Package 'tinkr'

Title: Cast '(R)Markdown' Files to 'XML' and Back Again
Description: Parsing '(R)Markdown' files with numerous regular expressions can be fraught with peril, but it does not have to be this way. Converting '(R)Markdown' files to 'XML' using the 'commonmark' package allows in-memory editing via of 'markdown' elements via 'XPath' through the extensible 'R6' class called 'yarn'. These modified 'XML' representations can be written to '(R)Markdown' documents via an 'xslt' stylesheet which implements an extended version of 'GitHub'-flavoured 'markdown' so that you can tinker to your hearts content.
Authors: Maëlle Salmon [aut] , Zhian N. Kamvar [aut, cre] , Jeroen Ooms [aut], Nick Wellnhofer [cph] (Nick Wellnhofer wrote the XSLT stylesheet.), rOpenSci [fnd] (https://ropensci.org/), Peter Daengeli [ctb]
Maintainer: Zhian N. Kamvar <[email protected]>
License: GPL-3
Version: 0.2.0.9001
Built: 2024-11-25 16:30:16 UTC
Source: https://github.com/ropensci/tinkr

Help Index

Find between a pattern

Description

Helper function to find all nodes between a standard pattern. This is useful if you want to find unnested pandoc tags.

Usage

find_between(
  body,
  ns,
  pattern = "md:paragraph[md:text[starts-with(text(), ':::')]]",
  include = FALSE
)

Arguments

body

and XML document
ns

the namespace of the document
pattern

an XPath expression that defines characteristics of nodes between which you want to extract everything.
include

if TRUE, the tags matching pattern will be included in the output, defaults to FALSE, which only gives you the nodes in between pattern.

Value

a nodeset

Examples

md <- glue::glue("
 h1
 ====

 ::: section

 h2
 ----

 section *text* with [a link](https://ropensci.org/)
 
 :::
")
x <- xml2::read_xml(commonmark::markdown_xml(md))
ns <- xml2::xml_ns_rename(xml2::xml_ns(x), d1 = "md")
res <- find_between(x, ns)
res
xml2::xml_text(res)
xml2::xml_find_all(res, ".//descendant-or-self::md:*", ns = ns)

Get protected nodes

Description

Get protected nodes

Usage

get_protected(body, type = NULL, ns = md_ns())

Arguments

body

an xml_document object
type

a character vector listing the protections to be included. Defaults to NULL, which includes all protected nodes:

  • math: via the protect_math() function

  • curly: via the protect_curly() function

  • unescaped: via the protect_unescaped() function

ns

the namespace of the document (defaults to md_ns())

Value

an xml_nodelist object.

Examples

path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE)
# protect curly braces
ex$protect_curly()
# add math and protect it
ex$add_md(c("## math\n", 
  "$c^2 = a^2 + b^2$\n", 
  "$$",
  "\\sum_{i}^k = x_i + 1",
  "$$\n")
)
ex$protect_math()
# get protected now shows all the protected nodes
get_protected(ex$body)
get_protected(ex$body, c("math", "curly")) # only show the math and curly

Aliased namespace prefix for commonmark

Description

The commonmark package is used to translate markdown to XML, but it does not assign a namespace prefix, which means that xml2 will auto-assign a default prefix of d1.

Usage

md_ns()

Details

This function renames the default prefix to md, so that you can use XPath queries that are slightly more descriptive.

Value

an xml_namespace object (see xml2::xml_ns())

Examples

tink <- tinkr::to_xml(system.file("extdata", "example1.md", package = "tinkr"))
# with default namespace
xml2::xml_find_all(tink$body, 
  ".//d1:link[starts-with(@destination, 'https://ropensci')]"
)
# with tinkr namespace
xml2::xml_find_all(tink$body, 
  ".//md:link[starts-with(@destination, 'https://ropensci')]",
  tinkr::md_ns()
)

Protect curly elements for further processing

Description

Protect curly elements for further processing

Usage

protect_curly(body, ns = md_ns())

Arguments

body

an XML object
ns

an XML namespace object (defaults: md_ns()).

Details

Commonmark will render text such as {.unnumbered} (Pandoc/Quarto option) or ⁠{#hello .greeting .message style="color: red;"}⁠ (Markdown custom block) as normal text which might be problematic if trying to extract real text from the XML.

If sending the XML to, say, a translation API that allows some tags to be ignored, you could first transform the text tags with the attribute curly to curly tags, and then transform them back to text tags before using to_md().

Value

a copy of the modified XML object

Note

this function is also a method in the yarn object.

Examples

m <- tinkr::to_xml(system.file("extdata", "basic-curly.md", package = "tinkr"))
xml2::xml_child(m$body)
m$body <- protect_curly(m$body)
xml2::xml_child(m$body)

Protect math elements from commonmark's character escape

Description

Protect math elements from commonmark's character escape

Usage

protect_math(body, ns = md_ns())

Arguments

body

an XML object
ns

an XML namespace object (defaults: md_ns()).

Details

Commonmark does not know what LaTeX is and will LaTeX equations as normal text. This means that content surrounded by underscores are interpreted as ⁠<emph>⁠ elements and all backslashes are escaped by default. This function protects inline and block math elements that use $ and ⁠$$⁠ for delimiters, respectively.

Value

a copy of the modified XML object

Note

this function is also a method in the yarn object.

Examples

m <- tinkr::to_xml(system.file("extdata", "math-example.md", package = "tinkr"))
txt <- textConnection(tinkr::to_md(m))
cat(tail(readLines(txt)), sep = "\n") # broken math
close(txt)
m$body <- protect_math(m$body)
txt <- textConnection(tinkr::to_md(m))
cat(tail(readLines(txt)), sep = "\n") # fixed math
close(txt)

Display a node or nodelist as markdown

Description

When inspecting the results of an XPath query, displaying the text often

Usage

show_list(nodelist, stylesheet_path = stylesheet())

show_block(nodelist, mark = FALSE, stylesheet_path = stylesheet())

show_censor(nodelist, stylesheet_path = stylesheet())

Arguments

nodelist

an object of class xml_nodeset OR xml_node OR a list of either.
stylesheet_path

path to the XSL stylesheet
mark

[bool] When TRUE markers (⁠[...]⁠) are added to replace nodes that come before or after the islated nodes. Defaults to FALSE, which only shows the isolated nodes in their respective blocks. Note that the default state may cause nodes within the same block to appear adjacent to each other.

Value

a character vector, invisibly. The result of these functions are displayed to the screen

See Also

to_md_vec() to get a vector of these elements in isolation.

Examples

path <- system.file("extdata", "show-example.md", package = "tinkr")
y <- tinkr::yarn$new(path, sourcepos = TRUE)
y$protect_math()$protect_curly()
items <- xml2::xml_find_all(y$body, ".//md:item", tinkr::md_ns())
imgs <- xml2::xml_find_all(y$body, ".//md:image | .//node()[@curly]", 
  tinkr::md_ns())
links <- xml2::xml_find_all(y$body, ".//md:link", tinkr::md_ns())
code <- xml2::xml_find_all(y$body, ".//md:code", tinkr::md_ns())
blocks <- xml2::xml_find_all(y$body, ".//md:code_block", tinkr::md_ns())

# show a list of items 
show_list(links)
show_list(code)
show_list(blocks)

# show the items in their local structure
show_block(items)
show_block(links, mark = TRUE)

# show the items in the full document censored (everything but whitespace):
show_censor(imgs)

# You can also adjust the censorship parameters. There are two paramters
# available: the mark, which chooses what character you want to use to
# replace characters (default: `\u2587`); and the regex which specifies 
# characters to replace (default: `[^[:space:]]`, which replaces all
# non-whitespace characters.
# 
# The following will replace everything that is not a whitespace
# or punctuation character with "o" for a very ghostly document
op <- options()
options(tinkr.censor.regex = "[^[:space:][:punct:]]")
options(tinkr.censor.mark = "o")
show_censor(links)
options(tinkr.censor.regex = NULL)
options(tinkr.censor.mark = NULL)

The tinkr stylesheet

Description

This function returns the path to the tinkr stylesheet

Usage

stylesheet()

Value

a single element character vector representing the path to the stylesheet used by tinkr.

Examples

tinkr::stylesheet()

Write YAML and XML back to disk as (R)Markdown

Description

Write YAML and XML back to disk as (R)Markdown

Usage

to_md(yaml_xml_list, path = NULL, stylesheet_path = stylesheet())

to_md_vec(nodelist, stylesheet_path = stylesheet())

Arguments

yaml_xml_list

result from a call to to_xml() and editing.
path

path of the new file. Defaults to NULL, which will not write any file, but will still produce the conversion and pass the output as a character vector.
stylesheet_path

path to the XSL stylesheet
nodelist

an object of xml_nodelist or xml_node

Details

The stylesheet you use will decide whether lists are built using "*" or "-" for instance. If you're keen to keep your own Markdown style when using to_md() after to_xml(), you can tweak the XSL stylesheet a bit and provide the path to your XSL stylesheet as argument.

Value

  • to_md(): ⁠\[character\]⁠ the converted document, invisibly as a character vector containing two elements: the yaml list and the markdown body.

  • to_md_vec(): ⁠\[character\]⁠ the markdown representation of each node.

Examples

path <- system.file("extdata", "example1.md", package = "tinkr")
yaml_xml_list <- to_xml(path)
names(yaml_xml_list)
# extract the level 3 headers from the body
headers3 <- xml2::xml_find_all(
  yaml_xml_list$body,
  xpath = './/md:heading[@level="3"]', 
  ns = md_ns()
)
# show the headers
print(h3 <- to_md_vec(headers3))
# transform level 3 headers into level 1 headers
# NOTE: these nodes are still associated with the document and this is done
# in place.
xml2::xml_set_attr(headers3, "level", 1)
# preview the new headers
print(h1 <- to_md_vec(headers3))
# save back and have a look
newmd <- tempfile("newmd", fileext = ".md")
res <- to_md(yaml_xml_list, newmd)
# show that it works
regmatches(res[[2]], gregexpr(h1[1], res[[2]], fixed = TRUE))
# file.edit("newmd.md")
file.remove(newmd)

Transform file to XML

Description

Transform file to XML

Usage

to_xml(
  path,
  encoding = "UTF-8",
  sourcepos = FALSE,
  anchor_links = TRUE,
  unescaped = TRUE
)

Arguments

path

Path to the file.
encoding

Encoding to be used by readLines.
sourcepos

passed to commonmark::markdown_xml(). If TRUE, the source position of the file will be included as a "sourcepos" attribute. Defaults to FALSE.
anchor_links

if TRUE (default), reference-style links with anchors (in the style of ⁠[key]: https://example.com/link "title"⁠) will be preserved as best as possible. If this is FALSE, the anchors disappear and the links will appear as normal links. See resolve_anchor_links() for details.
unescaped

if TRUE (default) AND sourcepos = TRUE, square braces that were unescaped in the original document will be preserved as best as possible. If this is FALSE, these braces will be escaped in the output document. See protect_unescaped() for details.

Details

This function will take a (R)markdown file, split the yaml header from the body, and read in the body through commonmark::markdown_xml(). Any RMarkdown code fences will be parsed to expose the chunk options in XML and tickboxes (aka checkboxes) in GitHub-flavored markdown will be preserved (both modifications from the commonmark standard).

Value

A list containing the YAML of the file (yaml) and its body (body) as XML.

Note

Math elements are not protected by default. You can use protect_math() to address this if needed.

Examples

path <- system.file("extdata", "example1.md", package = "tinkr")
post_list <- to_xml(path)
names(post_list)
path2 <- system.file("extdata", "example2.Rmd", package = "tinkr")
post_list2 <- to_xml(path2)
post_list2

R6 class containing XML representation of Markdown

Description

Wrapper around an XML representation of a Markdown document. It contains four publicly accessible slots: path, yaml, body, and ns.

Details

This class is a fancy wrapper around the results of to_xml() and has methods that make it easier to add, analyze, remove, or write elements of your markdown document.

Public fields

path

[character] path to file on disk

yaml

[character] text block at head of file

body

[xml_document] an xml document of the (R)Markdown file.

ns

[xml_document] an xml namespace object defining "md" to commonmark.

Methods

Public methods

Method new()

Create a new yarn document

Usage
yarn$new(path = NULL, encoding = "UTF-8", sourcepos = FALSE, ...)
Arguments
path

[character] path to a markdown episode file on disk

encoding

[character] encoding passed to readLines()

sourcepos

passed to commonmark::markdown_xml(). If TRUE, the source position of the file will be included as a "sourcepos" attribute. Defaults to FALSE.

...

arguments passed on to to_xml().

Returns

A new yarn object containing an XML representation of a (R)Markdown file.

Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
path2 <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path2)
ex2

Method reset()

reset a yarn document from the original file

Usage
yarn$reset()
Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
# OH NO
ex1$body
ex1$body <- xml2::xml_missing()
ex1$reset()
ex1$body

Method write()

Write a yarn document to Markdown/R Markdown

Usage
yarn$write(path = NULL, stylesheet_path = stylesheet())
Arguments
path

path to the file you want to write

stylesheet_path

path to the xsl stylesheet to convert XML to markdown.

Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
tmp <- tempfile()
try(readLines(tmp)) # nothing in the file
ex1$write(tmp)
head(readLines(tmp)) # now a markdown file
unlink(tmp)

Method show()

show the markdown contents on the screen

Usage
yarn$show(lines = TRUE, stylesheet_path = stylesheet())
Arguments
lines

a subset of elements to show. Defaults to TRUE, which shows all lines of the output. This can be either logical or numeric.

stylesheet_path

path to the xsl stylesheet to convert XML to markdown.

Returns

a character vector with one line for each line in the output

Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path)
ex2$head(5)
ex2$tail(5)
ex2$show()

Method head()

show the head of the markdown contents on the screen

Usage
yarn$head(n = 6L, stylesheet_path = stylesheet())
Arguments
n

the number of elements to show from the top. Negative numbers

stylesheet_path

path to the xsl stylesheet to convert XML to markdown.

Returns

a character vector with n elements

Method tail()

show the tail of the markdown contents on the screen

Usage
yarn$tail(n = 6L, stylesheet_path = stylesheet())
Arguments
n

the number of elements to show from the bottom. Negative numbers

stylesheet_path

path to the xsl stylesheet to convert XML to markdown.

Returns

a character vector with n elements

Method md_vec()

query and extract markdown elements

Usage
yarn$md_vec(xpath = NULL, stylesheet_path = stylesheet())
Arguments
xpath

a valid XPath expression

stylesheet_path

path to the xsl stylesheet to convert XML to markdown.

Returns

a vector of markdown elements generated from the query

Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
# all headings
ex$md_vec(".//md:heading")
# all headings greater than level 3
ex$md_vec(".//md:heading[@level>3]")
# all links
ex$md_vec(".//md:link")
# all links that are part of lists
ex$md_vec(".//md:list//md:link")
# all code
ex$md_vec(".//md:code | .//md:code_block")

Method add_md()

add an arbitrary Markdown element to the document

Usage
yarn$add_md(md, where = 0L)
Arguments
md

a string of markdown formatted text.

where

the location in the document to add your markdown text. This is passed on to xml2::xml_add_child(). Defaults to 0, which indicates the very top of the document.

Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# two headings, no lists
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
ex$add_md(
  "# Hello\n\nThis is *new* formatted text from `{tinkr}`!",
  where = 1L
)$add_md(
  " - This\n - is\n - a new list",
  where = 2L
)
# three headings
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
tmp <- tempfile()
ex$write(tmp)
readLines(tmp, n = 20)

Method protect_math()

Protect math blocks from being escaped

Usage
yarn$protect_math()
Examples
path <- system.file("extdata", "math-example.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$tail() # math blocks are escaped :(
ex$protect_math()$tail() # math blocks are no longer escaped :)

Method protect_curly()

Protect curly phrases {likethat} from being escaped

Usage
yarn$protect_curly()
Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$protect_curly()$head()

Method protect_unescaped()

Protect unescaped square braces from being escaped.

This is applied by default when you use yarn$new(sourcepos = TRUE).

Usage
yarn$protect_unescaped()
Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE, unescaped = FALSE)
ex$tail()
ex$protect_unescaped()$tail()

Method get_protected()

Return nodes whose contents are protected from being escaped

Usage
yarn$get_protected(type = NULL)
Arguments
type

a character vector listing the protections to be included. Defaults to NULL, which includes all protected nodes:

  • math: via the protect_math() function

  • curly: via the protect_curly() function

  • unescaped: via the protect_unescaped() function

Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE)
# protect curly braces
ex$protect_curly()
# add math and protect it
ex$add_md(c("## math\n", 
  "$c^2 = a^2 + b^2$\n", 
  "$$",
  "\\sum_{i}^k = x_i + 1",
  "$$\n")
)
ex$protect_math()
# get protected now shows all the protected nodes
ex$get_protected()
ex$get_protected(c("math", "curly")) # only show the math and curly

Method clone()

The objects of this class are cloneable with this method.

Usage
yarn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

this requires the sourcepos attribute to be recorded when the object is initialised. See protect_unescaped() for details.

See Also

to_md_vec() for a way to generate the same vector from a nodelist without a yarn object

Examples

## ------------------------------------------------
## Method `yarn$new`
## ------------------------------------------------

path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
path2 <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path2)
ex2

## ------------------------------------------------
## Method `yarn$reset`
## ------------------------------------------------


path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
# OH NO
ex1$body
ex1$body <- xml2::xml_missing()
ex1$reset()
ex1$body

## ------------------------------------------------
## Method `yarn$write`
## ------------------------------------------------

path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
tmp <- tempfile()
try(readLines(tmp)) # nothing in the file
ex1$write(tmp)
head(readLines(tmp)) # now a markdown file
unlink(tmp)

## ------------------------------------------------
## Method `yarn$show`
## ------------------------------------------------

path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path)
ex2$head(5)
ex2$tail(5)
ex2$show()

## ------------------------------------------------
## Method `yarn$md_vec`
## ------------------------------------------------

path <- system.file("extdata", "example1.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
# all headings
ex$md_vec(".//md:heading")
# all headings greater than level 3
ex$md_vec(".//md:heading[@level>3]")
# all links
ex$md_vec(".//md:link")
# all links that are part of lists
ex$md_vec(".//md:list//md:link")
# all code
ex$md_vec(".//md:code | .//md:code_block")

## ------------------------------------------------
## Method `yarn$add_md`
## ------------------------------------------------

path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# two headings, no lists
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
ex$add_md(
  "# Hello\n\nThis is *new* formatted text from `{tinkr}`!",
  where = 1L
)$add_md(
  " - This\n - is\n - a new list",
  where = 2L
)
# three headings
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
tmp <- tempfile()
ex$write(tmp)
readLines(tmp, n = 20)

## ------------------------------------------------
## Method `yarn$protect_math`
## ------------------------------------------------

path <- system.file("extdata", "math-example.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$tail() # math blocks are escaped :(
ex$protect_math()$tail() # math blocks are no longer escaped :)

## ------------------------------------------------
## Method `yarn$protect_curly`
## ------------------------------------------------

path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$protect_curly()$head()

## ------------------------------------------------
## Method `yarn$protect_unescaped`
## ------------------------------------------------

path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE, unescaped = FALSE)
ex$tail()
ex$protect_unescaped()$tail()

## ------------------------------------------------
## Method `yarn$get_protected`
## ------------------------------------------------

path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE)
# protect curly braces
ex$protect_curly()
# add math and protect it
ex$add_md(c("## math\n", 
  "$c^2 = a^2 + b^2$\n", 
  "$$",
  "\\sum_{i}^k = x_i + 1",
  "$$\n")
)
ex$protect_math()
# get protected now shows all the protected nodes
ex$get_protected()
ex$get_protected(c("math", "curly")) # only show the math and curly