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

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revision 87, Sat May 1 12:21:27 2010 UTC revision 115, Fri Jun 18 10:35:11 2010 UTC
# Line 1  Line 1 
1    ### combine lists or character strings
2    combine <- function(x,y)UseMethod("combine")
3    
4    ### combine character strings by pasting them together
5    combine.character <- function(x,y)
6        paste(x,y,sep="\n")
7    
8    ### combine lists by adding elements or adding to existing elements
9    combine.list <- function(x,y){
10      toadd <- !names(y)%in%names(x)
11      toup <- names(y)[names(y)%in%names(x)]
12      x[names(y)[toadd]] <- y[toadd]
13      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
14      return(x)
15    ### A list, same type as x, but with added elements from y.
16    }
17    
18    ### Prefix for code comments used with grep and gsub.
19    prefix <- "^[ \t]*###[ \t]"
20    
21    decomment <- function
22    ### Remove comment prefix and join lines of code to form a
23    ### documentation string.
24    (comments
25    ### Character vector of prefixed comment lines.
26     ){
27      paste(gsub(prefix,"",comments),collapse="\n")
28    ### String without prefixes or newlines.
29    }
30    
31  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
32  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
33  ### documentation list.  ### documentation list.
# Line 12  Line 42 
42    function(objs,docs,...){    function(objs,docs,...){
43      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
44      L <- list()      L <- list()
45      for(N in names(objs)){      for(N in names(docs)){
46        o <- objs[[N]]        o <- objs[[N]]
47        L[[N]] <- FUN(src=attr(o,"source"),name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)        L[[N]] <- FUN(src=attr(o,"source"),
48                        name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
49      }      }
50      L      L
51    }    }
# Line 24  Line 55 
55  ### For each function in the package, do something.  ### For each function in the package, do something.
56  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
57    
58  ### Get last line (test)  ### Parsers for each object/function that are constructed
59  parsefuns <- forfun(function(src,name,...){  ### automatically. This is a named list, each element is a list of 2
60    ### elements: forfun/forall, then a parser function for an individual
61    ### object.
62    forall.parsers <-
63      list(## Extract lots of info from normal functions.
64           parsefun=list(forfun,function(src,name,...){
65    extract.docs.fun(src,name)    extract.docs.fun(src,name)
66  })         }),
67           ## Fill in author from DESCRIPTION and titles.
68  ### Fill in author from DESCRIPTION and titles.         author.from.description=list(forall,function(desc,...){
 author.from.description <- forall(function(desc,...){  
69    list(author=desc[,"Maintainer"])    list(author=desc[,"Maintainer"])
70  })         }),
71           ## The format section sometimes causes problems, so erase it.
72  ### The format section sometimes causes problems, so erase it.         erase.format=list(forall,function(...){
 erase.format <- forall(function(...){  
73    list(format="")    list(format="")
74  })         }),
75           ## Convert the function name to a title.
76  ### Convert the function name to a title.         title.from.name=list(forall,function(name,doc,...){
77  title.from.name <- forall(function(name,...){           if("title"%in%names(doc))list() else
78    list(title=gsub("[._]"," ",name))    list(title=gsub("[._]"," ",name))
79  })         }),
80           # PhG: it is tests/FUN.R!!! I would like more flexibility here
81  ### Get examples for FUN from the file test/FUN.R             # please, let me choose which dir to use for examples!
82  examples.from.testfile <- forfun(function(name,...){             ## Get examples for FUN from the file tests/FUN.R
83    tfile <- file.path("..","tests",paste(name,".R",sep=""))         examples.from.testfile=list(forfun,function(name,...){
84             tsubdir <- getOption("inlinedocs.exdir")
85                     if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
86                     tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
87    if(file.exists(tfile))    if(file.exists(tfile))
88      list(examples=paste(readLines(tfile),collapse="\n"))      list(examples=paste(readLines(tfile),collapse="\n"))
89    else list()    else list()
90  })         }),
91           ## Get examples from inline definitions after return()
92               # PhG: this does not work well! Think at these situations:
93               # 1) You have multiple return() in the code of your function,
94               # 2) You have return() appearing is some example code, ...
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
97               # of code that is actually executed.
98               #
99               # I make two propositions here
100               # 1) to keep the same mechanism that has the advantage of simplicity
101               #    but to use a special tag ##examples<< or #{{{examples to separate
102               #    function code from examples explicitly, and
103               # 2) to place the example in an "ex" attribute attached to the function
104               #    (see next parser). That solution will be also interesting for
105               #    documenting datasets, something not done yet by inlinedocs!
106               examples.after.return = list(forfun, function(name, src, ...) {
107                            # Look for the examples mark
108                            m <- grep("##examples<<|#\\{\\{\\{examples", src)
109                            if (!length(m)) return(list())
110                            if (length(m) > 1)
111                                    warning("More than one examples tag for ", name, ". Taking the last one")
112                            m <- m[length(m)]
113                            # Look for the lines containing return value comments just before
114                            r <- grep("\\s*### ", src[1:(m-1)])
115                            if (!length(r)) {
116                                    value <- NULL
117                            } else {
118                                    # Only take consecutive lines before the mark
119                                    keep <- rev((m - rev(r)) == 1:length(r))
120                                    if (!any(keep)) {
121                                            value <- NULL
122                                    } else {
123                                            value <- decomment(src[r[keep]])
124                                    }
125                            }
126                            # Collect now the example code beneath the mark
127                            ex <- src[(m + 1):(length(src) - 1)]
128                            # Possibly eliminate a #}}} tag
129                            ex <- ex[!grepl("#}}}", ex)]
130                            # Eliminate leading tabulations or four spaces
131                            ex <- sub("^\t|    ", "", ex)
132                            # Add an empty line before and after example
133                            ex <- c("", ex, "")
134                            # Return examples and value
135                            list(examples = paste(ex, collapse = "\n"), value = value)
136               }),
137               # PhG: here is what I propose for examples code in the 'ex' attribute
138               examples.in.attr = list(forfun, function (name, o, ...) {
139                            ex <- attr(o, "ex")
140                            if (!is.null(ex)) {
141                                    # Special case for code contained in a function
142                                    if (inherits(ex, "function")) {
143                                            # If source is available, start from there
144                                            src <- attr(ex, "source")
145                                            if (!is.null(src)) {
146                                                    ex <- src
147                                            } else { # Use the body of the function
148                                                    ex <- deparse(body(ex))
149                                            }
150                                            # Eliminate leading and trailing code
151                                            ex <- ex[-c(1, length(ex))]
152                                            # Eliminate leading tabulations or four spaces
153                                            ex <- sub("^\t|    ", "", ex)
154                                            # Add an empty line before and after example
155                                            ex <- c("", ex, "")
156                                    }
157                                    list(examples = paste(ex, collapse = "\n"))
158                            } else list()
159               }))
160    
161    ### List of parser functions that operate on single objects. This list
162    ### is useful for testing these functions, ie
163    ### lonely$parsefun(attr(extract.docs.file,"source"),"extract.docs.file")
164    lonely <- sapply(forall.parsers,function(L)L[[2]])
165    
166  ### Get examples from inline definitions after return()  extra.code.docs <- function # Extract documentation from code chunks
 examples.after.return <- forfun(function(src,...){  
   rline <- grep("return([^)]*)",src)  
   if(length(rline)==0)return(list())  
   rline <- rline[length(rline)]  
   comment.line.nums <- grep(prefix,src)  
   if(!(comment.end <- rline+1)%in%comment.line.nums)return(list())  
   while(comment.end%in%comment.line.nums)comment.end <- comment.end+1  
   excode <- src[comment.end:(length(src)-1)]  
   list(examples=paste(gsub("^\\W*","",excode),collapse="\n"))  
 })  
   
 extract.docs.file <- function # Extract documentation from a file  
167  ### Parse R code to extract inline documentation from comments around  ### Parse R code to extract inline documentation from comments around
168  ### each function. These are not able to be retreived simply by  ### each function. These are not able to be retreived simply by
169  ### looking at the "source" attribute. This is a Parser Function that  ### looking at the "source" attribute. This is a Parser Function that
170  ### can be used in the parser list of package.skeleton.dx().  ### can be used in the parser list of package.skeleton.dx(). TODO:
171    ### Modularize this into separate Parsers Functions for S4 classes,
172    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
173  (code,  (code,
174  ### Code lines in a character vector containing multiple R objects to  ### Code lines in a character vector containing multiple R objects to
175  ### parse for documentation.  ### parse for documentation.
# Line 91  Line 192 
192            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
193          }          }
194          if ( "setMethodS3" == parsed[[on]]@created ){          if ( "setMethodS3" == parsed[[on]]@created ){
195              # PhG: this may be wrong! It does not catch correctly how the method
196                      # must be splitted in case of methods containing dots. for instance,
197                      # as.data.frame.matrix must be split into: m1 = as.data.frame and
198                      # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!
199            pattern <- "^([^\\.]+)\\.(.*)$"            pattern <- "^([^\\.]+)\\.(.*)$"
200            doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),            doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),
201                m2 <- gsub(pattern,"\\2",on,perl=TRUE))                m2 <- gsub(pattern,"\\2",on,perl=TRUE))
# Line 175  Line 280 
280  ### named list of lists, one for each object to document.  ### named list of lists, one for each object to document.
281  }  }
282    
283  ### Default parsers to use with package.skeleton.dx  ### List of parsers to use by default with package.skeleton.dx.
284  default.parsers <- list("parsefuns","extract.docs.file",  default.parsers <-
285                          "examples.after.return","examples.from.testfile",    c(extra.code.docs=extra.code.docs,
286                          "author.from.description","erase.format","title.from.name")      sapply(forall.parsers,function(L)L[[1]](L[[2]])),
287        edit.package.file=function(desc,...){
288          in.details <- setdiff(colnames(desc),"Description")
289          details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",
290                                 sep=""),collapse="\n")
291          L <-
292            list(list(title=desc[,"Title"],
293                      description=desc[,"Description"],
294                      `tabular{ll}`=details,
295                      author=desc[,"Maintainer"]))
296          names(L) <- paste(desc[,"Package"],"-package",sep="")
297          L
298        })
299    
300  extract.docs.fun <- function # Extract documentation from a function  extract.docs.fun <- function # Extract documentation from a function
301  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
# Line 187  Line 304 
304  ### The function to examine.  ### The function to examine.
305   name.fun   name.fun
306  ### The name of the function/chunk to use in warning messages.  ### The name of the function/chunk to use in warning messages.
307   )   ){
 {  
308    res <- list()    res <- list()
309    clines <- grep(prefix,code)    clines <- grep(prefix,code)
310    if(length(grep("#",code[1]))){    if(length(grep("#",code[1]))){
# Line 407  Line 523 
523        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
524        in.chunk <- TRUE        in.chunk <- TRUE
525        if ( not.describe ){        if ( not.describe ){
526            ## TDH 2010-06-18 For item{}s in the documentation list names,
527            ## we don't need to have a backslash before, so delete it.
528            arg <- gsub("^[\\]+","",arg)
529          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
530          payload <- comment          payload <- comment
531        } else {        } else {
# Line 574  Line 693 
693  ### Using the same conventions as for functions, definitions of S4 classes  ### Using the same conventions as for functions, definitions of S4 classes
694  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
695  ### scanned for inline comments.  ### scanned for inline comments.
696  (doc.link)  (doc.link
697  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{\link{extract.file.parse}}.
698  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
699  ### class definitions.  ### class definitions.
700  {   ){
701    chunk.source <- doc.link@code    chunk.source <- doc.link@code
702    ##details<<    ##details<<
703    ## Extraction of S4 class documentation is currently limited to expressions    ## Extraction of S4 class documentation is currently limited to expressions
# Line 619  Line 738 
738    }    }
739    invisible(docs)    invisible(docs)
740  }  }
741    
742    apply.parsers <- function
743    ### Parse code to r objs, then run all the parsers and return the
744    ### documentation list.
745    (code,
746    ### Character vector of code lines.
747     parsers=default.parsers,
748    ### List of Parser Functions.
749     verbose=FALSE,
750    ### Echo names of Parser Functions?
751     ...
752    ### Additional arguments to pass to Parser Functions.
753     ){
754      e <- new.env()
755      old <- options(keep.source=TRUE)
756      on.exit(options(old))
757      exprs <- parse(text=code)
758      for (i in exprs) eval(i, e)
759      objs <- sapply(ls(e),get,e,simplify=FALSE)
760    
761      docs <- list()
762    
763      # PhG: Automatically determine who is S3 methods
764      for (name in names(objs)) {
765        parts <- strsplit(name, ".", fixed = TRUE)[[1]]
766            l <- length(parts)
767            if (l > 1) {
768            for (i in 1:(l - 1)) {
769                # Look for a generic function (known by the system or defined
770                # in the package) that matches that part of the function name
771                generic <- paste(parts[1:i], collapse = ".")
772                if (any(generic %in% utils:::getKnownS3generics()) ||
773                    utils:::findGeneric(generic, e) != "") {
774                    object <- paste(parts[(i + 1):l], collapse = ".")
775                    docs[[name]]$s3method <- c(generic, object)
776                    break
777                }
778            }
779        }
780      }
781      ## apply parsers in sequence to code and objs
782      for(i in seq_along(parsers)){
783        N <- names(parsers[i])
784        if(verbose){
785          if(is.character(N) && N!=""){
786            cat(N," ",sep="")
787          }else cat('. ')
788        }
789        p <- parsers[[i]]
790        ## This is the argument list that each parser receives:
791        L <- p(code=code,objs=objs,docs=docs,...)
792        docs <- combine(docs,L)
793      }
794      if(verbose)cat("\n")
795      docs
796    ### A list of extracted documentation from code.
797    }
798    
799    extract.docs.file <- function
800    ### Apply all parsers relevant to extract info from just 1 code file.
801    (f,
802    ### File name of R code to read and parse.
803     parsers=list(extra.code.docs,default.parsers$parsefun),
804    ### Parser Functions to use to parse the code and extract
805    ### documentation.
806     ...
807    ### Other arguments to pass to Parser Functions.
808     ){
809      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
810    }

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