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

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revision 204, Fri Feb 18 16:48:22 2011 UTC revision 335, Thu Apr 5 12:08:07 2012 UTC
# Line 1  Line 1 
1    do.not.generate <- 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    }
18    
19  ### combine lists or character strings  ### combine lists or character strings
20  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y)UseMethod("combine")
21    
# Line 20  Line 38 
38  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
39  }  }
40    
41    
42    getSource <- function
43    ### Extract a function's source code.
44    (fun.obj
45    ### A function.
46     ) {
47          srcref <- attr(fun.obj, "srcref")
48          if (!is.null(srcref)) {
49            ##unlist(strsplit(as.character(srcref), "\n"))
50            as.character(srcref)
51          }
52          else attr(fun.obj, "source")
53    ### Source code lines as a character vector.
54    }
55    
56  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
57  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
58    
59  decomment <- function  decomment <- function
60  ### Remove comment prefix and join lines of code to form a  ### Remove comment prefix and join lines of code to form a
# Line 46  Line 79 
79   ){   ){
80    FUN <- FUN    FUN <- FUN
81    f <- function(objs,docs,...){    f <- function(objs,docs,...){
82        if(length(objs)==0)return(list())
83      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
84      L <- list()      L <- list()
85      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
86      for(N in union(names(docs),names(objs))){      for(N in union(names(docs),names(objs))){
87        o <- objs[[N]]        o <- objs[[N]]
88        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
89                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
90      }      }
91      on.exit()## remove warning message      on.exit()## remove warning message
# Line 89  Line 123 
123  ### Character vector of code lines with preceding whitespace removed.  ### Character vector of code lines with preceding whitespace removed.
124  }  }
125    
 examples.after.return <- function  
 ### Get examples from inline definitions after return()  
 ### PhG: this does not work well! Think of these situations:  
 ### 1) You have multiple return() in the code of your function,  
 ### 2) You have return() appearing is some example code, ...  
 ### I can hardly propose a hack here. The whole code of the function  
 ### must be parsed, and one must determine which one is the last line  
 ### of code that is actually executed.  
 ###  
 ### I make two propositions here  
 ### 1) to keep the same mechanism that has the advantage of simplicity  
 ###    but to use a special tag  
 ###    ##examples<< or #{{{examples to separate  
 ###    function code from examples explicitly, and  
 ### 2) to place the example in an "ex" attribute  
 ###    attached to the function  
 ###    (see next parser). That solution will be also interesting for  
 ###    documenting datasets, something not done yet by inlinedocs!  
 (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  
   ex <- kill.prefix.whitespace(ex)  
   ## Add an empty line before and after example  
   ex <- c("", ex, "")  
   ## Return examples and value  
   list(examples = ex, value = value)  
 }  
   
126  prefixed.lines <- structure(function(src,...){  prefixed.lines <- structure(function(src,...){
127  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
128  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
# Line 169  Line 152 
152    for(i in seq_along(starts)){    for(i in seq_along(starts)){
153      start <- clines[starts[i]]      start <- clines[starts[i]]
154      end <- clines[ends[i]]      end <- clines[ends[i]]
155      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
156        lab <- if(all(processed==""))"value"
157      else if(start==2)"description"      else if(start==2)"description"
158      else if(is.arg()){      else if(is.arg()){
159        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 196  Line 180 
180  ### the return value  ### the return value
181  ##seealso<< foobar  ##seealso<< foobar
182  }  }
183  src <- attr(test,"source")  src <- getSource(test)
184  prefixed.lines(src)  prefixed.lines(src)
185  extract.xxx.chunks(src)  extract.xxx.chunks(src)
186  })  })
# Line 293  Line 277 
277      }      }
278    while ( k <= length(src) ){    while ( k <= length(src) ){
279      line <- src[k]      line <- src[k]
280        ##print(line)
281        ##if(grepl("^$",line))browser()
282      if ( grepl(extra.regexp,line,perl=TRUE) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
283        ## 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
284        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
285        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
286          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
287        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
288        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
289        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 306  Line 292 
292        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
293        if ( "describe" == new.field ){        if ( "describe" == new.field ){
294          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
295          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
296          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
297          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
298            ## \code{##describe<<} comments.
299          if ( first.describe ){          if ( first.describe ){
300            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
301          } else {          } else {
# Line 445  Line 432 
432  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
433  }  }
434    
435    leadingS3generic <- function # check whether function name is an S3 generic
436    ### Determines whether a function name looks like an S3 generic function
437    (name,                     ##<< name of function
438     env,                      ##<< environment to search for additional generics
439     ...)                      ##<< ignored here
440    {
441      ##details<< This function is one of the default parsers, but exposed as
442      ## possibly of more general interest. Given a function name of the form
443      ## x.y.z it looks for the generic function x applying to objects of class
444      ## y.z and also for generic function x.y applying to objects of class z.
445      ##
446      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
447      l <- length(parts)
448      if (l > 1) {
449        for (i in 1:(l - 1)) {
450          ## Look for a generic function (known by the system or defined
451          ## in the package) that matches that part of the function name
452          generic <- paste(parts[1:i], collapse = ".")
453          if (any(generic %in% utils:::getKnownS3generics()) ||
454              utils:::findGeneric(generic, env) != "") {
455            object <- paste(parts[(i + 1):l], collapse = ".")
456            ##details<< Assumes that the first name which matches any known
457            ## generics is the target generic function, so if both x and x.y
458            ## are generic functions, will assume generic x applying to objects
459            ## of class y.z
460            ##value<< If a matching generic found returns a list with a single component:
461            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
462          }
463        }
464      }
465      ##value<< If no matching generic functions are found, returns an empty list.
466      list()
467    }
468    
469  ### Parsers for each function that are constructed automatically. This  ### Parsers for each function that are constructed automatically. This
470  ### is a named list, and each element is a parser function for an  ### is a named list, and each element is a parser function for an
471  ### individual object.  ### individual object.
472  forfun.parsers <-  forfun.parsers <-
473    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
474         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
475         ## title from first line of function def         ## title from first line of function def
476         title.from.firstline=function(src,...){         title.from.firstline=function(src,...){
# Line 482  Line 502 
502  forall.parsers <-  forall.parsers <-
503    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
504         author.from.description=function(desc,...){         author.from.description=function(desc,...){
505           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
506         },         },
507         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
508         erase.format=function(...){         erase.format=function(...){
# Line 500  Line 520 
520             ## Special case for code contained in a function             ## Special case for code contained in a function
521             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
522               ## If source is available, start from there               ## If source is available, start from there
523               src <- attr(ex, "source")               src <- getSource(ex)
524               if (!is.null(src)) {               if (!is.null(src)) {
525                 ex <- src                 ex <- src
526               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 508  Line 528 
528               }               }
529               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
530               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
531                 if(ex[1]=="{")ex <- ex[-1]
532               ## all the prefixes               ## all the prefixes
533               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
534               ## Add an empty line before and after example               ## Add an empty line before and after example
# Line 519  Line 540 
540           L <- lapply(doc,paste,collapse="\n")           L <- lapply(doc,paste,collapse="\n")
541           L$.overwrite <- TRUE           L$.overwrite <- TRUE
542           L           L
543         },tag.s3methods=function(name,env,...){         },tag.s3methods=leadingS3generic
          parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
          l <- length(parts)  
          if (l > 1) {  
            for (i in 1:(l - 1)) {  
              ## Look for a generic function (known by the system or defined  
              ## in the package) that matches that part of the function name  
              generic <- paste(parts[1:i], collapse = ".")  
              if (any(generic %in% utils:::getKnownS3generics()) ||  
                  utils:::findGeneric(generic, env) != "") {  
                object <- paste(parts[(i + 1):l], collapse = ".")  
                return(list(.s3method=c(generic, object)))  
              }  
            }  
          }  
          list()  
        }  
544         )         )
545    
546  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
# Line 553  Line 558 
558           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
559      ##end<<      ##end<<
560    }    }
561    src <- attr(f,"source")    src <- getSource(f)
562    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
563    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
564  })  })
# Line 586  Line 591 
591          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
592            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
593          }          }
594          if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "setMethodS3" == parsed[[on]]@created ){
595            # PhG: this may be wrong! It does not catch correctly how the method          ##   gen <- leadingS3generic(on,topenv())
596            # must be splitted in case of methods containing dots. for instance,          ##   if ( 0 < length(gen) ){
597            # as.data.frame.matrix must be split into: m1 = as.data.frame and          ##     doc$.s3method <- gen$.s3method
598            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!          ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
599                    pattern <- "^([^\\.]+)\\.(.*)$"          ##   }
600            doc$.s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),          ## }
               m2 <- gsub(pattern,"\\2",on,perl=TRUE))  
           if ( grepl("\\W",m1,perl=TRUE) ){  
                           m1 <- paste("`",m1,"`",sep="")  
           }  
           cat("S3method(",m1,",",m2,")\n",sep="")  
         }  
601        }        }
602        if("title" %in% names(doc) && !"description" %in% names(doc) ){        if("title" %in% names(doc) && !"description" %in% names(doc) ){
603          ## For short functions having both would duplicate, but a          ## For short functions having both would duplicate, but a
# Line 617  Line 616 
616      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
617        NULL        NULL
618      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
619                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
620                && grepl(paste("UseMethod(",on,")",sep="\""),osource)                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
621                ){                ){
622        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
# Line 695  Line 694 
694  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
695  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
696  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
697  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
698    ### the parent class.
699           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
700                          created="character", ##<< how created                          created="character", ##<< how created
701                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 836  Line 836 
836    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
837    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
838    ##details<<    ##details<<
839      ## If there is no explicit title on the first line of setClass, then
840      ## one is made up from the class name.
841      if ( 0 == length(docs$title) ){
842        docs$title <- list(title=paste(class.name,"S4 class"))
843      }
844      ##details<<
845    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
846    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
847    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 872  Line 878 
878  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
879   ){   ){
880    e <- new.env()    e <- new.env()
881    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
882      ## Error in assignClassDef(Class, classDef, where) :
883      ##   Class "DocLink" has a locked definition in package "inlinedocs"
884      ## Traced to "where" argument in setClassDef which defaults to topenv()
885      ## which in turn is inlinedocs when processing inlinedocs package, hence
886      ## the clash. The following works (under R 2.12.2), so that the topenv()
887      ## now finds e before finding the inlinedocs environment.
888      old <- options(keep.source=TRUE,topLevelEnvironment=e)
889    on.exit(options(old))    on.exit(options(old))
890    exprs <- parse(text=code)    exprs <- parse(text=code)
891      ## TDH 2011-04-07 set this so that no warnings about creating a fake
892      ## package when we try to process S4 classes defined in code
893      e$.packageName <- "inlinedocs.processor"
894    for (i in exprs){    for (i in exprs){
895      tryCatch(eval(i, e),error=function(e){        eval(i, e)
       ##print(e)  
     })  
896    }    }
897    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
898    
899    docs <- list()    docs <- list()
900    
901    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
902      if(verbose)cat("Applying parsers:\n")
903    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
904      N <- names(parsers[i])      N <- names(parsers[i])
905      if(verbose){      if(verbose){
906        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
907          cat(N," ",sep="")          cat(N,"\n",sep="")
908        }else cat('. ')        }else cat('.\n')
909      }      }
910      p <- parsers[[i]]      p <- parsers[[i]]
911      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
912      L <- p(code=code,objs=objs,docs=docs,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
913        #print(paste(L,"\n"))
914        #if(N=="exclude")browser()
915      docs <- combine(docs,L)      docs <- combine(docs,L)
916    }    }
917    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
# Line 905  Line 922 
922      }      }
923    }    }
924    if(verbose)cat("\n")    if(verbose)cat("\n")
925    docs    return(docs)
926  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
927  }  }
928    
# Line 920  Line 937 
937  ### description file.  ### description file.
938  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
939    
940  extract.docs.file <- function  extract.docs.file <- structure(function
941  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
942  (f,  (f,
943  ### File name of R code to read and parse.  ### File name of R code to read and parse.
# Line 932  Line 949 
949   ){   ){
950    if(is.null(parsers))parsers <- nondesc.parsers    if(is.null(parsers))parsers <- nondesc.parsers
951    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
952  }  },ex=function(){
953      f <- system.file("silly","R","silly.R",package="inlinedocs")
954      extract.docs.file(f)
955    })
956    

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