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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 302, Tue Jul 12 12:06:42 2011 UTC
# Line 7  Line 7 
7    
8  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
9  combine.list <- function(x,y){  combine.list <- function(x,y){
10    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
11    toup <- names(y)[names(y)%in%names(x)]      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]    x[names(y)[toadd]] <- y[toadd]
18    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
19    return(x)    x
20  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
21  }  }
22    
23    
24    getSource <- function
25    ### Extract a function's source code.
26    (fun.obj
27    ### A function.
28     ) {
29          srcref <- attr(fun.obj, "srcref")
30          if (!is.null(srcref)) unlist(strsplit(as.character(srcref), "\n"))
31          else attr(fun.obj, "source")
32    ### Source code lines as a character vector.
33    }
34    
35  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
36  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
37    
38  decomment <- function  decomment <- function
39  ### 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 41 
41  (comments  (comments
42  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
43   ){   ){
44    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
45  ### String without prefixes or newlines.  ### String without prefixes or newlines.
46  }  }
47    
 ### For each object in the package that satisfies the criterion#  
 ## checked by subfun, parse source using FUN and return the resulting  
 ### documentation list.  
48  forall <- function  forall <- function
49    ### For each object in the package that satisfies the criterion
50    ### checked by subfun, parse source using FUN and return the resulting
51    ### documentation list.
52  (FUN,  (FUN,
53  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
54   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 41  Line 58 
58   ){   ){
59    FUN <- FUN    FUN <- FUN
60    f <- function(objs,docs,...){    f <- function(objs,docs,...){
61        if(length(objs)==0)return(list())
62      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
63      L <- list()      L <- list()
64      for(N in names(docs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
65        for(N in union(names(docs),names(objs))){
66        o <- objs[[N]]        o <- objs[[N]]
67        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
68                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
69      }      }
70        on.exit()## remove warning message
71      L      L
72    }    }
73    class(f) <- c("allfun","function")    class(f) <- c("allfun","function")
# Line 67  Line 87 
87  ### For each function in the package, do something.  ### For each function in the package, do something.
88  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
89    
90  examples.after.return <- function  kill.prefix.whitespace <- function
91  ### Get examples from inline definitions after return()  ### Figure out what the whitespace preceding the example code is, and
92  ### PhG: this does not work well! Think of these situations:  ### then delete that from every line.
93  ### 1) You have multiple return() in the code of your function,  (ex
94  ### 2) You have return() appearing is some example code, ...  ### character vector of example code lines.
95  ### I can hardly propose a hack here. The whole code of the function   ){
96  ### must be parsed, and one must determine which one is the last line    tlines <- gsub("\\s*","",ex)
97  ### of code that is actually executed.    ##tlines <- gsub("#.*","",tlines)
98  ###    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)]  
99    FIND <- prefixes[which.min(nchar(prefixes))]    FIND <- prefixes[which.min(nchar(prefixes))]
100    ex <- sub(FIND,"",ex)    ## Eliminate leading tabulations or 2/4 spaces
101    ## Add an empty line before and after example    sub(FIND, "", ex)
102    ex <- c("", ex, "")  ### Character vector of code lines with preceding whitespace removed.
   ## Return examples and value  
   list(examples = paste(ex, collapse = "\n"), value = value)  
103  }  }
104    
105  prefixed.lines <- function(src,...){  prefixed.lines <- structure(function(src,...){
106  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
107  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
108  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 136  Line 118 
118    starts <- c(1,bounds+1)    starts <- c(1,bounds+1)
119    ends <- c(bounds,length(clines))    ends <- c(bounds,length(clines))
120    ## detect body of function using paren matching    ## detect body of function using paren matching
121    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",src)))    code <- gsub("#.*","",src)
122      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
123    parens <- f("(")-f(")")    parens <- f("(")-f(")")
124    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
125      if(length(body.begin)==0)body.begin <- 1 ## rare cases
126    is.arg <- function(){    is.arg <- function(){
127      0 == length(grep("^\\s*#",src[start-1],perl=TRUE)) &&      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
128        start<=body.begin      0 == length(gres) && start<=body.begin
129      }      }
130    res <- list()    res <- list()
131    for(i in seq_along(starts)){    for(i in seq_along(starts)){
132      start <- clines[starts[i]]      start <- clines[starts[i]]
133      end <- clines[ends[i]]      end <- clines[ends[i]]
134      lab <- if(end+1==length(src))"value"      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"
135      else if(start==2)"description"      else if(start==2)"description"
136      else if(is.arg()){      else if(is.arg()){
137        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 163  Line 147 
147      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
148    }    }
149    res    res
150  }  },ex=function(){
151    test <- function
152  ### Parsers for each object/function that are constructed  ### the description
153  ### automatically. This is a named list, each element is a list of 2  (x,
154  ### elements: forfun/forall, then a parser function for an individual  ### the first argument
155  ### 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  
156   ){   ){
157    parsed <- extract.file.parse(code)    5
158    extract.docs.try <- function(o,on)  ### the return value
159      {  ##seealso<< foobar
160        ## Note: we could use parsed information here too, but that  }
161        ## would produce different results for setMethodS3 etc.  src <- getSource(test)
162        doc <- list()  prefixed.lines(src)
163        if ( !is.null(parsed[[on]]) ){  extract.xxx.chunks(src)
         if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics  
           doc$definition <- paste(parsed[[on]]@code,collapse="\n")  
         }  
         if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){  
           doc$description <- parsed[[on]]@description  
         }  
         if ( "setMethodS3" == parsed[[on]]@created ){  
           # PhG: this may be wrong! It does not catch correctly how the method  
           # must be splitted in case of methods containing dots. for instance,  
           # as.data.frame.matrix must be split into: m1 = as.data.frame and  
           # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!  
                   pattern <- "^([^\\.]+)\\.(.*)$"  
           doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),  
               m2 <- gsub(pattern,"\\2",on,perl=TRUE))  
           if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){  
                           m1 <- paste("`",m1,"`",sep="")  
           }  
           cat("S3method(",m1,",",m2,")\n",sep="")  
         }  
       }  
       if("title" %in% names(doc) && !"description" %in% names(doc) ){  
         ## For short functions having both would duplicate, but a  
         ## description is required. Therefore automatically copy title  
         ## across to avoid errors at package build time.  
         doc$description <- doc$title  
       }  
       doc  
     }  
   extract.docs <- function(on){  
     res <- try({o <- objs[[on]]  
                 extract.docs.try(o, on)},FALSE)  
     if(class(res)=="try-error"){  
       cat("Failed to extract docs for: ",on,"\n\n")  
       list()  
     } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){  
       NULL  
     } else if(0 == length(res) && "function" %in% class(o)  
               && 1 == length(osource <- attr(o,"source"))  
               && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))  
               ){  
       ## phew - this should only pick up R.oo S3 generic definitions like:  
       ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"  
       NULL  
     } else res  
   }  
   doc.names <- names(objs)  
   res <- sapply(doc.names,extract.docs,simplify=FALSE)  
   ## Special processing for S4 classes as they do not appear in normal ls()  
   for ( nn in names(parsed) ){  
     if ( parsed[[nn]]@created == "setClass" ){  
       S4class.docs <- extract.docs.setClass(parsed[[nn]])  
       docname <- paste(nn,"class",sep="-")  
       if ( is.null(res[[docname]]) ){  
         res[[docname]] <- S4class.docs  
         doc.names <- c(doc.names,docname)  
       } else {  
         stop(nn," appears as both S4 class and some other definition")  
       }  
     }  
   }  
   inherit.docs <- function(on){  
     in.res <- res[[on]]  
     if ( !is.null(parsed[[on]]) ){  
       for ( parent in parsed[[on]]@parent ){  
         if ( !is.na(parent) ){  
           if ( is.null(in.res) ){  
             in.res <- res[[parent]]  
           } else if ( parent %in% names(res) ){  
             parent.docs <- res[[parent]]  
             for ( nn in names(parent.docs) ){  
               if ( !nn %in% names(in.res) ){  
                 in.res[[nn]] <- parent.docs[[nn]]  
               }  
             }  
           }  
         }  
       }  
     }  
     invisible(in.res)  
   }  
   all.done <- FALSE  
   while ( !all.done ){  
     res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)  
     all.done <- identical(res1,res)  
     res <- res1  
   }  
   ## now strip out any generics (which have value NULL in res):  
   res.not.null <- sapply(res,function(x){!is.null(x)})  
   if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){  
     res <- res[res.not.null]  
   }  
   res  
 ### named list of lists, one for each object to document.  
 }  
   
 ### 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  
164      })      })
165    
166  extract.docs.fun <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
167  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
168  ### documentation in that source code.  ### documentation in that source code.
169  (code,  (src,
170  ### The function to examine.  ### The source lines of the function to examine, as a character
171   name.fun  ### vector.
172     name.fun="(unnamed function)",
173  ### The name of the function/chunk to use in warning messages.  ### The name of the function/chunk to use in warning messages.
174     ...
175    ### ignored.
176   ){   ){
177    res <- list()    res <- list()
178    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
# Line 462  Line 247 
247          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
248        }        }
249        chunk.res <- NULL        chunk.res <- NULL
250        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
251          chunk.res <-          chunk.res <-
252            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
253            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
254        invisible(chunk.res)        invisible(chunk.res)
255      }      }
256    while ( k <= length(code) ){    while ( k <= length(src) ){
257      line <- code[k]      line <- src[k]
258      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
259        ## 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
260        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
261        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 545  Line 330 
330            first.describe <- TRUE;            first.describe <- TRUE;
331          }          }
332        }        }
333      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
334        ## append this line to current chunk        ## append this line to current chunk
335        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
336          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
337          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
338          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 560  Line 345 
345            payload <- stripped            payload <- stripped
346          }          }
347        }        }
348      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
349        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
350        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
351          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 622  Line 407 
407  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
408  }  }
409    
410    leadingS3generic <- function # check whether function name is an S3 generic
411    ### Determines whether a function name looks like an S3 generic function
412    (name,                     ##<< name of function
413     env,                      ##<< environment to search for additional generics
414     ...)                      ##<< ignored here
415    {
416      ##details<< This function is one of the default parsers, but exposed as
417      ## possibly of more general interest. Given a function name of the form
418      ## x.y.z it looks for the generic function x applying to objects of class
419      ## y.z and also for generic function x.y applying to objects of class z.
420      ##
421      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
422      l <- length(parts)
423      if (l > 1) {
424        for (i in 1:(l - 1)) {
425          ## Look for a generic function (known by the system or defined
426          ## in the package) that matches that part of the function name
427          generic <- paste(parts[1:i], collapse = ".")
428          if (any(generic %in% utils:::getKnownS3generics()) ||
429              utils:::findGeneric(generic, env) != "") {
430            object <- paste(parts[(i + 1):l], collapse = ".")
431            ##details<< Assumes that the first name which matches any known
432            ## generics is the target generic function, so if both x and x.y
433            ## are generic functions, will assume generic x applying to objects
434            ## of class y.z
435            ##value<< If a matching generic found returns a list with a single component:
436            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
437          }
438        }
439      }
440      ##value<< If no matching generic functions are found, returns an empty list.
441      list()
442    }
443    
444    ### Parsers for each function that are constructed automatically. This
445    ### is a named list, and each element is a parser function for an
446    ### individual object.
447    forfun.parsers <-
448      list(prefixed.lines=prefixed.lines,
449           extract.xxx.chunks=extract.xxx.chunks,
450           ## title from first line of function def
451           title.from.firstline=function(src,...){
452             first <- src[1]
453             if(!is.character(first))return(list())
454             if(!grepl("#",first))return(list())
455             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
456           },
457           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
458           ## please, let me choose which dir to use for examples!
459           ## Get examples for FUN from the file tests/FUN.R
460           examples.from.testfile=function(name,...){
461             tsubdir <- getOption("inlinedocs.exdir")
462             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
463             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
464             if(file.exists(tfile))
465               list(examples=readLines(tfile))
466             else list()
467           },
468           definition.from.source=function(doc,src,...){
469             def <- doc$definition
470             is.empty <- function(x)is.null(x)||x==""
471             if(is.empty(def) && !is.empty(src))
472               list(definition=src)
473             else list()
474           })
475    
476    ### List of Parser Functions that can be applied to any object.
477    forall.parsers <-
478      list(## Fill in author from DESCRIPTION and titles.
479           author.from.description=function(desc,...){
480             list(author=desc[,"Maintainer"])
481           },
482           ## The format section sometimes causes problems, so erase it.
483           erase.format=function(...){
484             list(format="")
485           },
486           ## Convert the function name to a title.
487           title.from.name=function(name,doc,...){
488             if("title"%in%names(doc))list() else
489             list(title=gsub("[._]"," ",name))
490           },
491           ## PhG: here is what I propose for examples code in the 'ex' attribute
492           examples.in.attr =  function (name, o, ...) {
493             ex <- attr(o, "ex")
494             if (!is.null(ex)) {
495               ## Special case for code contained in a function
496               if (inherits(ex, "function")) {
497                 ## If source is available, start from there
498                 src <- getSource(ex)
499                 if (!is.null(src)) {
500                   ex <- src
501                 } else { ## Use the body of the function
502                   ex <- deparse(body(ex))
503                 }
504                 ## Eliminate leading and trailing code
505                 ex <- ex[-c(1, length(ex))]
506                 ## all the prefixes
507                 ex <- kill.prefix.whitespace(ex)
508                 ## Add an empty line before and after example
509                 ex <- c("", ex, "")
510               }
511               list(examples = ex)
512             } else list()
513           },collapse=function(doc,...){
514             L <- lapply(doc,paste,collapse="\n")
515             L$.overwrite <- TRUE
516             L
517           },tag.s3methods=leadingS3generic
518           )
519    
520    ### List of parser functions that operate on single objects. This list
521    ### is useful for testing these functions.
522    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
523      f <- function # title
524    ### description
525      (x, ##<< arg x
526       y
527    ### arg y
528       ){
529        ##value<< a list with elements
530        list(x=x, ##<< original x value
531             y=y, ##<< original y value
532             sum=x+y) ##<< their sum
533        ##end<<
534      }
535      src <- getSource(f)
536      lonely$extract.xxx.chunks(src)
537      lonely$prefixed.lines(src)
538    })
539    
540    extra.code.docs <- function # Extract documentation from code chunks
541    ### Parse R code to extract inline documentation from comments around
542    ### each function. These are not able to be retreived simply by
543    ### looking at the "source" attribute. This is a Parser Function that
544    ### can be used in the parser list of package.skeleton.dx(). TODO:
545    ### Modularize this into separate Parsers Functions for S4 classes,
546    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
547    (code,
548    ### Code lines in a character vector containing multiple R objects to
549    ### parse for documentation.
550     objs,
551    ### The objects defined in the code.
552     ...
553    ### ignored
554     ){
555      parsed <- extract.file.parse(code)
556      extract.docs.try <- function(o,on)
557        {
558          ## Note: we could use parsed information here too, but that
559          ## would produce different results for setMethodS3 etc.
560          doc <- list()
561          if ( !is.null(parsed[[on]]) ){
562            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
563              doc$definition <- paste(parsed[[on]]@code)
564            }
565            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
566              doc$description <- parsed[[on]]@description
567            }
568            ## if ( "setMethodS3" == parsed[[on]]@created ){
569            ##   gen <- leadingS3generic(on,topenv())
570            ##   if ( 0 < length(gen) ){
571            ##     doc$.s3method <- gen$.s3method
572            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
573            ##   }
574            ## }
575          }
576          if("title" %in% names(doc) && !"description" %in% names(doc) ){
577            ## For short functions having both would duplicate, but a
578            ## description is required. Therefore automatically copy title
579            ## across to avoid errors at package build time.
580            doc$description <- doc$title
581          }
582          doc
583        }
584      extract.docs <- function(on){
585        res <- try({o <- objs[[on]]
586                    extract.docs.try(o, on)},FALSE)
587        if(class(res)=="try-error"){
588          cat("Failed to extract docs for: ",on,"\n\n")
589          list()
590        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
591          NULL
592        } else if(0 == length(res) && "function" %in% class(o)
593                  && 1 == length(osource <- getSource(o))
594                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
595                  ){
596          ## phew - this should only pick up R.oo S3 generic definitions like:
597          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
598          NULL
599        } else res
600      }
601      doc.names <- names(objs)
602      res <- sapply(doc.names,extract.docs,simplify=FALSE)
603      ## Special processing for S4 classes as they do not appear in normal ls()
604      for ( nn in names(parsed) ){
605        if ( parsed[[nn]]@created == "setClass" ){
606          S4class.docs <- extract.docs.setClass(parsed[[nn]])
607          docname <- paste(nn,"class",sep="-")
608          if ( is.null(res[[docname]]) ){
609            res[[docname]] <- S4class.docs
610            doc.names <- c(doc.names,docname)
611          } else {
612            stop(nn," appears as both S4 class and some other definition")
613          }
614        }
615      }
616      inherit.docs <- function(on){
617        in.res <- res[[on]]
618        if ( !is.null(parsed[[on]]) ){
619          for ( parent in parsed[[on]]@parent ){
620            if ( !is.na(parent) ){
621              if ( is.null(in.res) ){
622                in.res <- res[[parent]]
623              } else if ( parent %in% names(res) ){
624                parent.docs <- res[[parent]]
625                for ( nn in names(parent.docs) ){
626                  if ( !nn %in% names(in.res) ){
627                    in.res[[nn]] <- parent.docs[[nn]]
628                  }
629                }
630              }
631            }
632          }
633        }
634        invisible(in.res)
635      }
636      all.done <- FALSE
637      while ( !all.done ){
638        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
639        all.done <- identical(res1,res)
640        res <- res1
641      }
642      ## now strip out any generics (which have value NULL in res):
643      res.not.null <- sapply(res,function(x){!is.null(x)})
644      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
645        res <- res[res.not.null]
646      }
647      res
648    ### named list of lists, one for each object to document.
649    }
650    
651    ### List of parsers to use by default with package.skeleton.dx.
652    default.parsers <-
653      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
654        sapply(forfun.parsers,forfun),
655        edit.package.file=function(desc,...){
656          in.details <- setdiff(colnames(desc),"Description")
657          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
658          L <-
659            list(list(title=desc[,"Title"],
660                      description=desc[,"Description"],
661                      `tabular{ll}`=details))
662          names(L) <- paste(desc[,"Package"],"-package",sep="")
663          L
664        },
665        sapply(forall.parsers,forall)
666        )
667    
668  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
669  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
670  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
671  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
672    ### the parent class.
673           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
674                          created="character", ##<< how created                          created="character", ##<< how created
675                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 660  Line 704 
704      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
705      default.description <- NULL      default.description <- NULL
706      while ( start > last.end+1      while ( start > last.end+1
707             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
708        start <- start-1        start <- start-1
709      }      }
710      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 687  Line 731 
731        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
732        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
733        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
734        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
735          parent <- chars[3]          parent <- chars[3]
736        }        }
737        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 719  Line 763 
763        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
764        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
765        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
766        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
767          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
768        }        }
769        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 760  Line 804 
804    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
805    ## following line.    ## following line.
806    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
807    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
808    ## also apply source parsing functions that I separated out into    ## also apply source parsing functions that I separated out into
809    ## separate functions    ## separate functions
810    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
# Line 802  Line 846 
846  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
847   ){   ){
848    e <- new.env()    e <- new.env()
849    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
850      ## Error in assignClassDef(Class, classDef, where) :
851      ##   Class "DocLink" has a locked definition in package "inlinedocs"
852      ## Traced to "where" argument in setClassDef which defaults to topenv()
853      ## which in turn is inlinedocs when processing inlinedocs package, hence
854      ## the clash. The following works (under R 2.12.2), so that the topenv()
855      ## now finds e before finding the inlinedocs environment.
856      old <- options(keep.source=TRUE,topLevelEnvironment=e)
857    on.exit(options(old))    on.exit(options(old))
858    exprs <- parse(text=code)    exprs <- parse(text=code)
859    for (i in exprs) eval(i, e)    ## TDH 2011-04-07 set this so that no warnings about creating a fake
860      ## package when we try to process S4 classes defined in code
861      e$.packageName <- "inlinedocs.processor"
862      for (i in exprs){
863        ## TDH 2011-04-07 Disable this tryCatch since it makes it harder
864        ##to debug errors/warnings in the evaluated code
865    
866        ##tryCatch({
867          eval(i, e)
868        ##},error=function(e){
869          ##print(e)
870        ##})
871      }
872    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
873    
874    docs <- list()    docs <- list()
875    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
876    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
877    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
878      N <- names(parsers[i])      N <- names(parsers[i])
# Line 838  Line 883 
883      }      }
884      p <- parsers[[i]]      p <- parsers[[i]]
885      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
886      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
887      docs <- combine(docs,L)      docs <- combine(docs,L)
888    }    }
889      ## post-process to collapse all character vectors
890      for(i in seq_along(docs)){
891        for(j in seq_along(docs[[i]])){
892          if(names(docs[[i]])[j]!=".s3method")
893          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
894        }
895      }
896    if(verbose)cat("\n")    if(verbose)cat("\n")
897    docs    docs
898  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
# Line 857  Line 909 
909  ### description file.  ### description file.
910  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
911    
912  extract.docs.file <- function  extract.docs.file <- structure(function
913  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
914  (f,  (f,
915  ### File name of R code to read and parse.  ### File name of R code to read and parse.
916   parsers=nondesc.parsers,   parsers=NULL,
917  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
918  ### documentation.  ### documentation.
919   ...   ...
920  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
921   ){   ){
922      if(is.null(parsers))parsers <- nondesc.parsers
923    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
924  }  },ex=function(){
925      f <- system.file("silly","R","silly.R",package="inlinedocs")
926      extract.docs.file(f)
927    })
928    

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