res.not.null <- sapply(res,function(x){!is.null(x)})
728      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
729        res <- res[res.not.null]
730      }
731      res
732    ### named list of lists, one for each object to document.
733    }
734    
735    ### List of parsers to use by default with package.skeleton.dx.
736    default.parsers <-
737      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
738        sapply(forfun.parsers,forfun),
739        edit.package.file=function(desc,...){
740          in.details <- setdiff(colnames(desc),"Description")
741          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
742          L <-
743            list(list(title=desc[,"Title"],
744                      description=desc[,"Description"],
745                      `tabular{ll}`=details))
746          names(L) <- paste(desc[,"Package"],"-package",sep="")
747          L
748        },
749        sapply(forall.parsers,forall)
750        )
751    
752  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
753  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
754  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
755  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
756    ### the parent class.
757           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
758                          created="character", ##<< how created                          created="character", ##<< how created
759                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 634  Line 762 
762           )           )
763    
764  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
765  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
766  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
767  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
768  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 660  Line 788 
788      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
789      default.description <- NULL      default.description <- NULL
790      while ( start > last.end+1      while ( start > last.end+1
791             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
792        start <- start-1        start <- start-1
793      }      }
794      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 687  Line 815 
815        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
816        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
817        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
818        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
819          parent <- chars[3]          parent <- chars[3]
820        }        }
821        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 706  Line 834 
834        generic.name <- chars[2]        generic.name <- chars[2]
835        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
836        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
837          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
838            ## since it causes problems on R CMD check.
839            ##* checking Rd cross-references ... WARNING
840            ##Error in find.package(package, lib.loc) :
841            ##  there is no package called ‘MASS’
842            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
843    
844            generic.desc <-
845              paste("Generic method behind \\code{",object.name,"}",sep="")
846          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
847                                     name=generic.name,                                     name=generic.name,
848                                     created=expr.type,                                     created=expr.type,
# Line 719  Line 855 
855        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
856        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
857        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
858        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
859          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
860        }        }
861        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 740  Line 876 
876  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
877  ### scanned for inline comments.  ### scanned for inline comments.
878  (doc.link  (doc.link
879  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
880  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
881  ### class definitions.  ### class definitions.
882   ){   ){
# Line 760  Line 896 
896    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
897    ## following line.    ## following line.
898    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
899    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
900    ## also apply source parsing functions that I separated out into    ## also apply source parsing functions that I separated out into
901    ## separate functions    ## separate functions
902    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
903    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
904    ##details<<    ##details<<
905      ## If there is no explicit title on the first line of setClass, then
906      ## one is made up from the class name.
907      if ( 0 == length(docs$title) ){
908        docs$title <- list(title=paste(class.name,"S4 class"))
909      }
910      ##details<<
911    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
912    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
913    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 802  Line 944 
944  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
945   ){   ){
946    e <- new.env()    e <- new.env()
947    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
948      ## Error in assignClassDef(Class, classDef, where) :
949      ##   Class "DocLink" has a locked definition in package "inlinedocs"
950      ## Traced to "where" argument in setClassDef which defaults to topenv()
951      ## which in turn is inlinedocs when processing inlinedocs package, hence
952      ## the clash. The following works (under R 2.12.2), so that the topenv()
953      ## now finds e before finding the inlinedocs environment.
954      old <- options(keep.source=TRUE,topLevelEnvironment=e)
955    on.exit(options(old))    on.exit(options(old))
956    exprs <- parse(text=code)    exprs <- parse(text=code)
957    for (i in exprs) eval(i, e)    ## TDH 2011-04-07 set this so that no warnings about creating a fake
958      ## package when we try to process S4 classes defined in code
959      e$.packageName <- "inlinedocs.processor"
960      for (i in exprs){
961          eval(i, e)
962      }
963    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
964    
965    docs <- list()    docs <- list()
966    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
967    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
968      if(verbose)cat("Applying parsers:\n")
969    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
970      N <- names(parsers[i])      N <- names(parsers[i])
971      if(verbose){      #mm if(verbose){
972        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
973          cat(N," ",sep="")          cat(" this is parser:",N,"\n",sep="")
974        }else cat('. ')        }else cat('.\n')
975      }      #mm }
976      p <- parsers[[i]]      p <- parsers[[i]]
977      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
978      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
979      docs <- combine(docs,L)      # print("mm point1")
980        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
981        #print(paste(L,"\n"))
982        #if(N=="exclude")browser()
983        docs <- combine(docs,L) #mm
984      }
985      ## post-process to collapse all character vectors
986      for(i in seq_along(docs)){
987        for(j in seq_along(docs[[i]])){
988          if(names(docs[[i]])[j]!=".s3method")
989          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
990        }
991    }    }
992    if(verbose)cat("\n")    if(verbose)cat("\n")
993    docs    return(docs)
994  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
995  }  }
996    
# Line 857  Line 1005 
1005  ### description file.  ### description file.
1006  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
1007    
1008  extract.docs.file <- function  extract.docs.file <- structure(function
1009  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
1010  (f,  (f,
1011  ### File name of R code to read and parse.  ### File name of R code to read and parse.
1012   parsers=nondesc.parsers,   parsers=NULL,
1013  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
1014  ### documentation.  ### documentation.
1015   ...   ...
1016  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
1017   ){   ){
1018      if(is.null(parsers))parsers <- nondesc.parsers
1019    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
1020  }  },ex=function(){
1021      f <- system.file("silly","R","silly.R",package="inlinedocs")
1022      extract.docs.file(f)
1023    })
1024    

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