| Title: | Re-using Content in Bioconductor Books |
|---|---|
| Description: | Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment. |
| Authors: | Aaron Lun [aut, cre, cph] |
| Maintainer: | Aaron Lun <[email protected]> |
| License: | GPL-3 |
| Version: | 1.17.0 |
| Built: | 2024-12-18 03:54:37 UTC |
| Source: | https://github.com/bioc/rebook |
Helper functions to pull down images to use in the book. These aim to provide a sensible default for Bioconductor-related books.
BiocFavicon() BiocSticker(mode = c("static", "animated"))BiocFavicon() BiocSticker(mode = c("static", "animated"))
mode |
String specifying the type of sticker to show. |
BiocFavicon will return a path to a favicon.ico file.
BiocSticker will return a URL or path to a sticker.
Aaron Lun
BiocFavicon() BiocSticker()BiocFavicon() BiocSticker()
Get the path to the cache directory in which the book will be built.
bookCache(package) bookCacheExpiry()bookCache(package) bookCacheExpiry()
package |
String containing the name of the book package. |
For bookCache, the last elements of the output path are the package and version, consistent with the expectations of dir.expiry functions.
This path is located in a directory determined by rappdirs.
If the environment variable REBOOK_CACHE is set, it is used to obtain the root of the path instead.
If the environment variable REBOOK_CACHE_EXPIRY is set, it is coerced into an integer and returned by bookCacheExpiry.
This allows users to tune the expiry interval for older cached books.
For bookCache, a string containing the path to the cache directory for this book package.
For bookCacheExpiry, an integer specifying the maximum number of days from last access for a book cache.
Any unaccessed caches are subject to deletion by various rebook functions.
Aaron Lun
configureBook, where this function is used in the Makefile.
extractFromPackage, which populates the cache directory if this is not supplied.
bookCache('OSCA.workflows') bookCacheExpiry()bookCache('OSCA.workflows') bookCacheExpiry()
Build the dependency graph between chapter based on their extractCached calls to each other.
buildChapterGraph(dir, recursive = TRUE, pattern = "\\.Rmd$")buildChapterGraph(dir, recursive = TRUE, pattern = "\\.Rmd$")
dir |
String containing the path to the directory containing Rmarkdown reports.
This is searched recursively for all files ending in |
recursive, pattern
|
Further arguments to pass to |
A directed graph object from the igraph package, where each node is a chapter and is connected to its dependencies by an edge.
Aaron Lun
dir <- tempfile() dir.create(dir) tmp1 <- file.path(dir, "alpha.Rmd") write(file=tmp1, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") tmp2 <- file.path(dir, "bravo.Rmd") write(file=tmp2, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} extractCached('alpha.Rmd') ```") # Building the chapter graph: g <- buildChapterGraph(dir) plot(g)dir <- tempfile() dir.create(dir) tmp1 <- file.path(dir, "alpha.Rmd") write(file=tmp1, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") tmp2 <- file.path(dir, "bravo.Rmd") write(file=tmp2, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} extractCached('alpha.Rmd') ```") # Building the chapter graph: g <- buildChapterGraph(dir) plot(g)
Execute code to set up the compilation environment at the start of every chapter.
chapterPreamble(cache = TRUE)chapterPreamble(cache = TRUE)
cache |
Logical indicating whether to cache code chunks. |
Compilation is performed with no tolerance for errors, no printing of package start-up messages, and no printing of warnings.
Numbers are printed to 4 digits of precision.
The BiocStyle package is automatically attached, primarily for use of Biocpkg and similar functions.
HTML elements are defined using setupHTML.
HTML is printed to standard output, see setupHTML.
Aaron Lun
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} pi # four digits! ``` ```{r} warning('ASDASD') # warnings and messages are not saved in the HTML. ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} pi # four digits! ``` ```{r} warning('ASDASD') # warnings and messages are not saved in the HTML. ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))
Print HTML tags to open and close the collapsible chunks.
collapseStart(message) collapseEnd()collapseStart(message) collapseEnd()
message |
String containing a message to insert in the collapsible header. |
Both functions will cat HTML tags; one to start and another to end each collapsible chunk.
Aaron Lun
collapseStart("This is collapsible") cat("something inside the chunk\n") collapseEnd()collapseStart("This is collapsible") cat("something inside the chunk\n") collapseEnd()
Copy a bookdown book to a separate workspace prior to compilation, and then copy the compiled book to a final location.
preCompileBook(src.dir, work.dir, desc = NULL) postCompileBook(work.dir, final.dir, handle = NULL)preCompileBook(src.dir, work.dir, desc = NULL) postCompileBook(work.dir, final.dir, handle = NULL)
src.dir |
String containing the path to the book Rmarkdown sources. |
work.dir |
String containing the path to the versioned cache directory used to compile the book, see the dir.expiry package for details. |
desc |
String containing the path to a |
final.dir |
String containing the path to the final location for the compiled book's HTMLs. |
handle |
The lock handle returned by |
These two functions should bracket a render_book call.
We do not make these into a single function as calling render_book inside another function inside a package does not interact properly with some imports.
The offending example is that of cbind, which fails to be converted into an S4 generic (this would normally happen when BiocGenerics gets attached).
preCompileBook may take some time as it will compile all chapters via compileChapter.
It does so by locking and unlocking each chapter as it is compiled, thus avoiding problems with concurrent attempts to compile the same chapter via extractFromPackage.
(Concurrent compilation of different chapters is still supported and allows for parallel package builds.)
The actual compilation of the book with bookdown will simply re-use these caches for efficiency.
After compilation of the individual chapters, preCompileBook will lock the entire work.dir.
This ensures that bookdown's directory shuffling does not break concurrent processes using the knitr cache directories.
The lock can be released by passing the returned handle to handle in postCompileBook.
For preCompileBook, work is populated with the book sources and intermediate content (e.g., caches).
A lock handle is returned.
For postCompileBook, final is populated with the HTMLs.
Cache directories are moved out of _bookdown_files into their original location.
In both cases, a NULL is invisibly returned.
Aaron Lun
configureBook, where this function is called in the Makefile.
bookCache, the default choice for work.dir.
Compile a Rmarkdown file - typically a chapter of a book -
so that extractCached calls work correctly in other chapters.
compileChapter(path, cache = TRUE)compileChapter(path, cache = TRUE)
path |
String containing a path to an Rmarkdown file. |
cache |
Logical scalar indicating whether the compilation should be cached. |
Compilation is performed in a completely fresh R session, to ensure that objects, globals and loaded packages from one chapter do not affect the next chapter.
If an error is encountered during compilation of any Rmarkdown file,
the standard output of render leading up to the error is printed out before the function exists.
The specified file is (re)compiled to generate the corresponding *_cache directories.
NULL is invisibly returned.
Aaron Lun
extractCached, which calls this function.
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") compileChapter(tmp) file.exists(sub(".Rmd$", ".html", tmp)) # output HTML exists. file.exists(sub(".Rmd$", "_cache", tmp)) # output cache exists. exists("rodan") # FALSEtmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") compileChapter(tmp) file.exists(sub(".Rmd$", ".html", tmp)) # output HTML exists. file.exists(sub(".Rmd$", "_cache", tmp)) # output cache exists. exists("rodan") # FALSE
Helper function to run at the top-level directory of Bioconductor book packages,
to prepare for book compilation and to set up install-time resources for linking from other books.
configureBook(prefix = NULL, input = "index.Rmd", redirect = NULL)configureBook(prefix = NULL, input = "index.Rmd", redirect = NULL)
prefix |
Optional string containing the prefix to be used when |
input |
Name of the index file for the book, see |
redirect |
Optional name of the file containing redirection information, to be passed to |
This function assumes that the bookdown-formatted book is located at inst/book inside the package.
input is interpreted relative to this location, e.g., if input="index.Rmd", the file should be located at inst/book/index.Rmd.
Similarly, redirect is provided, the file should already be present in vignettes/.
For example, if redirect="redirect.txt", the file should be located at vignettes/redirect.txt.
A number of files are created in the package directory.
A "references.csv" file is created in the inst/rebook directory,
containing the table of references from scrapeReferences.
If prefix is specified, a "prefix.csv" file is also created in inst/rebook.
This contains the preferred prefix of the book.
A Makefile is created in vignettes/ that triggers book compilation.
This will also generate HTMLs for redirection via createRedirects if redirect is provided.
A stub vignette at vignettes/stub.Rmd is created that redirects to the deployed book location.
Aaron Lun
scrapeReferences, which is called by this function to create the reference table.
link, which is used by other books to link to the configured book.
Create a Makefile for compiling individual chapters, in a manner that respects the dependencies between chapters.
createMakefile(dir = ".", pattern = "\\.Rmd$", ..., fname = "Makefile")createMakefile(dir = ".", pattern = "\\.Rmd$", ..., fname = "Makefile")
dir |
String containing the path to the directory containing Rmarkdown reports.
This is searched recursively for all files ending in |
... |
Further arguments to pass to |
fname |
String containing the name of the output Makefile. |
The main benefit of using a Makefile is that the generation of the chapter caches can be done in parallel. Then, the bookdown step can just serially retrieve the cache contents for rapid rendering.
The Makefile uses the markdown output file as an indicator of successful knitting of a chapter.
Caches are left in the current working directory after the compilation of each report.
It is assumed that bookdown's render_book is smart enough to find and use these caches.
A Makefile is created in dir with the name fname
and a NULL is invisibly returned.
Aaron Lun
buildChapterGraph, to detect dependencies between chapters.
dir <- tempfile() dir.create(dir) tmp1 <- file.path(dir, "alpha.Rmd") write(file=tmp1, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") tmp2 <- file.path(dir, "bravo.Rmd") write(file=tmp2, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} extractCached('alpha.Rmd') ```") # Creating the Makefile: createMakefile(dir) cat(readLines(file.path(dir, "Makefile")), sep="\n")dir <- tempfile() dir.create(dir) tmp1 <- file.path(dir, "alpha.Rmd") write(file=tmp1, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} rodan <- 1 ```") tmp2 <- file.path(dir, "bravo.Rmd") write(file=tmp2, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} extractCached('alpha.Rmd') ```") # Creating the Makefile: createMakefile(dir) cat(readLines(file.path(dir, "Makefile")), sep="\n")
Create HTML pages to redirect users to the latest version of the relevant Bioconductor book. This is useful for preserving compatibility with old links when reorganizing the contents of a book.
createRedirects( name, pkg, page, dir = "../inst/doc/book", file = NULL, check = FALSE, include.gif = TRUE )createRedirects( name, pkg, page, dir = "../inst/doc/book", file = NULL, check = FALSE, include.gif = TRUE )
name |
Character vector containing the name of each HTML. |
pkg |
Character vector containing the name of the Bioconductor book package to redirect to. |
page |
Character vector containing the name of the new chapter to redirect to. |
dir |
String containing the path to the output directory for the HTMLs. |
file |
String containing the name of a comma-separate file with three unnamed columns, from which to derive |
check |
Logical scalar indicating whether to check if the destination URL exists. |
include.gif |
Logical scalar indicating whether a GIF should be included in the redirection notice. |
This function is intended to be called inside the Makefile generated by configureBook,
which will create the necessary HTMLs at package build time.
The expectation is that there is a file like redirect.txt that can be passed in as the file argument.
The default dir is the same as the final destination for all HTMLs that is defined in the Makefile.
In file, the last column can be left empty for any row.
This will instruct createRedirects to re-use name as page,
which is convenient when a chapter is simply moved to another package without a change in the HTML file name.
It is probably a good idea to run with check=TRUE on occasion, to verify that the redirections are working.
This is not done by default to avoid a chicken-and-egg situation where two books cannot build because they redirect to each other.
HTMLs of the specified name are created in dir, redirected to the sites defined by their respective pkg and page entries.
A NULL is invisibly returned.
Aaron Lun
tmp <- tempfile() dir.create(tmp) createRedirects("BLAH.html", pkg="OSCA.intro", page="installation.html", dir=tmp) if (interactive()) { browseURL(file.path(tmp, "BLAH.html")) }tmp <- tempfile() dir.create(tmp) createRedirects("BLAH.html", pkg="OSCA.intro", page="installation.html", dir=tmp) if (interactive()) { browseURL(file.path(tmp, "BLAH.html")) }
Deploy a custom CSS to change the colors of the book's section headers, mostly to add some flavor to the book.
deployCustomCSS(path = "style.css", h2.col = "#87b13f", h3.col = "#1a81c2")deployCustomCSS(path = "style.css", h2.col = "#87b13f", h3.col = "#1a81c2")
path |
String containing the path to the output CSS file. |
h2.col |
String containing the color to use for the section headers. |
h3.col |
String containing the color to use for the subsection headers. |
We quickly learned that it was unwise to be too adventurous with the colors. In particular, changing the colors of the table of contents was quite distracting. Altering the colors of the section headers provides a tasteful level of customization, with the default colors set (almost) to the Bioconductor color palette.
The CSS file is overwritten at path.
A NULL is invisibly returned.
Aaron Lun, based on work by Rob Amezquita and Kevin Rue-Albrecht
fname <- tempfile(fileext=".css") deployCustomCSS(fname) cat(readLines(fname), sep="\n")fname <- tempfile(fileext=".css") deployCustomCSS(fname) cat(readLines(fname), sep="\n")
Extract specific R objects from the knitr cache of a previously compiled Rmarkdown file (the “donor”) so that it can be used in the compilation process of another Rmarkdown file (the “acceptor”).
extractCached(path, chunk, objects, envir = parent.frame(1), link.text = NULL)extractCached(path, chunk, objects, envir = parent.frame(1), link.text = NULL)
path |
String containing the path to the donor Rmarkdown file. |
chunk |
String containing the name of the requested chunk. |
objects |
Character vector containing variable names for one or more objects to be extracted. |
envir |
Environment where the loaded objects should be stored. Defaults to the environment in which this function is called. |
link.text |
String containing an Rmarkdown-formatted link to the donor file, to be inserted in the collapsible element's title.
If |
Each R object is extracted in its state at the requested chunk and inserted into envir.
Note that the object does not have to be generated or even referenced in the requested chunk,
provided it was generated in a previous named chunk.
The parser in this function is rather limited, so the donor Rmarkdown file is subject to several constraints:
All chunks involved in generating the requested objects (indirectly or otherwise) should be named.
All named chunks should be executed; eval=FALSE is not respected.
All relevant code occurs within triple backticks, i.e., any inline code should be read-only.
Unnamed chunks are allowed but cannot be referenced and will not be used for searching for objects.
Chunks with names starting with unref- are considered to be the same as unnamed chunks and will be ignored;
this is useful for figure-generating chunks that need to be referenced inside the donor report.
In general, neither of these should be used for code that might affect variables in the named chunks,
i.e., code in unnamed chunks should be “read-only” with respect to variables in the named chunks.
Obviously, this entire process assumes that donor report has already been compiled with cache=TRUE.
If not, extractCached will compile it (and thus generate the cache) using compileChapter.
A report-specific lock is applied during this process to avoid problems with concurrent compilation.
Variables with names objects are created in envir.
A markdown chunk (wrapped in a collapsible element) is printed that contains all commands needed to generate those objects,
based on the code in the named chunks of the donor Rmarkdown file.
Aaron Lun
setupHTML and chapterPreamble, to set up the code for the collapsible element.
compileChapter, to compile a Rmarkdown report to generate the cache.
# Mocking up an Rmarkdown report. donor <- tempfile(fileext=".Rmd") write(file=donor, "```{r some-monsters} destoroyah <- 1 mecha.king.ghidorah <- 2 ``` ```{r more-monsters} space.godzilla <- 3 ``` ```{r} msg <- 'I am not referenced.' ``` ```{r unref-figure} plot(1, 1, main='I am also not referenced.') ``` ```{r even-more-monsters} megalon <- 4 ```") # Extracting stuff from it in another report. acceptor <- tempfile(fileext=".Rmd") dpb <- deparse(basename(donor)) write(file=acceptor, sprintf("```{r, echo=FALSE, results='asis'} chapterPreamble() ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='more-monsters', objects=c('space.godzilla', 'destoroyah')) ``` ```{r} space.godzilla * destoroyah ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='even-more-monsters', objects=c('megalon', 'mecha.king.ghidorah')) ``` ```{r} mecha.king.ghidorah * megalon ```", dpb, dpb)) rmarkdown::render(acceptor) if (interactive()) browseURL(sub(".Rmd$", ".html", acceptor))# Mocking up an Rmarkdown report. donor <- tempfile(fileext=".Rmd") write(file=donor, "```{r some-monsters} destoroyah <- 1 mecha.king.ghidorah <- 2 ``` ```{r more-monsters} space.godzilla <- 3 ``` ```{r} msg <- 'I am not referenced.' ``` ```{r unref-figure} plot(1, 1, main='I am also not referenced.') ``` ```{r even-more-monsters} megalon <- 4 ```") # Extracting stuff from it in another report. acceptor <- tempfile(fileext=".Rmd") dpb <- deparse(basename(donor)) write(file=acceptor, sprintf("```{r, echo=FALSE, results='asis'} chapterPreamble() ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='more-monsters', objects=c('space.godzilla', 'destoroyah')) ``` ```{r} space.godzilla * destoroyah ``` ```{r, results='asis', echo=FALSE} extractCached(%s, chunk='even-more-monsters', objects=c('megalon', 'mecha.king.ghidorah')) ``` ```{r} mecha.king.ghidorah * megalon ```", dpb, dpb)) rmarkdown::render(acceptor) if (interactive()) browseURL(sub(".Rmd$", ".html", acceptor))
Extract and compile Rmarkdown files from a “donor” package's installation directory, extracting cached objects from the subsequent knitr cache.
extractFromPackage( rmd.name, ..., package, envir = parent.frame(1), src.name = "book", work.dir = bookCache(package) )extractFromPackage( rmd.name, ..., package, envir = parent.frame(1), src.name = "book", work.dir = bookCache(package) )
rmd.name |
String containing the path to the donor Rmarkdown file, relative to |
..., envir
|
Further arguments to pass to |
package |
String containing the name of the donor package. |
src.name |
String containing the name or relative path of the subdirectory in the donor package's installation directory that contains all the Rmarkdown files. |
work.dir |
String containing the path to a versioned cache directory to hold the contents of donor book, see the dir.expiry package for details. |
This function assumes that all potential donor Rmarkdown files for package are present in the directory src.name.
It copies the contents of src.name into work.dir and calls extractCached on the rmd.name inside.
The desired objects are then extracted from the subsequent knitr cache.
The work.dir directory should be set to a persistent cache to enable greater re-use of the cache across calls and R sessions.
Indeed, the default here is the same as that used by preCompileBook, so we can avoid recopmilation if the donor book has already been compiled via the latter function.
This function will respect any global locks imposed by other functions in the process of performing the copy (or other rearrangements).
A NULL is invisibly returned.
Objects are created in envir and a code chunk is printed; see extractCached for more details.
Aaron Lun
# Only specifyin 'work.dir' here for demonstration purposes. # For actual use, just leave it as the default. tmp <- file.path(tempfile(), "1.0.0") extractFromPackage("test.Rmd", chunk="ghidorah-1964", src.name="example", objects="godzilla", package="rebook", work.dir=tmp) list.files(tmp) godzilla# Only specifyin 'work.dir' here for demonstration purposes. # For actual use, just leave it as the default. tmp <- file.path(tempfile(), "1.0.0") extractFromPackage("test.Rmd", chunk="ghidorah-1964", src.name="example", objects="godzilla", package="rebook", work.dir=tmp) list.files(tmp) godzilla
From another Rmarkdown file, create a link to a section or figure of a rebook-configured book.
link(id, package, type = NULL, prefix = NULL, df = NULL, error = TRUE)link(id, package, type = NULL, prefix = NULL, df = NULL, error = TRUE)
id |
String containing an identifier for a section or figure. |
package |
String containing the name of the package containing the target book. |
type |
String containing the type of the link, e.g., |
prefix |
String specifying the prefix to use on |
df |
A data.frame containing all links for |
error |
Logical scalar indicating whether an error should be raised if the link cannot be found. |
We expect that the target book is set up as a Bioconductor package with a configure file that runs configureBook.
This function will then retrieve install-time information from that package to create necessary hyperlinks to the Bioconductor-hosted book content.
String containing a markdown-formatted link to the relevant part of the target book.
If the link cannot be constructed and error=FALSE, a NULL is instead returned.
Aaron Lun
configureBook, which should be run by the authors of package.
scrapeReferences, to generate a df for testing.
# Only using 'df=' here because 'testpackage' doesn't actually exist. link("fig:xxx", package="testpackage", df=data.frame(id='fig:xxx', file='whee.html', text='3.1')) link("fig:xxx", package="testpackage", type=NA, df=data.frame(id='fig:xxx', file='whee.html', text='3.1')) link("fig:xxx", package="testpackage", prefix=NA, df=data.frame(id='fig:xxx', file='whee.html', text='3.1'))# Only using 'df=' here because 'testpackage' doesn't actually exist. link("fig:xxx", package="testpackage", df=data.frame(id='fig:xxx', file='whee.html', text='3.1')) link("fig:xxx", package="testpackage", type=NA, df=data.frame(id='fig:xxx', file='whee.html', text='3.1')) link("fig:xxx", package="testpackage", prefix=NA, df=data.frame(id='fig:xxx', file='whee.html', text='3.1'))
Report opening details about the book, to be executed as an R expression in the Date: field.
openingDetails(..., Copyright = NULL)openingDetails(..., Copyright = NULL)
... |
Further named strings to be included in the opening details. |
Copyright |
String containing copyright information; defaults to |
It is usually sufficient to set something like
date: "`r rebook::openingDetails()`"
in the YAML header of the book, thereby ensuring that the book details are printed after the title but before any contents. This assumes that none of the details have problematic characters, particularly double quotes.
Details are extracted from a DESCRIPTION file in the current or any parent directory.
This assumes that authors are formatted as Authors@R and the License and Date fields are specified.
A string containing the formatted details for inclusion into a YAML header.
Aaron Lun
wd <- getwd() setwd(system.file(package="rebook")) cat(openingDetails(), '\n') setwd(wd)wd <- getwd() setwd(system.file(package="rebook")) cat(openingDetails(), '\n') setwd(wd)
Wraps the session information output chunk in a collapsible HTML element so that it doesn't dominate the compiled chapter.
prettySessionInfo()prettySessionInfo()
Prints a HTML block containing a collapsible section with session information.
Aaron Lun
setupHTML and chapterPreamble, to set up the code for the collapsible element.
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::setupHTML() ``` ```{r, results='asis'} prettySessionInfo() ```") rmarkdown::render(tmp) if (interactive()) browseURL(sub(".Rmd$", ".html", tmp))
Get the identifier for a book chapter given the Rmarkdown source code. This is usually derived from the chapter title but can also be explicitly specified.
rmd2id(path)rmd2id(path)
path |
String containing the path to the Rmarkdown file for a chapter. |
String containing the identifier for this chapter.
If no identifier can be determined, NULL is returned.
Aaron Lun
tmp <- tempfile(fileext='.Rmd') write('# some chapter name blah', file=tmp) rmd2id(tmp) tmp2 <- tempfile(fileext='.Rmd') write('# some chapter name {#chapter-id} blah', file=tmp2) rmd2id(tmp2)tmp <- tempfile(fileext='.Rmd') write('# some chapter name blah', file=tmp) rmd2id(tmp) tmp2 <- tempfile(fileext='.Rmd') write('# some chapter name {#chapter-id} blah', file=tmp2) rmd2id(tmp2)
Scrape Rmarkdown reports in the book for all required dependencies.
scrapeDependencies(dir, recursive = TRUE, pattern = "\\.Rmd$")scrapeDependencies(dir, recursive = TRUE, pattern = "\\.Rmd$")
dir |
String containing the path to the directory containing Rmarkdown reports.
This is searched recursively for all files ending in |
recursive, pattern
|
Further arguments to pass to |
The output of this should be added to the Suggests field of the book's DESCRIPTION,
to make it easier to simply install all of its required dependencies.
Note that dependencies in inline code sections are not detected, so these should be explicitly mentioned in a standalone code chunk to be captured.
Character vector of required packages.
Aaron Lun
tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r} A::a() ``` ```{r} library(B) require(C) ```") scrapeDependencies(tempdir())tmp <- tempfile(fileext=".Rmd") write(file=tmp, "```{r} A::a() ``` ```{r} library(B) require(C) ```") scrapeDependencies(tempdir())
Scrape references to sections and figures from all Rmarkdown files in a bookdown directory.
scrapeReferences(dir, input = "index.Rmd", workdir = tempfile(), clean = TRUE)scrapeReferences(dir, input = "index.Rmd", workdir = tempfile(), clean = TRUE)
dir |
String containing a path to a bookdown-containing directory. |
input |
String containing the name of the file to use in the |
workdir |
String containing a path to a working directory to use to store bits and pieces. |
clean |
Logical scalar indicating whether the working directory should be removed upon function completion. |
This function works by performing a quick dummy compilation of the book, turning off all evaluations with a global eval=FALSE.
It then trawls the set of newly created HTML files, pulling out the section/figure identifiers and collating them into a data.frame.
The goal is to facilitate convenient linking between books by automatically filling in the file and text for a given link.
Packages that deploy books should run this in their configure scripts to obtain a reference mapping that they can serve to other packages via link.
Extraction of the figure text assumes that the figure prefix ends with a non-numeric character, e.g., "Figure " or "Figure S".
A data.frame where each row corresponds to a reference.
It has id, the name of the reference;
file, the compiled HTML file that the reference comes from;
and text, the text to be associated with that reference.
Aaron Lun
link, to create links given a package name and identifier.
book.dir <- system.file("example", package="rebook") df <- scrapeReferences(book.dir) dfbook.dir <- system.file("example", package="rebook") df <- scrapeReferences(book.dir) df
Set up Javascript and CSS elements for each chapter, primarily for the custom collapsible class.
setupHTML()setupHTML()
The custom collapsible class allows us to hide details until requested by the user. This improves readability by reducing the clutter in the compiled chapter.
Prints HTML to standard output set up JS and CSS elements.
Aaron Lun
chapterPreamble, which calls this function.
extractCached and prettySessionInfo, which use the custom collapsible class.
setupHTML()setupHTML()
Update the book package's DESCRIPTION file with the latest dependencies.
updateDependencies( dir = ".", path = file.path(dir, "DESCRIPTION"), extra = NULL, indent = 4, field = "Depends", ... )updateDependencies( dir = ".", path = file.path(dir, "DESCRIPTION"), extra = NULL, indent = 4, field = "Depends", ... )
dir |
String containing the path to the directory containing the book. |
path |
String containing the path to the DESCRIPTION file. |
extra |
Character vector of extra packages to be added to imports,
usually from packages that are in |
indent |
Integer scalar specifying the size of the indent to use when listing packages. |
field |
String specifying the dependency field to store the packages in.
Defaults to |
... |
Further arguments to pass to |
The book DESCRIPTION is useful for quick installation of all packages required across all chapters.
For example, it is used by https://github.com/LTLA/TrojanBookBuilder to populate a trojan package's dependencies,
ensuring that all packages are available when the book itself is compiled.
The specified field in the DESCRIPTION file in dir is updated.
NULL is invisibly returned.
Aaron Lun
dir <- tempfile() dir.create(dir) write(file=file.path(dir, "DESCRIPTION"), "Package: son.of.godzilla Version: 0.0.1 Description: Like godzilla, but smaller.") tmp <- file.path(dir, "alpha.Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} A::func library(C) ```") tmp <- file.path(dir, "bravo.Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} require(D) B::more ```") updateDependencies(dir) cat(readLines(file.path(dir, "DESCRIPTION")), sep="\n")dir <- tempfile() dir.create(dir) write(file=file.path(dir, "DESCRIPTION"), "Package: son.of.godzilla Version: 0.0.1 Description: Like godzilla, but smaller.") tmp <- file.path(dir, "alpha.Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} A::func library(C) ```") tmp <- file.path(dir, "bravo.Rmd") write(file=tmp, "```{r, echo=FALSE, results='asis'} rebook::chapterPreamble() ``` ```{r} require(D) B::more ```") updateDependencies(dir) cat(readLines(file.path(dir, "DESCRIPTION")), sep="\n")