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render_site.R
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render_site.R
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#' Render multiple documents as a website
#'
#' Render all of the R Markdown documents within a directory as a website.
#'
#' The \code{render_site} function enables you to render a collection of
#' markdown documents within a directory as a website. There are two
#' requirements for a directory to be rendered as a website:
#' \enumerate{
#' \item{It must contain either an "index.Rmd" or "index.md" file.}
#' \item{It must contain a site configuration file ("_site.yml").}
#' }
#'
#' The most minimal valid website is an empty "index.Rmd" and an empty
#' "_site.yml". With this configuration a single empty webpage would be
#' generated via a call to \code{render_site}. If you add additional markdown
#' documents to the directory they will also be rendered. By default a site is
#' rendered in the following fashion:
#'
#' \enumerate{
#' \item{R Markdown (.Rmd) and plain markdown (.md) files in the root
#' directory are rendered. Note however that markdown files beginning with "_"
#' are not rendered (this is a convention to designate files that are included
#' by top level documents).}
#' \item{All output and supporting files are copied to a "_site" subdirectory
#' of the website directory (this is configurable, see discussion below).}
#' \item{The following files are \bold{not} copied to the "_site"
#' sub-directory:
#' \itemize{
#' \item{Files beginning with "." (hidden files).}
#' \item{Files beginning with "_"}
#' \item{Files known to contain R source code (e.g. ".R", ".s", ".Rmd"), R
#' data (e.g. ".RData", ".rds"), or configuration data (e.g. ".Rproj",
#' "rsconnect")).}
#' }
#' Note that you can override which files are included or excluded via
#' settings in "_site.yml" (described below).}
#' \item{Normally R Markdown renders documents as self-contained HTML.
#' However, \code{render_site} ensures that dependencies (e.g. CSS,
#' JavaScript, images, etc.) remain in external files. CSS/JavaScript
#' libraries are copied to a "site_libs" sub-directory and plots/images are
#' copied to "_files" sub-directories.}
#' }
#'
#' You can remove the files generated by \code{render_site} using the
#' \code{clean_site} function.
#'
#' @section Configuration:
#' A "_site.yml" file can be used to configure the behavior of site generation.
#' Here is an example configuration file:
#'
#' \preformatted{
#' name: my-website
#' output_dir: _site
#' include: ["demo.R"]
#' exclude: ["docs.txt", "*.csv"]
#' navbar:
#' title: "My Website"
#' left:
#' - text: "Home"
#' href: index.html
#' - text: "About"
#' href: about.html
#' output:
#' html_document:
#' toc: true
#' highlight: textmate
#' }
#'
#' The \code{name} field provides a suggested URL path for your website when it
#' is published (by default this is just the name of the directory containing
#' the site). The \code{output_dir} indicates which directory to copy site
#' content into ("_site" is the default if none is specified). Note that this
#' can be "." to keep all content within the root website directory alongside
#' the source code.
#'
#' The \code{include} and \code{exclude} fields enable you to override the
#' default behavior vis-a-vis what files are copied into the "_site" directory
#' (wildcards can be used as in the above example).
#'
#' The \code{navbar} field can be used to define a navigation bar for websites
#' based on the \code{\link{html_document}} format.
#'
#' Finally, the \code{output} field enables you to specify output options that
#' are common to all documents within the website (you can also still provide
#' local options within each document that override any common options).
#'
#' \code{new_session: true} causes each file to be rendered in a new R session.
#' This prevents the masking problem that arises when different files use
#' functions from different packages (namespaces) that share a common name, such
#' as \code{here::here} and \code{lubridate::here} or \code{dplyr::filter} and
#' \code{MASS::filter}. The default behaviour of \code{render_site} is to use a
#' common R session.
#'
#' \code{autospin: true} causes \code{.R} files to be spinned and rendered
#' (as well as \code{.Rmd} files). If \code{autospin} is set to false (the default),
#' \code{.R} files will not be spinned nor rendered. \code{autospin} can also
#' enumerate a list of .R files to be spinned and rendered.
#'
#' @section Custom Site Generation:
#' The behavior of the default site generation function
#' (\code{rmarkdown::default_site}) is described above. It is also possible to
#' define a custom site generator that has alternate behavior. A site generator
#' is an R function that is bound to by including it in the "site:" field of the
#' "index.Rmd" or "index.md" file. For example:
#'
#' \preformatted{
#' title: "My Book"
#' output: bookdown::gitbook
#' site: bookdown::bookdown_site
#' }
#'
#' A site generation function should return a list with the following elements:
#' \itemize{
#' \item{\code{name}} {The name for the website (e.g. the parent directory
#' name).}
#' \item{\code{output_dir} {The directory where the website output is written
#' to. This path should be relative to the site directory (e.g. "." or
#' "_site")}}
#' \item{\code{render}} {An R function that can be called to generate the
#' site. The function should accept the \code{input_file},
#' \code{output_format}, \code{envir}, and \code{quiet} arguments.}
#' \item{\code{clean}} {An R function that returns relative paths to the files
#' generated by \code{render_site} (these files are the ones which will be
#' removed by the \code{clean_site} function.}
#' }
#'
#' Note that the \code{input_file} argument will be \code{NULL} when the entire
#' site is being generated. It will be set to a specific file name if a
#' front-end tool is attempting to preview it (e.g. RStudio IDE via the Knit
#' button).
#'
#' When \code{quiet = FALSE} the \code{render} function should also print a line
#' of output using the \code{\link{message}} function indicating which output
#' file should be previewed, for example:
#'
#' \preformatted{if (!quiet)
#' message("\nOutput created: ", output)
#' }
#'
#' Emitting this line enables front-ends like RStudio to determine which file
#' they should open to preview the website.
#'
#' See the source code of the \code{rmarkdown::default_site} function for a
#' example of a site generation function.
#'
#' @param input Website directory (or the name of a file within the directory).
#' @param output_format R Markdown format to convert to (defaults to "all").
#' @param envir The environment in which the code chunks are to be evaluated
#' during knitting (can use \code{\link{new.env}} to guarantee an empty new
#' environment).
#' @param quiet \code{TRUE} to suppress messages and other output.
#' @inheritParams render
#'
#' @return \code{render_site} returns the name of the site output file (relative
#' to the input directory). \code{clean_site} returns the names of the
#' generated files removed during cleaning. \code{site_config} returns the
#' contents of _site.yml as an R list. \code{default_site_generator} returns
#' the default site generator for R Markdown websites.
#' @export
render_site <- function(input = ".",
output_format = "all",
envir = parent.frame(),
quiet = FALSE,
encoding = "UTF-8") {
# capture original input
original_input <- input
# normalize to a directory
input <- input_as_dir(input)
# if it's a file then capture that and force output_format to be NULL
# (to only render a single format for incremental/previewing)
input_file <- NULL
if (!dir_exists(original_input)) {
input_file <- original_input
if (output_format == "all")
output_format <- NULL
}
# find the site generator
generator <- site_generator(input, output_format)
if (is.null(generator))
stop("No site generator found.")
# execute it
generator$render(input_file = input_file,
output_format = output_format,
envir = envir,
quiet = quiet)
# compute the name of the output file. if the input was a filename
# use that as a base (otherwise use index.html)
if (!dir_exists(original_input))
output <- file_with_ext(basename(original_input), "html")
else
output <- "index.html"
output <- file.path(input, generator$output_dir, output)
output <- normalized_relative_to(input, output)
# return it invisibly
invisible(output)
}
#' @rdname render_site
#' @param preview Whether to list the files to be removed rather than actually
#' removing them.
#' @export
clean_site <- function(input = ".", preview = FALSE, quiet = FALSE,
encoding = "UTF-8") {
# normalize to a directory
input <- input_as_dir(input)
# find the site generator
generator <- site_generator(input, output_format = NULL)
if (is.null(generator))
stop("No site generator found.")
# get the files to be cleaned
files <- generator$clean()
# if it's just a preview then return the files, otherwise
# actually remove the files
if (preview)
files
else {
if (!quiet) {
cat("Removing files: \n")
cat(paste0(" ", files), sep = "\n")
}
unlink(file.path(input, files), recursive = TRUE)
}
}
#' @rdname render_site
#' @export
site_generator <- function(input = ".", output_format = NULL) {
# look for the closest index file with 'site' metadata
root <- tryCatch(
proj_root(input, "^index.R?md$", "^\\s*site:.*::.*$"),
error = function(e) NULL
)
# normalize input
input <- input_as_dir(input)
# if none found then look for a _site.yml file
if (is.null(root)) {
if (file.exists(site_config_file(input))) {
return (default_site(input))
} else {
return(NULL)
}
}
# determine the index file (will be index.Rmd or index.md)
index <- file.path(root, "index.Rmd")
if (!file.exists(index))
index <- file.path(root, "index.md")
# is this in a subdir of the site root? (only some generators support this)
in_subdir <- !same_path(input, root)
# read index.Rmd and extract the front matter
front_matter <- yaml_front_matter(index)
# create the site generator (passing the root dir)
create_site_generator <- eval(parse(text = front_matter$site))
generator <- create_site_generator(root)
# if it's in a subdir check to see if the generator supports nested files
if (in_subdir) {
if (isTRUE(generator$subdirs)) {
generator
} else {
NULL
}
} else {
generator
}
}
#' @rdname render_site
#' @export
site_config <- function(input = ".", encoding = "UTF-8") {
# normalize input
input <- input_as_dir(input)
# check for config file
config_file <- site_config_file(input)
if (file.exists(config_file)) {
# parse the yaml
config_lines <- read_utf8(config_file)
config <- yaml_load(config_lines)
if (!is.list(config))
config <- list()
# provide defaults if necessary
if (is.null(config$name))
config$name <- basename(normalize_path(input))
if (is.null(config$output_dir))
config$output_dir <- "_site"
if (is.null(config$new_session))
config$new_session <- FALSE
# return config
config
# no _site.yml
} else {
NULL
}
}
# default site implementation (can be overridden by custom site generators)
#' @rdname render_site
#' @param ... Currently unused.
#' @export
default_site_generator <- default_site <- function(input, ...) {
# get the site config
config <- site_config(input)
if (is.null(config))
stop("No site configuration (_site.yml) file found.")
# helper function to get all input files. includes all .Rmd and
# .md files that don't start with "_" (note that we don't do this
# recursively because rmarkdown in general handles applying common
# options/elements across subdirectories poorly). Also excludes
# README.R?md as those files are intended for GitHub. If
# config$autospin is TRUE, we also spin and render .R files.
input_files <- function() {
pattern <- sprintf(
"^[^_].*\\.%s$", if (isTRUE(config$autospin)) {
"([Rr]|[Rr]?md)"
} else {
"[Rr]?md"
}
)
files <- list.files(input, pattern)
if (is.character(config$autospin)) files <- c(files, config$autospin)
files[!grepl("^README\\.R?md$", files)]
}
# define render function (use ... to gracefully handle future args)
render <- function(input_file,
output_format,
envir,
quiet,
...) {
# track outputs
outputs <- c()
# see if this is an incremental render
incremental <- !is.null(input_file)
# files list is either a single file (for incremental) or all
# file within the input directory
if (incremental)
files <- input_file
else {
files <- file.path(input, input_files())
}
sapply(files, function(x) {
render_one <- if (isTRUE(config$new_session)) {
render_new_session
} else {
render_current_session
}
# log the file being rendered
if (!quiet) message("\nRendering: ", x)
output <- render_one(input = x,
output_format = output_format,
output_options = list(lib_dir = "site_libs",
self_contained = FALSE),
envir = envir,
quiet = quiet)
# add to global list of outputs
outputs <<- c(outputs, output)
# check for files dir and add that as well
sidecar_files_dir <- knitr_files_dir(output)
files_dir_info <- file.info(sidecar_files_dir)
if (isTRUE(files_dir_info$isdir))
outputs <<- c(outputs, sidecar_files_dir)
})
# do we have a relative output directory? if so then remove,
# recreate, and copy outputs to it (we don't however remove
# it for incremental builds)
if (config$output_dir != '.') {
# remove and recreate output dir if necessary
output_dir <- file.path(input, config$output_dir)
if (file.exists(output_dir)) {
if (!incremental) {
unlink(output_dir, recursive = TRUE)
dir.create(output_dir)
}
} else {
dir.create(output_dir)
}
# move outputs
for (output in outputs) {
# don't move it if it's a _files dir that has a _cache dir
if (grepl("^.*_files$", output)) {
cache_dir <- gsub("_files$", "_cache", output)
if (dir_exists(cache_dir))
next;
}
output_dest <- file.path(output_dir, basename(output))
if (dir_exists(output_dest))
unlink(output_dest, recursive = TRUE)
file.rename(output, output_dest)
}
# copy lib dir a directory at a time (allows it to work with incremental)
lib_dir <- file.path(input, "site_libs")
output_lib_dir <- file.path(output_dir, "site_libs")
if (!file.exists(output_lib_dir))
dir.create(output_lib_dir)
libs <- list.files(lib_dir)
for (lib in libs)
file.copy(file.path(lib_dir, lib), output_lib_dir, recursive = TRUE)
unlink(lib_dir, recursive = TRUE)
# copy other files
copy_site_resources(input)
}
# Print output created for rstudio preview
if (!quiet) {
# determine output file
output_file <- ifelse(is.null(input_file),
"index.html",
file_with_ext(basename(input_file), "html"))
if (config$output_dir != ".")
output_file <- file.path(config$output_dir, output_file)
message("\nOutput created: ", output_file)
}
}
# define clean function
clean <- function() {
# build list of generated files
generated <- c()
# enumerate rendered markdown files
files <- input_files()
# get html files
html_files <- file_with_ext(files, "html")
# _files peers are always removed (they could be here due to
# output_dir == "." or due to a _cache existing for the page)
html_supporting <- paste0(knitr_files_dir(html_files), '/')
generated <- c(generated, html_supporting)
# _cache peers are always removed
html_cache <- paste0(knitr_root_cache_dir(html_files), '/')
generated <- c(generated, html_cache)
# for rendering in the current directory we need to eliminate
# output files for our inputs (including _files) and the lib dir
if (config$output_dir == ".") {
# .html peers
generated <- c(generated, html_files)
# site_libs dir
generated <- c(generated, "site_libs/")
# for an explicit output_dir just remove the directory
} else {
generated <- c(generated, paste0(config$output_dir, '/'))
}
# filter out by existence
generated[file.exists(file.path(input, generated))]
}
# return site generator
list(
name = config$name,
output_dir = config$output_dir,
render = render,
clean = clean
)
}
# we suppress messages during render so that "Output created" isn't emitted
# (which could result in RStudio previewing the wrong file)
render_current_session <- function(...) suppressMessages(rmarkdown::render(...))
render_new_session <- function(...) {
xfun::Rscript_call(
function(...) { suppressMessages(rmarkdown::render(...)) },
args = list(...)
)
}
# utility function to copy all files into the _site directory
copy_site_resources <- function(input) {
# get the site config
config <- site_config(input)
if (config$output_dir != ".") {
# get the list of files
files <- copyable_site_resources(input = input, config = config)
# perform the copy
output_dir <- file.path(input, config$output_dir)
file.copy(from = file.path(input, files),
to = output_dir,
recursive = TRUE)
}
}
#' Determine website resource files for a directory
#'
#' Determine which files within a given directory should be copied in
#' order to serve a website from the directory. Attempts to automatically
#' exclude source, data, hidden, and other files not required to serve
#' website content.
#'
#' @param site_dir Site directory to analyze
#' @param include Additional files to include (glob wildcards supported)
#' @param exclude Files to exclude (glob wildcards supported)
#' @param recursive \code{TRUE} to return a full recursive file listing;
#' \code{FALSE} to just provide top-level files and directories.
#'
#' @return Character vector of files and directories to copy
#'
#' @export
site_resources <- function(site_dir, include = NULL, exclude = NULL, recursive = FALSE) {
# get the original file list (we'll need it to apply includes)
all_files <- list.files(site_dir, all.files = TRUE)
# excludes:
# - known source/data extensions
# - anything that starts w/ '.' or '_'
# - rsconnect and packrat directories
# - user excludes
extensions <- c("R", "r", "S", "s",
"Rmd", "rmd", "md", "Rmarkdown", "rmarkdown",
"Rproj", "rproj",
"RData", "rdata", "rds")
extensions_regex <- utils::glob2rx(paste0("*.", extensions))
excludes <- c("^rsconnect$", "^packrat$", "^\\..*$", "^_.*$", "^.*_cache$",
extensions_regex,
utils::glob2rx(exclude))
files <- all_files
for (exclude in excludes)
files <- files[!grepl(exclude, files)]
# allow back in anything specified as an explicit "include"
includes <- utils::glob2rx(include)
for (include in includes) {
include_files <- all_files[grepl(include, all_files)]
files <- unique(c(files, include_files))
}
# if this is recursive then we need to blow out the directories
if (recursive) {
recursive_files <- c()
for (file in files) {
file_path <- file.path(site_dir, file)
if (dir_exists(file_path)) {
dir_files <- file.path(list.files(file_path,
full.names = FALSE,
recursive = TRUE))
dir_files <- file.path(file, dir_files)
recursive_files <- c(recursive_files, dir_files)
} else {
recursive_files <- c(recursive_files, file)
}
}
recursive_files
} else {
files
}
}
# utility function to list the files that should be copied
#
# NOTE: '...' is kept for backwards compatibility with older versions of
# RStudio which called 'copyable_site_resources(encoding = "UTF-8")'
copyable_site_resources <- function(input, config = site_config(input), ...) {
include <- config$include
exclude <- config$exclude
if (config$output_dir != ".")
exclude <- c(exclude, config$output_dir)
site_resources(input, include, exclude)
}
# utility function to ensure that 'input' is a valid directory
# (converts from file to parent directory as necessary)
input_as_dir <- function(input) {
# ensure the input dir exists
if (!file.exists(input)) {
input <- normalize_path(input, mustWork = FALSE)
if (!file.exists(input)) stop(
"The specified directory '", input, "' does not exist.", call. = FALSE
)
}
# convert from file to directory if necessary
if (!dir_exists(input))
input <- dirname(input)
# return it
input
}
# get the path to the site config file
site_config_file <- function(input) {
file.path(input, "_site.yml")
}
site_skeleton <- function(path, ...) {
dir.create(path, recursive = TRUE, showWarnings = FALSE)
file.copy(
list.files(pkg_file('rmd', 'site'), full.names = TRUE),
path, overwrite = TRUE
)
}