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Extending roxygen2

Source: vignettes/extending.Rmd
extending.Rmd

Basics

Roxygen is extensible with user-defined roclets. It means that you can take advantage of Roxygen’s parser and extend it with your own @tags.

There are two primary ways to extend roxygen2:

  • Add a new tag that generates a new top-level section in .Rd files.

  • Add a new roclet that does anything you like.

This vignette will introduce you to the key data structures in roxygen2, and then show you how to use these two extension points. This vignette is very rough, so you are expected to have also read some roxygen2 source code to understand all the extension points. Hopefully, it’s useful enough to help you get started, and if you have problems, please file an issue!

Key data structures

Before we talk about extending roxygen2, we need to first discuss two important data structures that power roxygen: tags and blocks.

Tags

A tag (a list with S3 class roxy_tag) represents a single tag. It has the following fields:

  • tag: the name of the tag.

  • raw: the raw contents of the tag (i.e. everything from the end of this tag to the beginning of the next).

  • val: the parsed value, which we’ll come back to shortly.

  • file and line: the location of the tag in the package. Used with roxy_tag_warning() to produce informative error messages.

You can construct tag objects by hand with roxy_tag():

roxy_tag("name", "Hadley")
#> [????:???] @name 'Hadley' {unparsed}
str(roxy_tag("name", "Hadley"))
#> List of 5
#>  $ file: chr NA
#>  $ line: chr NA
#>  $ raw : chr "Hadley"
#>  $ tag : chr "name"
#>  $ val : NULL
#>  - attr(*, "class")= chr [1:2] "roxy_tag_name" "roxy_tag"

However, you should rarely need to do so, because you’ll typically have them given to you in a block object, as you’ll see shortly.

Blocks

A block (a list with S3 class roxy_block) represents a single roxygen block. It has the following fields:

  • tags: a list of roxy_tags.
  • call: the R code associated with the block (usually a function call).
  • file and line: the location of the R code.
  • object: the evaluated R object associated with the code.

The easiest way to see the basic structure of a roxy_block() is to generate one by parsing a roxygen block with parse_text():

text <- "
  #' This is a title
  #'
  #' This is the description.
  #'
  #' @param x,y A number
  #' @export
  f <- function(x, y) x + y
"

# parse_text() returns a list of blocks, so I extract the first
block <- parse_text(text)[[1]]
block
#> <roxy_block> [<text>:8]
#>   $tag
#>     [line:  2] @title 'This is a title' {parsed}
#>     [line:  4] @description 'This is the description.' {parsed}
#>     [line:  6] @param 'x,y A number' {parsed}
#>     [line:  7] @export '' {parsed}
#>     [line:  8] @usage '<generated>' {parsed}
#>     [line:  8] @.formals '<generated>' {parsed}
#>     [line:  8] @backref '<generated>' {parsed}
#>   $call   f <- function(x, y) x + y
#>   $object <function> 
#>     $topic f
#>     $alias f

Adding a new .Rd tag

The easiest way to extend roxygen2 is to create a new tag that adds output to .Rd files. This requires two steps:

  1. Define a roxy_tag_parse() method that describes how to parse our new tag.

  2. Define a roxy_tag_rd() method that describes how to convert the tag into .Rd commands.

To illustrate the basic idea, we’ll create a new @tip tag that will create a bulleted list of tips about how to use a function. The idea is to take something like this:

#' @tip The mean of a logical vector is the proportion of `TRUE` values.
#' @tip You can compute means of dates and date-times!

And generate Rd like this:

\section{Tips and tricks}{
\itemize{
  \item The mean of a logical vector is the proportion of \code{TRUE} values.
  \item You can compute means of dates and date-times!
}
}

The first step is to define a method for roxy_tag_parse() that describes how to parse the tag text. The name of the class will be roxy_tag_{tag}, which in this case is roxy_tag_tip. This function takes a roxy_tag as input, and it’s job is to set x$val to a convenient parsed value that will be used later by the roclet. Here we want to process the text using Markdown so we can just use tag_markdown():

roxy_tag_parse.roxy_tag_tip <- function(x) {
  tag_markdown(x)
}

We check this works by using parse_text():

text <- "
  #' Title
  #'
  #' @tip The mean of a logical vector is the proportion of `TRUE` values.
  #' @tip You can compute means of dates and date-times!
  #' @md
  f <- function(x, y) {
    # ...
  }
"
block <- parse_text(text)[[1]]
block
#> <roxy_block> [<text>:7]
#>   $tag
#>     [line:  2] @title 'Title' {parsed}
#>     [line:  4] @tip 'The mean of a logical vector is the proportion ...' {parsed}
#>     [line:  5] @tip 'You can compute means of dates and date-times!' {parsed}
#>     [line:  6] @md '' {parsed}
#>     [line:  7] @usage '<generated>' {parsed}
#>     [line:  7] @.formals '<generated>' {parsed}
#>     [line:  7] @backref '<generated>' {parsed}
#>   $call   f <- function(x, y) { ...
#>   $object <function> 
#>     $topic f
#>     $alias f

str(block$tags[[2]])
#> List of 5
#>  $ file: chr "<text>"
#>  $ line: int 4
#>  $ tag : chr "tip"
#>  $ raw : chr "The mean of a logical vector is the proportion of `TRUE` values."
#>  $ val : chr "The mean of a logical vector is the proportion of \\code{TRUE} values."
#>  - attr(*, "class")= chr [1:2] "roxy_tag_tip" "roxy_tag"

(Here I explicitly turn Markdown parsing on using @md; it’s usually turned on for a package using roxygen options).

Next, we define a method for roxy_tag_rd(), which must create an rd_section(). We’re going to create a new section called tip. It will contain a character vector of tips:

roxy_tag_rd.roxy_tag_tip <- function(x, base_path, env) {
  rd_section("tip", x$val)
}

This additional layer is needed because there can be multiple tags of the same type in a single block, and multiple blocks can contribute to the same .Rd file. The job of the rd_section is to combine all the tags into a single top-level Rd section. Each tag generates an rd_section which is then combined with any previous section using merge(). The default merge.rd_section() just concatenates the values together (rd_section(x$type, c(x$value, y$value))); you can override this method if you need more sophisticated behaviour.

We then need to define a format() method to convert this object into text for the .Rd file:

format.rd_section_tip <- function(x, ...) {
  paste0(
    "\\section{Tips and tricks}{\n",
    "\\itemize{\n",
    paste0("  \\item ", x$value, "\n", collapse = ""),
    "}\n",
    "}\n"
  )
}

We can now try this out with roclet_text():

topic <- roc_proc_text(rd_roclet(), text)[[1]]
topic$get_section("tip")
#> \section{Tips and tricks}{
#> \itemize{
#>   \item The mean of a logical vector is the proportion of \code{TRUE} values.
#>   \item You can compute means of dates and date-times!
#> }
#> }
#>

Note that there is no namespacing so if you’re defining multiple new tags I recommend using your package name as the common prefix.

Creating a new roclet

Creating a new roclet is usually a two part process. First, you define new tags that your roclet will work with. Second, you define a roclet that tells roxygen how to process an entire package.

Custom tags

In this example we will make a new @memo tag to enable printing the memos at the console when the roclet runs. We choose that the @memo has this syntax:

@memo [Headline] Description

As an example:

@memo [EFFICIENCY] Currently brute-force; find better algorithm.

As above, we first define a parse method:

roxy_tag_parse.roxy_tag_memo <- function(x) {
  if (!grepl("^\\[.*\\].*$", x$raw)) {
    roxy_tag_warning(x, "Invalid memo format")
    return()
  }

  parsed <- stringi::stri_match(str = x$raw, regex = "\\[(.*)\\](.*)")[1, ]

  x$val <- list(
    header = parsed[[2]], 
    message = parsed[[3]]
  )
  x
}

Then check if it works with parse_text():

text <- "
  #' @memo [TBI] Remember to implement this!
  #' @memo [API] Check best API
  f <- function(x, y) {
    # ...
  }
"
block <- parse_text(text)[[1]]
block
#> <roxy_block> [<text>:4]
#>   $tag
#>     [line:  2] @memo '[TBI] Remember to implement this!' {parsed}
#>     [line:  3] @memo '[API] Check best API' {parsed}
#>     [line:  4] @usage '<generated>' {parsed}
#>     [line:  4] @.formals '<generated>' {parsed}
#>     [line:  4] @backref '<generated>' {parsed}
#>   $call   f <- function(x, y) { ...
#>   $object <function> 
#>     $topic f
#>     $alias f

str(block$tags[[1]])
#> List of 5
#>  $ file: chr "<text>"
#>  $ line: int 2
#>  $ tag : chr "memo"
#>  $ raw : chr "[TBI] Remember to implement this!"
#>  $ val :List of 2
#>   ..$ header : chr "TBI"
#>   ..$ message: chr " Remember to implement this!"
#>  - attr(*, "class")= chr [1:2] "roxy_tag_memo" "roxy_tag"

The roclet

Next, we create a constructor for the roclet, which uses roclet(). Our memo roclet doesn’t have any options so this is very simple:

memo_roclet <- function() {
  roclet("memo")
}

To give the roclet behaviour, you need to define methods. There are two methods that almost every roclet will use:

For this roclet, we’ll have roclet_process() collect all the memo tags into a named list:

roclet_process.roclet_memo <- function(x, blocks, env, base_path) {
  results <- list()
  
  for (block in blocks) {
    tags <- block_get_tags(block, "memo")

    for (tag in tags) {
      msg <- paste0("[", tag$file, ":", tag$line, "] ", tag$val$message)
      results[[tag$val$header]] <- c(results[[tag$val$header]], msg)
    }
  }
  
  results
}

And then have roclet_output() just print them to the screen:

roclet_output.roclet_memo <- function(x, results, base_path, ...) {
  for (header in names(results)) {
    messages <- results[[header]]
    cat(paste0(header, ": ", "\n"))
    cat(paste0(" * ", messages, "\n", collapse = ""))
  }

  invisible(NULL)
}

Then you can test if it works by using roc_proc_text():

results <- roc_proc_text(memo_roclet(), "
#' @memo [TBI] Remember to implement this!
#' @memo [API] Check best API
f <- function(x, y) {
  # ...
}

#' @memo [API] Consider passing z option
g <- function(x, y) {
  # ...
}
")
roclet_output(memo_roclet(), results)
#> TBI: 
#>  * [<text>:2]  Remember to implement this!
#> API: 
#>  * [<text>:3]  Check best API
#>  * [<text>:8]  Consider passing z option

Adding a roclet to your workflow

To use a roclet when developing a package, call

roxygen2::roxygenize(roclets = "yourPackage::roclet")

where yourPackage::roclet is the function which creates the roclet, e.g. memo_roclet above.

You can also add the roclet to the target package’s DESCRIPTION file, like this:

Roxygen: list(roclets = c("collate", "rd", "namespace", "yourPackage::roclet"))

Optionally, you can add your roclet package to the target package as a Suggests: dependency:

usethis::use_dev_package("yourPackage", type = "Suggests", remote = "yourGithubID/yourPackage")

You don’t have to do this, but it will help other developers working on the target package.