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

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revision 302, Tue Jul 12 12:06:42 2011 UTC revision 356, Mon Apr 9 15:39:09 2012 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 lists or character strings  ### combine lists or character strings
61  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y)UseMethod("combine")
62    
# Line 27  Line 86 
86  ### A function.  ### A function.
87   ) {   ) {
88        srcref <- attr(fun.obj, "srcref")        srcref <- attr(fun.obj, "srcref")
89        if (!is.null(srcref)) unlist(strsplit(as.character(srcref), "\n"))        if (!is.null(srcref)) {
90            ##unlist(strsplit(as.character(srcref), "\n"))
91            as.character(srcref)
92          }
93        else attr(fun.obj, "source")        else attr(fun.obj, "source")
94  ### Source code lines as a character vector.  ### Source code lines as a character vector.
95  }  }
# Line 131  Line 193 
193    for(i in seq_along(starts)){    for(i in seq_along(starts)){
194      start <- clines[starts[i]]      start <- clines[starts[i]]
195      end <- clines[ends[i]]      end <- clines[ends[i]]
196      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
197        lab <- if(all(processed==""))"value"
198      else if(start==2)"description"      else if(start==2)"description"
199      else if(is.arg()){      else if(is.arg()){
200        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 139  Line 202 
202        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
203        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
204        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
205        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
206        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
207      } else {      } else {
208        next;        next;
# Line 255  Line 318 
318      }      }
319    while ( k <= length(src) ){    while ( k <= length(src) ){
320      line <- src[k]      line <- src[k]
321        ##print(line)
322        ##if(grepl("^$",line))browser()
323      if ( grepl(extra.regexp,line,perl=TRUE) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
324        ## 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
325        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
326        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
327          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
328        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
329        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
330        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 268  Line 333 
333        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
334        if ( "describe" == new.field ){        if ( "describe" == new.field ){
335          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
336          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
337          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
338          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
339            ## \code{##describe<<} comments.
340          if ( first.describe ){          if ( first.describe ){
341            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
342          } else {          } else {
# Line 357  Line 423 
423          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
424          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
425          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
426          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
427          payload <- comment          payload <- comment
428        } else {        } else {
429          ## 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 477  Line 543 
543  forall.parsers <-  forall.parsers <-
544    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
545         author.from.description=function(desc,...){         author.from.description=function(desc,...){
546           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
547         },         },
548         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
549         erase.format=function(...){         erase.format=function(...){
# Line 503  Line 569 
569               }               }
570               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
571               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
572                 if(ex[1]=="{")ex <- ex[-1]
573               ## all the prefixes               ## all the prefixes
574               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
575               ## Add an empty line before and after example               ## Add an empty line before and after example
# Line 678  Line 745 
745           )           )
746    
747  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
748  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
749  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
750  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
751  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 750  Line 817 
817        generic.name <- chars[2]        generic.name <- chars[2]
818        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
819        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
820          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
821            ## since it causes problems on R CMD check.
822            ##* checking Rd cross-references ... WARNING
823            ##Error in find.package(package, lib.loc) :
824            ##  there is no package called ‘MASS’
825            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
826    
827            generic.desc <-
828              paste("Generic method behind \\code{",object.name,"}",sep="")
829          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
830                                     name=generic.name,                                     name=generic.name,
831                                     created=expr.type,                                     created=expr.type,
# Line 784  Line 859 
859  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
860  ### scanned for inline comments.  ### scanned for inline comments.
861  (doc.link  (doc.link
862  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
863  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
864  ### class definitions.  ### class definitions.
865   ){   ){
# Line 810  Line 885 
885    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
886    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
887    ##details<<    ##details<<
888      ## If there is no explicit title on the first line of setClass, then
889      ## one is made up from the class name.
890      if ( 0 == length(docs$title) ){
891        docs$title <- list(title=paste(class.name,"S4 class"))
892      }
893      ##details<<
894    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
895    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
896    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 860  Line 941 
941    ## package when we try to process S4 classes defined in code    ## package when we try to process S4 classes defined in code
942    e$.packageName <- "inlinedocs.processor"    e$.packageName <- "inlinedocs.processor"
943    for (i in exprs){    for (i in exprs){
     ## TDH 2011-04-07 Disable this tryCatch since it makes it harder  
     ##to debug errors/warnings in the evaluated code  
   
     ##tryCatch({  
944        eval(i, e)        eval(i, e)
     ##},error=function(e){  
       ##print(e)  
     ##})  
945    }    }
946    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
947    
948    docs <- list()    docs <- list()
949    
950    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
951      if(verbose)cat("Applying parsers:\n")
952    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
953      N <- names(parsers[i])      N <- names(parsers[i])
954      if(verbose){      if(verbose){
955        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
956          cat(N," ",sep="")          cat(N,"\n",sep="")
957        }else cat('. ')        }else cat('.\n')
958      }      }
959      p <- parsers[[i]]      p <- parsers[[i]]
960      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
961      L <- p(code=code,objs=objs,docs=docs,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
962        #print(paste(L,"\n"))
963        #if(N=="exclude")browser()
964      docs <- combine(docs,L)      docs <- combine(docs,L)
965    }    }
966    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
# Line 894  Line 971 
971      }      }
972    }    }
973    if(verbose)cat("\n")    if(verbose)cat("\n")
974    docs    return(docs)
975  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
976  }  }
977    

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