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

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revision 246, Thu Apr 7 13:21:39 2011 UTC revision 370, Fri Nov 9 19:48:27 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.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    combine <- function(x,y){
75        UseMethod("combine")
76    }
77    
78  ### combine character strings by pasting them together  ### combine character strings by pasting them together
79  combine.character <- function(x,y)  combine.character <- function(x,y)
# Line 20  Line 94 
94  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
95  }  }
96    
97    
98    getSource <- function
99    ### Extract a function's source code.
100    (fun.obj
101    ### A function.
102     ) {
103          srcref <- attr(fun.obj, "srcref")
104          if (!is.null(srcref)) {
105            ##unlist(strsplit(as.character(srcref), "\n"))
106            as.character(srcref)
107          }
108          else attr(fun.obj, "source")
109    ### Source code lines as a character vector.
110    }
111    
112  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
113  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
114    
115  decomment <- function  decomment <- function
116  ### 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 135 
135   ){   ){
136    FUN <- FUN    FUN <- FUN
137    f <- function(objs,docs,...){    f <- function(objs,docs,...){
138        if(length(objs)==0)return(list())
139      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
140      L <- list()      L <- list()
141      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
142      for(N in union(names(docs),names(objs))){      for(N in union(names(docs),names(objs))){
143        o <- objs[[N]]        o <- objs[[N]]
144        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
145                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
146      }      }
147      on.exit()## remove warning message      on.exit()## remove warning message
# Line 89  Line 179 
179  ### Character vector of code lines with preceding whitespace removed.  ### Character vector of code lines with preceding whitespace removed.
180  }  }
181    
 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)  
 }  
   
182  prefixed.lines <- structure(function(src,...){  prefixed.lines <- structure(function(src,...){
183  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
184  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
# Line 169  Line 208 
208    for(i in seq_along(starts)){    for(i in seq_along(starts)){
209      start <- clines[starts[i]]      start <- clines[starts[i]]
210      end <- clines[ends[i]]      end <- clines[ends[i]]
211      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
212        lab <- if(all(processed==""))"value"
213      else if(start==2)"description"      else if(start==2)"description"
214      else if(is.arg()){      else if(is.arg()){
215        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 177  Line 217 
217        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
218        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
219        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
220        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
221        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
222      } else {      } else {
223        next;        next;
# Line 196  Line 236 
236  ### the return value  ### the return value
237  ##seealso<< foobar  ##seealso<< foobar
238  }  }
239  src <- attr(test,"source")  src <- getSource(test)
240  prefixed.lines(src)  prefixed.lines(src)
241  extract.xxx.chunks(src)  extract.xxx.chunks(src)
242  })  })
# Line 293  Line 333 
333      }      }
334    while ( k <= length(src) ){    while ( k <= length(src) ){
335      line <- src[k]      line <- src[k]
336        ##print(line)
337        ##if(grepl("^$",line))browser()
338      if ( grepl(extra.regexp,line,perl=TRUE) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
339        ## 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
340        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
341        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
342          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
343        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
344        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
345        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 306  Line 348 
348        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
349        if ( "describe" == new.field ){        if ( "describe" == new.field ){
350          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
351          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
352          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
353          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
354            ## \code{##describe<<} comments.
355          if ( first.describe ){          if ( first.describe ){
356            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
357          } else {          } else {
# Line 395  Line 438 
438          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
439          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
440          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
441          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
442          payload <- comment          payload <- comment
443        } else {        } else {
444          ## 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 484  Line 527 
527  ### individual object.  ### individual object.
528  forfun.parsers <-  forfun.parsers <-
529    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
530         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
531         ## title from first line of function def         ## title from first line of function def
532         title.from.firstline=function(src,...){         title.from.firstline=function(src,...){
# Line 516  Line 558 
558  forall.parsers <-  forall.parsers <-
559    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
560         author.from.description=function(desc,...){         author.from.description=function(desc,...){
561           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
562         },         },
563         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
564         erase.format=function(...){         erase.format=function(...){
# Line 534  Line 576 
576             ## Special case for code contained in a function             ## Special case for code contained in a function
577             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
578               ## If source is available, start from there               ## If source is available, start from there
579               src <- attr(ex, "source")               src <- getSource(ex)
580               if (!is.null(src)) {               if (!is.null(src)) {
581                 ex <- src                 ex <- src
582               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 542  Line 584 
584               }               }
585               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
586               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
587                 if(ex[1]=="{")ex <- ex[-1]
588               ## all the prefixes               ## all the prefixes
589               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
590               ## Add an empty line before and after example               ## Add an empty line before and after example
# Line 571  Line 614 
614           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
615      ##end<<      ##end<<
616    }    }
617    src <- attr(f,"source")    src <- getSource(f)
618    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
619    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
620  })  })
# Line 629  Line 672 
672      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
673        NULL        NULL
674      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
675                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
676                && grepl(paste("UseMethod(",on,")",sep="\""),osource)                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
677                ){                ){
678        ## 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 717  Line 760 
760           )           )
761    
762  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
763  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
764  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
765  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
766  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 789  Line 832 
832        generic.name <- chars[2]        generic.name <- chars[2]
833        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
834        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
835          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
836            ## since it causes problems on R CMD check.
837            ##* checking Rd cross-references ... WARNING
838            ##Error in find.package(package, lib.loc) :
839            ##  there is no package called ‘MASS’
840            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
841    
842            generic.desc <-
843              paste("Generic method behind \\code{",object.name,"}",sep="")
844          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
845                                     name=generic.name,                                     name=generic.name,
846                                     created=expr.type,                                     created=expr.type,
# Line 823  Line 874 
874  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
875  ### scanned for inline comments.  ### scanned for inline comments.
876  (doc.link  (doc.link
877  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
878  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
879  ### class definitions.  ### class definitions.
880   ){   ){
# Line 849  Line 900 
900    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
901    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
902    ##details<<    ##details<<
903      ## If there is no explicit title on the first line of setClass, then
904      ## one is made up from the class name.
905      if ( 0 == length(docs$title) ){
906        docs$title <- list(title=paste(class.name,"S4 class"))
907      }
908      ##details<<
909    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
910    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
911    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 895  Line 952 
952    old <- options(keep.source=TRUE,topLevelEnvironment=e)    old <- options(keep.source=TRUE,topLevelEnvironment=e)
953    on.exit(options(old))    on.exit(options(old))
954    exprs <- parse(text=code)    exprs <- parse(text=code)
955      ## TDH 2011-04-07 set this so that no warnings about creating a fake
956      ## package when we try to process S4 classes defined in code
957      e$.packageName <- "inlinedocs.processor"
958    for (i in exprs){    for (i in exprs){
959      tryCatch(eval(i, e),error=function(e){        eval(i, e)
       ##print(e)  
     })  
960    }    }
961    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
962    
963    docs <- list()    docs <- list()
964    
965    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
966      if(verbose)cat("Applying parsers:\n")
967    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
968      N <- names(parsers[i])      N <- names(parsers[i])
969      if(verbose){      #mm if(verbose){
970        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
971          cat(N," ",sep="")          cat(" this is parser:",N,"\n",sep="")
972        }else cat('. ')        }else cat('.\n')
973      }      #mm }
974      p <- parsers[[i]]      p <- parsers[[i]]
975      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
976      L <- p(code=code,objs=objs,docs=docs,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
977      docs <- combine(docs,L)      # print("mm point1")
978        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
979        #print(paste(L,"\n"))
980        #if(N=="exclude")browser()
981        docs <- combine(docs,L) #mm
982    }    }
983    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
984    for(i in seq_along(docs)){    for(i in seq_along(docs)){
# Line 925  Line 988 
988      }      }
989    }    }
990    if(verbose)cat("\n")    if(verbose)cat("\n")
991    docs    return(docs)
992  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
993  }  }
994    
# Line 954  Line 1017 
1017    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
1018  },ex=function(){  },ex=function(){
1019    f <- system.file("silly","R","silly.R",package="inlinedocs")    f <- system.file("silly","R","silly.R",package="inlinedocs")
1020    extract.docs.file(f) ##FIXME: warning    extract.docs.file(f)
1021  })  })
1022    

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