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

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revision 162, Wed Nov 10 09:18:20 2010 UTC revision 204, Fri Feb 18 16:48:22 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    
# Line 24  Line 29 
29  (comments  (comments
30  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
31   ){   ){
32    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
33  ### String without prefixes or newlines.  ### String without prefixes or newlines.
34  }  }
35    
# Line 44  Line 49 
49      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
50      L <- list()      L <- list()
51      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
52      for(N in names(docs)){      for(N in union(names(docs),names(objs))){
53        o <- objs[[N]]        o <- objs[[N]]
54        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=attr(o,"source"),
55                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
# Line 69  Line 74 
74  ### For each function in the package, do something.  ### For each function in the package, do something.
75  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
76    
77    kill.prefix.whitespace <- function
78    ### Figure out what the whitespace preceding the example code is, and
79    ### then delete that from every line.
80    (ex
81    ### character vector of example code lines.
82     ){
83      tlines <- gsub("\\s*","",ex)
84      ##tlines <- gsub("#.*","",tlines)
85      prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
86      FIND <- prefixes[which.min(nchar(prefixes))]
87      ## Eliminate leading tabulations or 2/4 spaces
88      sub(FIND, "", ex)
89    ### Character vector of code lines with preceding whitespace removed.
90    }
91    
92  examples.after.return <- function  examples.after.return <- function
93  ### Get examples from inline definitions after return()  ### Get examples from inline definitions after return()
94  ### PhG: this does not work well! Think of these situations:  ### PhG: this does not work well! Think of these situations:
# Line 113  Line 133 
133    ## Possibly eliminate a #}}} tag    ## Possibly eliminate a #}}} tag
134    ex <- ex[!grepl("#}}}", ex)]    ex <- ex[!grepl("#}}}", ex)]
135    ## Eliminate leading tabulations or four spaces    ## Eliminate leading tabulations or four spaces
136    prefixes <- gsub("(\\s*).*","\\1",ex,perl=TRUE)[grep("\\w",ex)]    ex <- kill.prefix.whitespace(ex)
   FIND <- prefixes[which.min(nchar(prefixes))]  
   ex <- sub(FIND,"",ex)  
137    ## Add an empty line before and after example    ## Add an empty line before and after example
138    ex <- c("", ex, "")    ex <- c("", ex, "")
139    ## Return examples and value    ## Return examples and value
140    list(examples = paste(ex, collapse = "\n"), value = value)    list(examples = ex, value = value)
141  }  }
142    
143  prefixed.lines <- function(src,...){  prefixed.lines <- structure(function(src,...){
144  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
145  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
146  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 142  Line 160 
160    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
161    parens <- f("(")-f(")")    parens <- f("(")-f(")")
162    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
163      if(length(body.begin)==0)body.begin <- 1 ## rare cases
164    is.arg <- function(){    is.arg <- function(){
165      gres <- grep("^\\s*#",src[start-1],perl=TRUE)      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
166      0 == length(gres) && start<=body.begin      0 == length(gres) && start<=body.begin
# Line 150  Line 169 
169    for(i in seq_along(starts)){    for(i in seq_along(starts)){
170      start <- clines[starts[i]]      start <- clines[starts[i]]
171      end <- clines[ends[i]]      end <- clines[ends[i]]
172      lab <- if(end+1==length(src))"value"      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"
173      else if(start==2)"description"      else if(start==2)"description"
174      else if(is.arg()){      else if(is.arg()){
175        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 166  Line 185 
185      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
186    }    }
187    res    res
188  }  },ex=function(){
189    test <- function
190    ### the description
191    (x,
192    ### the first argument
193     y ##<< another argument
194     ){
195      5
196    ### the return value
197    ##seealso<< foobar
198    }
199    src <- attr(test,"source")
200    prefixed.lines(src)
201    extract.xxx.chunks(src)
202    })
203    
204  extract.xxx.chunks <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
205  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
# Line 252  Line 285 
285          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
286        }        }
287        chunk.res <- NULL        chunk.res <- NULL
288        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
289          chunk.res <-          chunk.res <-
290            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
291            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
# Line 260  Line 293 
293      }      }
294    while ( k <= length(src) ){    while ( k <= length(src) ){
295      line <- src[k]      line <- src[k]
296      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
297        ## 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
298        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
299        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 335  Line 368 
368            first.describe <- TRUE;            first.describe <- TRUE;
369          }          }
370        }        }
371      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
372        ## append this line to current chunk        ## append this line to current chunk
373        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
374          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
375          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
376          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 350  Line 383 
383            payload <- stripped            payload <- stripped
384          }          }
385        }        }
386      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
387        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
388        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
389          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 420  Line 453 
453         examples.after.return=examples.after.return,         examples.after.return=examples.after.return,
454         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
455         ## title from first line of function def         ## title from first line of function def
456         title.from.firstline=function(src,name,code,...){         title.from.firstline=function(src,...){
457           if(length(grep("#",src[1]))){           first <- src[1]
458             list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))           if(!is.character(first))return(list())
459           } else list()           if(!grepl("#",first))return(list())
460             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
461         },         },
462         ## PhG: it is tests/FUN.R!!! I would like more flexibility here         ## PhG: it is tests/FUN.R!!! I would like more flexibility here
463         ## please, let me choose which dir to use for examples!         ## please, let me choose which dir to use for examples!
# Line 433  Line 467 
467           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
468           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
469           if(file.exists(tfile))           if(file.exists(tfile))
470             list(examples=paste(readLines(tfile),collapse="\n"))             list(examples=readLines(tfile))
471           else list()           else list()
472         },         },
473         definition.from.source=function(doc,src,...){         definition.from.source=function(doc,src,...){
474           def <- doc$definition           def <- doc$definition
475           is.empty <- function(x)is.null(x)||x==""           is.empty <- function(x)is.null(x)||x==""
476           if(is.empty(def) && !is.empty(src))           if(is.empty(def) && !is.empty(src))
477             list(definition=paste(src,collapse="\n"))             list(definition=src)
478           else list()           else list()
479         })         })
480    
# Line 474  Line 508 
508               }               }
509               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
510               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
511               ## Eliminate leading tabulations or 2/4 spaces               ## all the prefixes
512               ex <- sub("^\t|    |  ", "", ex)               ex <- kill.prefix.whitespace(ex)
513               ## Add an empty line before and after example               ## Add an empty line before and after example
514               ex <- c("", ex, "")               ex <- c("", ex, "")
515             }             }
516             list(examples = paste(ex, collapse = "\n"))             list(examples = ex)
517           } else list()           } else list()
518         })         },collapse=function(doc,...){
519             L <- lapply(doc,paste,collapse="\n")
520             L$.overwrite <- TRUE
521             L
522           },tag.s3methods=function(name,env,...){
523             parts <- strsplit(name, ".", fixed = TRUE)[[1]]
524             l <- length(parts)
525             if (l > 1) {
526               for (i in 1:(l - 1)) {
527                 ## Look for a generic function (known by the system or defined
528                 ## in the package) that matches that part of the function name
529                 generic <- paste(parts[1:i], collapse = ".")
530                 if (any(generic %in% utils:::getKnownS3generics()) ||
531                     utils:::findGeneric(generic, env) != "") {
532                   object <- paste(parts[(i + 1):l], collapse = ".")
533                   return(list(.s3method=c(generic, object)))
534                 }
535               }
536             }
537             list()
538           }
539           )
540    
541  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
542  ### is useful for testing these functions.  ### is useful for testing these functions.
543  lonely <- c(forall.parsers,forfun.parsers)  lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
 attr(lonely,"ex") <- function(){  
544    f <- function # title    f <- function # title
545  ### description  ### description
546    (x, ##<< arg x    (x, ##<< arg x
# Line 502  Line 556 
556    src <- attr(f,"source")    src <- attr(f,"source")
557    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
558    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
559  }  })
560    
561  extra.code.docs <- function # Extract documentation from code chunks  extra.code.docs <- function # Extract documentation from code chunks
562  ### Parse R code to extract inline documentation from comments around  ### Parse R code to extract inline documentation from comments around
# Line 527  Line 581 
581        doc <- list()        doc <- list()
582        if ( !is.null(parsed[[on]]) ){        if ( !is.null(parsed[[on]]) ){
583          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
584            doc$definition <- paste(parsed[[on]]@code,collapse="\n")            doc$definition <- paste(parsed[[on]]@code)
585          }          }
586          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
587            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
# Line 538  Line 592 
592            # as.data.frame.matrix must be split into: m1 = as.data.frame and            # as.data.frame.matrix must be split into: m1 = as.data.frame and
593            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!
594                    pattern <- "^([^\\.]+)\\.(.*)$"                    pattern <- "^([^\\.]+)\\.(.*)$"
595            doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),            doc$.s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),
596                m2 <- gsub(pattern,"\\2",on,perl=TRUE))                m2 <- gsub(pattern,"\\2",on,perl=TRUE))
597            if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){            if ( grepl("\\W",m1,perl=TRUE) ){
598                            m1 <- paste("`",m1,"`",sep="")                            m1 <- paste("`",m1,"`",sep="")
599            }            }
600            cat("S3method(",m1,",",m2,")\n",sep="")            cat("S3method(",m1,",",m2,")\n",sep="")
# Line 564  Line 618 
618        NULL        NULL
619      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
620                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- attr(o,"source"))
621                && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
622                ){                ){
623        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
624        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
# Line 625  Line 679 
679  default.parsers <-  default.parsers <-
680    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
681      sapply(forfun.parsers,forfun),      sapply(forfun.parsers,forfun),
     sapply(forall.parsers,forall),  
682      edit.package.file=function(desc,...){      edit.package.file=function(desc,...){
683        in.details <- setdiff(colnames(desc),"Description")        in.details <- setdiff(colnames(desc),"Description")
684        details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
                              sep=""),collapse="\n")  
685        L <-        L <-
686          list(list(title=desc[,"Title"],          list(list(title=desc[,"Title"],
687                    description=desc[,"Description"],                    description=desc[,"Description"],
688                    `tabular{ll}`=details,                    `tabular{ll}`=details))
                   author=desc[,"Maintainer"]))  
689        names(L) <- paste(desc[,"Package"],"-package",sep="")        names(L) <- paste(desc[,"Package"],"-package",sep="")
690        L        L
691      })      },
692        sapply(forall.parsers,forall)
693        )
694    
695  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
696  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
# Line 677  Line 730 
730      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
731      default.description <- NULL      default.description <- NULL
732      while ( start > last.end+1      while ( start > last.end+1
733             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
734        start <- start-1        start <- start-1
735      }      }
736      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 704  Line 757 
757        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
758        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
759        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
760        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
761          parent <- chars[3]          parent <- chars[3]
762        }        }
763        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 736  Line 789 
789        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
790        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
791        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
792        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
793          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
794        }        }
795        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 831  Line 884 
884    
885    docs <- list()    docs <- list()
886    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
887    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
888    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
889      N <- names(parsers[i])      N <- names(parsers[i])
# Line 859  Line 894 
894      }      }
895      p <- parsers[[i]]      p <- parsers[[i]]
896      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
897      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
898      docs <- combine(docs,L)      docs <- combine(docs,L)
899    }    }
900      ## post-process to collapse all character vectors
901      for(i in seq_along(docs)){
902        for(j in seq_along(docs[[i]])){
903          if(names(docs[[i]])[j]!=".s3method")
904          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
905        }
906      }
907    if(verbose)cat("\n")    if(verbose)cat("\n")
908    docs    docs
909  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
# Line 882  Line 924 
924  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
925  (f,  (f,
926  ### File name of R code to read and parse.  ### File name of R code to read and parse.
927   parsers=nondesc.parsers,   parsers=NULL,
928  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
929  ### documentation.  ### documentation.
930   ...   ...
931  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
932   ){   ){
933      if(is.null(parsers))parsers <- nondesc.parsers
934    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
935  }  }

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